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<h3 style="margin-top: 20px; margin-bottom: 10px;">
Lance Lin pushed to branch upstream at <a href="https://salsa.debian.org/med-team/stacks">Debian Med / stacks</a>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
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<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1">fded9fa1</a></strong>
<div>
<span> by Lance Lin </span> <i> at 2024-08-10T18:43:35+07:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 2.67+dfsg</pre>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
22 changed files:
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<ul>
<li class="file-stats">
<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
ChangeLog
</a>
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<li class="file-stats">
<a href="#d5b4de16d947214ec306bd57bed1bd23a939b5f9">
Makefile.am
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<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
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<li class="file-stats">
<a href="#f80f154b64490a485c4418bd70f94184f6336dce">
scripts/denovo_map.pl
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<li class="file-stats">
<a href="#8035c04d156a13d0aefa8edc446bb296143294f8">
scripts/stacks-dist-extract
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<li class="file-stats">
<a href="#9af07f1911c400b9a3863d9a1ffe88c1793ff2c6">
<span class="new-file">
+
scripts/stacks-private-alleles
</span>
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</li>
<li class="file-stats">
<a href="#119d50f2f2d1e3f64b65bbd89f3cafcfb13ca0d4">
src/Seq.h
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<li class="file-stats">
<a href="#85c0ee6f77dd1ab892cf45bfd301d678f6ebec1f">
src/clean.cc
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<li class="file-stats">
<a href="#1644bd85290d6144938b4b136f22f9635a67964e">
src/clean.h
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<li class="file-stats">
<a href="#2f7325ed14b982f91f8a457bac8ca0389322f5a3">
src/clone_filter.cc
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<li class="file-stats">
<a href="#03f856e8b44c3c125706ba7e7a8c138a914e7063">
src/constants.h
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<li class="file-stats">
<a href="#9b5186210cef02bd7aa4ac577214b1ba3b2fa6a8">
src/cstacks.cc
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<li class="file-stats">
<a href="#930a2c5c4679e2fa7738631bb355df01e13be529">
src/file_io.cc
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<li class="file-stats">
<a href="#11bb84c7517c5dd061e913712c92d72cd6a698db">
src/file_io.h
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<li class="file-stats">
<a href="#5d057fdf8543f341f83844acdc94851f57407d44">
src/populations.cc
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<li class="file-stats">
<a href="#e4426463c64a505bc8fcb199c701d8e0003a4ab4">
src/populations.h
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<li class="file-stats">
<a href="#6b229f74a1c1dafec515b59e2082ef52596e4d1a">
src/process_radtags.cc
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<li class="file-stats">
<a href="#dc87fdb3f7c40b9a1ff34020178c9c55c2c063f7">
src/process_radtags.h
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<li class="file-stats">
<a href="#fd57d93bef1cff07dc69b266458b5e78af39be25">
src/process_shortreads.cc
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<li class="file-stats">
<a href="#a229ae1cb4c1ccb3f041e58c9ac02711c0114043">
src/sstacks.cc
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<li class="file-stats">
<a href="#115f7027957c0ea3ba55c87ad3b1eaea3b5ebe8d">
src/ustacks.cc
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<li class="file-stats">
<a href="#b44ce7d7ddbd794f98496d8179231949622e498e">
src/write.cc
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
Changes:
</h4>
<li id="00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#00fe7828d56d7a3ee4030d6cea057cf13f50e70c"><strong style="font-weight: 600;">ChangeLog</strong></a>
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<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1" class="line" lang="plaintext">Stacks 2.67 - July 18, 2024</span>
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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2" class="line" lang="plaintext">---------------------------</span>
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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="plaintext"> Feature: Added the --min-gt-depth filter to populations. Requires a called SNP to be supported</span>
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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4" class="line" lang="plaintext"> by a minimum number of reads, otherwise it is marked as missing data.</span>
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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="plaintext"> Feature: Added processing of UMI field to process_radtags. Raw Illumina data may include</span>
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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6" class="line" lang="plaintext"> an extra field in the FASTQ header which represents a unique molecular</span>
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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7" class="line" lang="plaintext"> identifier (UMI).</span>
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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC8" class="line" lang="plaintext"> Feature: Added detection for runs of G nucleotides to process_radtags. In recent two-color</span>
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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
9
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="plaintext"> chemistries from Illumina, 'no signal' can be mistaken for high quality runs of 'G'.</span>
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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10" class="line" lang="plaintext"> This feature detects high quality of runs of G nucleotides at the 3' end of the read</span>
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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
11
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC11" class="line" lang="plaintext"> and drops reads containing this loss of signal (if there are 10 or more Gs present).</span>
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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
12
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC12" class="line" lang="plaintext"> Feature: Added the --basename option to process_radtags so a user can sepcify an output </span>
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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
13
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC13" class="line" lang="plaintext"> filename when processing individual input files (i.e. -f, or -1/-2). (Useful, </span>
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<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
14
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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
15
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC15" class="line" lang="plaintext"> Bugfix: Corrected a bug in process_radtags when run with multiple threads: if more than one</span>
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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
16
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC16" class="line" lang="plaintext"> barcode mapped to the same output file it could crash due to a lack of thread</span>
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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
17
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC17" class="line" lang="plaintext"> synchronization. Code now assigns all barcodes pointing to the same output files to</span>
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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
18
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC18" class="line" lang="plaintext"> the same output thread.</span>
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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
19
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC19" class="line" lang="plaintext"> Bugfix: Corrected a bug in filtering adapter sequence in process_radtags that occurred</span>
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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
20
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC20" class="line" lang="plaintext"> when a barcode was part of the adaptor sequence, but near the end of that adaptor</span>
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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
21
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC21" class="line" lang="plaintext"> sequence, it could cause a read to be inadvertantly discarded.</span>
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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
22
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC22" class="line" lang="plaintext"> Bugfix: Corrected a regression in process_radtags where FASTQ custom</span>
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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
23
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23" class="line" lang="plaintext"> headers (e.g. from the Sequence Read Archive) were not properly parsed.</span>
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24
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC24" class="line" lang="plaintext"> Also added a check to ensure "/1" and/or "/2" are removed from the header</span>
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25
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC25" class="line" lang="plaintext"> if present so as not to be duplciated after processing.</span>
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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
26
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC26" class="line" lang="plaintext"> Bugfix: Corrected stacks-private-alleles to work properly with denovo</span>
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27
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC27" class="line" lang="plaintext"> data.</span>
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28
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC28" class="line" lang="plaintext"></span>
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1
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<td class="new_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC29" class="line" lang="plaintext">Stacks 2.66 - December 5, 2023</span>
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<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC30" class="line" lang="plaintext">------------------------------</span>
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3
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<td class="new_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
31
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC31" class="line" lang="plaintext"> Feature: Rewrote stacks-dist-extract in Python including new support for partial</span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#d5b4de16d947214ec306bd57bed1bd23a939b5f9"><strong style="font-weight: 600;">Makefile.am</strong></a>
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<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -86,7 +86,8 @@ kmer_filter_LDADD = $(LDADD) libclean.a</td>
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86
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<td class="new_line diff-line-num" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
86
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC86" class="line" lang="make"><span class="nv" style="color: teal;">populations_LDADD</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">$(</span>LDADD<span class="p">)</span> libpop.a</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC87" class="line" lang="make"></span>
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<td class="new_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
88
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC88" class="line" lang="make"><span class="nv" style="color: teal;">dist_bin_SCRIPTS</span> <span class="o" style="font-weight: 600;">=</span> scripts/denovo_map.pl scripts/ref_map.pl <span class="se" style="color: #d14;">\</span></span>
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89
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<td class="new_line diff-line-num old" data-linenumber="89" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC89" class="line" lang="make"> scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-gdb <span class="se" style="color: #d14;">\</span></span>
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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
89
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC89" class="line" lang="make"> scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-private-alleles <span class="se" style="color: #d14;">\</span></span>
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90
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC90" class="line" lang="make"> scripts/stacks-gdb <span class="se" style="color: #d14;">\</span></span>
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90
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<td class="new_line diff-line-num" data-linenumber="91" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
91
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC91" class="line" lang="make"> scripts/stacks-samtools-tview scripts/stacks-count-reads-per-sample-per-locus <span class="se" style="color: #d14;">\</span></span>
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91
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<td class="new_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
92
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC92" class="line" lang="make"> scripts/stacks-hist2d-loci-samples-coverage <span class="c" style="color: #998; font-style: italic;"># scripts/denovo_map.py</span></span>
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93
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC93" class="line" lang="make"></span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong style="font-weight: 600;">configure.ac</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2,7 +2,7 @@</td>
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<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2
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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="plaintext"># Process this file with autoconf to produce a configure script.</span>
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3
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3
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3" class="line" lang="plaintext"></span>
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4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="plaintext">AC_PREREQ(2.59)</span>
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<td class="old_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
5
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<td class="new_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="plaintext">AC_INIT([Stacks], [2.6<span class="idiff left right deletion" style="background-color: #fac5cd;">6</span>])</span>
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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="plaintext">AC_INIT([Stacks], [2.6<span class="idiff left right addition" style="background-color: #c7f0d2;">7</span>])</span>
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6
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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="plaintext">AC_CONFIG_AUX_DIR([config])</span>
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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7
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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7" class="line" lang="plaintext">AM_INIT_AUTOMAKE([-Wall -Werror foreign parallel-tests subdir-objects])</span>
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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
8
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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
8
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="plaintext">AC_CONFIG_SRCDIR([src/ustacks.cc])</span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#f80f154b64490a485c4418bd70f94184f6336dce"><strong style="font-weight: 600;">scripts/denovo_map.pl</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="163" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="163" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -163,7 +163,7 @@ sub execute_stacks {</td>
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163
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163
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC163" class="line" lang="perl"> <span class="k" style="font-weight: 600;">next</span><span class="p">;</span></span>
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164
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<td class="new_line diff-line-num" data-linenumber="164" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
164
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC164" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="165" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
165
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<td class="new_line diff-line-num" data-linenumber="165" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
165
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC165" class="line" lang="perl"></span>
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<td class="old_line diff-line-num old" data-linenumber="166" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
166
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<td class="new_line diff-line-num old" data-linenumber="166" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC166" class="line" lang="perl"> <span class="nv" style="color: teal;">$cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$exe_path</span> <span class="o" style="font-weight: 600;">.</span> <span class="p">"</span><span class="s2" style="color: #d14;">ustacks -<span class="idiff left deletion" style="background-color: #fac5cd;">t</span> </span><span class="si" style="color: #d14;">$sample</span><span class="s2" style="color: #d14;">->{'fmt'} -<span class="idiff deletion" style="background-color: #fac5cd;">f</span> </span><span class="si" style="color: #d14;">$sample</span><span class="s2" style="color: #d14;">->{'path'} -<span class="idiff right deletion" style="background-color: #fac5cd;">o</span> </span><span class="si" style="color: #d14;">$out_path</span><span class="p">"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$minc</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="167" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
166
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC166" class="line" lang="perl"> <span class="nv" style="color: teal;">$cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$exe_path</span> <span class="o" style="font-weight: 600;">.</span> <span class="p">"</span><span class="s2" style="color: #d14;">ustacks -<span class="idiff left addition" style="background-color: #c7f0d2;">-in-type</span> </span><span class="si" style="color: #d14;">$sample</span><span class="s2" style="color: #d14;">->{'fmt'} -<span class="idiff addition" style="background-color: #c7f0d2;">-file</span> </span><span class="si" style="color: #d14;">$sample</span><span class="s2" style="color: #d14;">->{'path'} -<span class="idiff right addition" style="background-color: #c7f0d2;">-out-path</span> </span><span class="si" style="color: #d14;">$out_path</span><span class="p">"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$minc</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="167" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
167
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<td class="new_line diff-line-num" data-linenumber="167" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
167
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC167" class="line" lang="perl"></span>
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<td class="old_line diff-line-num" data-linenumber="168" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
168
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<td class="new_line diff-line-num" data-linenumber="168" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
168
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC168" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$sample</span><span class="o" style="font-weight: 600;">-></span><span class="p">{'</span><span class="s1" style="color: #d14;">path</span><span class="p">'}</span> <span class="o" style="font-weight: 600;">!~</span> <span class="sr" style="color: #009926;">/$sample->{'file'}.$sample->{'suffix'}$/</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="169" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
169
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<td class="new_line diff-line-num" data-linenumber="169" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
169
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC169" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Guessing the sample name from the input path won't work.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="808" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="808" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -808,12 +808,12 @@ sub parse_command_line {</td>
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<td class="old_line diff-line-num" data-linenumber="808" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
808
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<td class="new_line diff-line-num" data-linenumber="808" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
808
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC808" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="vg" style="color: teal;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^--catalog-popmap$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$cpopmap_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="nv" style="color: teal;">@ARGV</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="809" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
809
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<td class="new_line diff-line-num" data-linenumber="809" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
809
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC809" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="vg" style="color: teal;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^-T$/</span> <span class="o" style="font-weight: 600;">||</span> <span class="vg" style="color: teal;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^--threads/</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="810" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
810
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<td class="new_line diff-line-num" data-linenumber="810" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
810
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC810" class="line" lang="perl"> <span class="nv" style="color: teal;">$arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="nv" style="color: teal;">@ARGV</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="811" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
811
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<td class="new_line diff-line-num old" data-linenumber="811" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC811" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: teal;">@_ustacks</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">-<span class="idiff left right deletion" style="background-color: #fac5cd;">p</span> </span><span class="p">"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$arg</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="812" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
812
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<td class="new_line diff-line-num old" data-linenumber="811" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC812" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: teal;">@_cstacks</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">-<span class="idiff left right deletion" style="background-color: #fac5cd;">p</span> </span><span class="p">"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$arg</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="813" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
813
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<td class="new_line diff-line-num old" data-linenumber="811" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC813" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: teal;">@_sstacks</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">-<span class="idiff left right deletion" style="background-color: #fac5cd;">p</span> </span><span class="p">"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$arg</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="814" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
814
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<td class="new_line diff-line-num old" data-linenumber="811" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC814" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: teal;">@_tsv2bam</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">-<span class="idiff left right deletion" style="background-color: #fac5cd;">t</span> </span><span class="p">"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$arg</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="815" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
815
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<td class="new_line diff-line-num old" data-linenumber="811" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC815" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: teal;">@_gstacks</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">-<span class="idiff left right deletion" style="background-color: #fac5cd;">t</span> </span><span class="p">"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$arg</span><span class="p">);</span></span>
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816
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<td class="new_line diff-line-num old" data-linenumber="811" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC816" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: teal;">@_populations</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">-<span class="idiff left right deletion" style="background-color: #fac5cd;">t</span> </span><span class="p">"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$arg</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="811" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
811
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC811" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: teal;">@_ustacks</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">-<span class="idiff left right addition" style="background-color: #c7f0d2;">-threads</span> </span><span class="p">"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$arg</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="817" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="812" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
812
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC812" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: teal;">@_cstacks</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">-<span class="idiff left right addition" style="background-color: #c7f0d2;">-threads</span> </span><span class="p">"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$arg</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="817" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="813" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
813
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC813" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: teal;">@_sstacks</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">-<span class="idiff left right addition" style="background-color: #c7f0d2;">-threads</span> </span><span class="p">"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$arg</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="817" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="814" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
814
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC814" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: teal;">@_tsv2bam</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">-<span class="idiff left right addition" style="background-color: #c7f0d2;">-threads</span> </span><span class="p">"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$arg</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="815" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
815
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC815" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: teal;">@_gstacks</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">-<span class="idiff left right addition" style="background-color: #c7f0d2;">-threads</span> </span><span class="p">"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$arg</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="817" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="816" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
816
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC816" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: teal;">@_populations</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">-<span class="idiff left right addition" style="background-color: #c7f0d2;">-threads</span> </span><span class="p">"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$arg</span><span class="p">);</span></span>
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817
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<td class="new_line diff-line-num" data-linenumber="817" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
817
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC817" class="line" lang="perl"></span>
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<td class="old_line diff-line-num" data-linenumber="818" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
818
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<td class="new_line diff-line-num" data-linenumber="818" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
818
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC818" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="vg" style="color: teal;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^-M$/</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="819" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
819
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<td class="new_line diff-line-num" data-linenumber="819" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
819
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC819" class="line" lang="perl"> <span class="nv" style="color: teal;">$ustacks_mismatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">(</span><span class="nv" style="color: teal;">@ARGV</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#8035c04d156a13d0aefa8edc446bb296143294f8"><strong style="font-weight: 600;">scripts/stacks-dist-extract</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="133" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="133" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -133,13 +133,16 @@ def find_section(sections, section):</td>
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<td class="old_line diff-line-num" data-linenumber="133" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
133
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<td class="new_line diff-line-num" data-linenumber="133" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
133
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC133" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pretty_print</span><span class="p">(</span><span class="n" style="color: #333;">stream</span><span class="p">):</span></span>
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<td class="old_line diff-line-num" data-linenumber="134" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
134
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<td class="new_line diff-line-num" data-linenumber="134" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
134
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">colcnts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="old_line diff-line-num" data-linenumber="135" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
135
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<td class="new_line diff-line-num" data-linenumber="135" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
135
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">stream</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
136
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">#</span><span class="sh" style="color: #d14;">'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
137
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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138
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC138" class="line" lang="python"></span>
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<td class="new_line diff-line-num" data-linenumber="139" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
139
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="sh" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="sh" style="color: #d14;">'</span><span class="p">)</span></span>
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140
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC140" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="138" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
138
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<td class="new_line diff-line-num" data-linenumber="141" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
141
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC141" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">colcnts</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">):</span></span>
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139
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<td class="new_line diff-line-num" data-linenumber="142" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
142
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">colcnts</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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140
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<td class="new_line diff-line-num old" data-linenumber="143" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC140" class="line" lang="python"><span class="idiff left right deletion" style="background-color: #fac5cd;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
143
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC143" class="line" lang="python"></span>
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141
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<td class="new_line diff-line-num" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
144
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nf" style="color: #900; font-weight: 600;">range</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">)):</span></span>
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142
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<td class="new_line diff-line-num old" data-linenumber="145" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">cols</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">i</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">][</span></span><span class="mi" style="color: #099;"><span class="idiff deletion" style="background-color: #fac5cd;">0</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">]</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">!=</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sh" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">#</span></span><span class="sh" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="ow" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">and</span></span><span class="idiff right deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;">colcnts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
145
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">colcnts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]):</span></span>
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<td class="old_line diff-line-num" data-linenumber="143" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
143
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<td class="new_line diff-line-num" data-linenumber="146" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
146
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">colcnts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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147
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC147" class="line" lang="python"></span>
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148
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">""</span></span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#9af07f1911c400b9a3863d9a1ffe88c1793ff2c6"><strong style="font-weight: 600;">scripts/stacks-private-alleles</strong></a>
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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python3</span></span>
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2
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright 2021-2024, Julian Catchen <jcatchen@illinois.edu></span></span>
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># This file is part of Stacks.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Stacks is free software: you can redistribute it and/or modify</span></span>
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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC8" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># it under the terms of the GNU General Public License as published by</span></span>
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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
9
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># the Free Software Foundation, either version 3 of the License, or</span></span>
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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># (at your option) any later version.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
11
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC11" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
12
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Stacks is distributed in the hope that it will be useful,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
13
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
14
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
15
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC15" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># GNU General Public License for more details.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
16
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC16" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
17
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC17" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># You should have received a copy of the GNU General Public License</span></span>
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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
18
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC18" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># along with Stacks. If not, see <http://www.gnu.org/licenses/>.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
19
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC19" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
20
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC20" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
21
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">argparse</span></span>
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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
22
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">sys</span></span>
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23
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">os</span></span>
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24
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">math</span></span>
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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
25
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">datetime</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">datetime</span></span>
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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
26
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC26" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">enum</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Enum</span></span>
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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
27
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">operator</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">itemgetter</span><span class="p">,</span> <span class="n" style="color: #333;">attrgetter</span></span>
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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
28
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC28" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
29
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC29" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
30
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC30" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Constant values</span></span>
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31
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC31" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
32
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC32" class="line" lang="python"><span class="n" style="color: #333;">SUMSTATS_COLS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">21</span></span>
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<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
33
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC33" class="line" lang="python"><span class="n" style="color: #333;">VCF_SAMP_STRT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">9</span></span>
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34
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC34" class="line" lang="python"></span>
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35
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC35" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
36
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC36" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Global configuration variables.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
37
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC37" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
38
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC38" class="line" lang="python"><span class="n" style="color: #333;">sumstats_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">""</span></span>
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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
39
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC39" class="line" lang="python"><span class="n" style="color: #333;">vcf_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">""</span></span>
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40
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC40" class="line" lang="python"><span class="n" style="color: #333;">popmap_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">""</span></span>
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41
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC41" class="line" lang="python"><span class="n" style="color: #333;">popmap_used</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
42
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC42" class="line" lang="python"><span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">""</span></span>
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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
43
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC43" class="line" lang="python"><span class="n" style="color: #333;">ref_aligned</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
44
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC44" class="line" lang="python"><span class="n" style="color: #333;">ctg_limit</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">500000</span></span>
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<td class="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
45
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC45" class="line" lang="python"><span class="n" style="color: #333;">polarize</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
46
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC46" class="line" lang="python"><span class="n" style="color: #333;">plots</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
47
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC47" class="line" lang="python"><span class="n" style="color: #333;">smooth</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
48
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC48" class="line" lang="python"><span class="n" style="color: #333;">sigma</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">150000.0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
49
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC49" class="line" lang="python"><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
50
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC50" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
51
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC51" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Strand</span><span class="p">(</span><span class="n" style="color: #333;">Enum</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
52
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">plus</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
53
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">minus</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
54
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC54" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
55
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC55" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SmoothStat</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
56
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">loc_id</span><span class="p">,</span> <span class="n" style="color: #333;">pop</span><span class="p">,</span> <span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">allele_cnt</span><span class="p">,</span> <span class="n" style="color: #333;">stat</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
57
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loc_id</span></span>
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<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
58
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">pop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pop</span></span>
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<td class="new_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
59
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">col</span></span>
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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
60
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">chr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">chr</span></span>
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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
61
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bp</span></span>
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<td class="new_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
62
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allele_cnt</span></span>
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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
63
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">stat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat</span></span>
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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
64
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">smoothed</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
65
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC65" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
66
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC66" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Pop</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
67
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">pop</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">cnt</span><span class="p">,</span> <span class="n" style="color: #333;">priv</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
68
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">pop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pop</span></span>
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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
69
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">p_freq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span></span>
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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
70
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">q_freq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q</span></span>
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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
71
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cnt</span></span>
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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
72
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">private</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">priv</span></span>
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<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
73
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">priv_all</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span> <span class="c1" style="color: #998; font-style: italic;"># If there is a private allele, which one is it?</span></span>
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<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
74
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC74" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
75
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__str__</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
76
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">{} - p freq: {:.3f}; q freq: {:.3f}; sample cnt: {}; private? {}</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>
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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
77
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">,</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">p_freq</span><span class="p">,</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">q_freq</span><span class="p">,</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">cnt</span><span class="p">,</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">private</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
78
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">private</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
79
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"> [allele: </span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">{}</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">]</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">priv_all</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
80
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC80" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
81
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="82" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
82
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC82" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
83
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC83" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SNP</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
84
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
85
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
86
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
87
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">p_allele</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">""</span></span>
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<td class="new_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
88
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">q_allele</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">""</span></span>
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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
89
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">pops</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span> <span class="c1" style="color: #998; font-style: italic;"># Includes parental populations and 'vcf' for all VCF samples.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
90
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span> <span class="c1" style="color: #998; font-style: italic;"># Indexed by population name; includes individual populations from VCF.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
91
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">priv_pop</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span> <span class="c1" style="color: #998; font-style: italic;"># True if there is a private allele in one or more of the populations at this site.</span></span>
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92
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">priv_hyb</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span> <span class="c1" style="color: #998; font-style: italic;"># Is the private allele present in the hybrids?</span></span>
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<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
93
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC93" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
94
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__str__</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
95
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">Column {}; P allele: </span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">{}</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">, Q allele </span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">{}</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">, private? {}</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">p_allele</span><span class="p">,</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">q_allele</span><span class="p">,</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">priv_pop</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
96
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span></span>
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<td class="new_line diff-line-num new" data-linenumber="97" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
97
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC97" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
98
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC98" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Locus</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
99
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">id</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
100
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">id</span></span>
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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
101
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">chr</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="new_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
102
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
103
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">snps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span> <span class="c1" style="color: #998; font-style: italic;"># Indexed by column.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
104
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">private</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span> <span class="c1" style="color: #998; font-style: italic;"># At least one SNP at this locus contains a private allele.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="105" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
105
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__str__</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
106
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">Locus {}</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
107
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">chr</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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108
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"> [{}:{}:{}]</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">strand</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
109
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">; {} snp(s)</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">snps</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="110" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
110
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">snp</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">snps</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
111
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"> </span><span class="sh" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="112" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
112
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">snps</span><span class="p">[</span><span class="n" style="color: #333;">snp</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">__str__</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
113
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pop</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">snps</span><span class="p">[</span><span class="n" style="color: #333;">snp</span><span class="p">].</span><span class="n" style="color: #333;">pops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
114
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"> </span><span class="sh" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
115
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">snps</span><span class="p">[</span><span class="n" style="color: #333;">snp</span><span class="p">].</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="n" style="color: #333;">pop</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">__str__</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="116" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
116
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC116" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span></span>
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<td class="new_line diff-line-num new" data-linenumber="117" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
117
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC117" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
118
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC118" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
119
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC119" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_command_line</span><span class="p">():</span></span>
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<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
120
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC120" class="line" lang="python"> <span class="k" style="font-weight: 600;">global</span> <span class="n" style="color: #333;">sumstats_path</span></span>
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<td class="new_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
121
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">global</span> <span class="n" style="color: #333;">vcf_path</span></span>
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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
122
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">global</span> <span class="n" style="color: #333;">popmap_path</span><span class="p">,</span> <span class="n" style="color: #333;">popmap_used</span></span>
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<td class="new_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
123
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC123" class="line" lang="python"> <span class="k" style="font-weight: 600;">global</span> <span class="n" style="color: #333;">out_path</span></span>
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124
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">global</span> <span class="n" style="color: #333;">polarize</span></span>
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<td class="new_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
125
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">global</span> <span class="n" style="color: #333;">plots</span><span class="p">,</span> <span class="n" style="color: #333;">smooth</span><span class="p">,</span> <span class="n" style="color: #333;">sigma</span></span>
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<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
126
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">global</span> <span class="n" style="color: #333;">verbose</span></span>
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<td class="new_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
127
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC127" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
128
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">desc</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">'''</span><span class="s" style="color: #d14;">Supply the populations.sumstats.tsv file containing the </span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">parental</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;"> populations </span><span class="se" style="color: #d14;">\</span></span>
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<td class="new_line diff-line-num new" data-linenumber="129" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
129
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC129" class="line" lang="python"><span class="s" style="color: #d14;"> which were used to define private alleles. Supply a VCF file from the </span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">hybrid</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
130
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC130" class="line" lang="python"><span class="s" style="color: #d14;"> populations which may contain those private alleles. Optionally export a set of VCF </span><span class="se" style="color: #d14;">\</span></span>
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<td class="new_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
131
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC131" class="line" lang="python"><span class="s" style="color: #d14;"> files, one per parental population, that list SNPs with the non-private allele as </span><span class="se" style="color: #d14;">\</span></span>
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<td class="new_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
132
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC132" class="line" lang="python"><span class="s" style="color: #d14;"> </span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">REF</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;"> and the private allele as </span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">ALT</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;"> for plotting.</span><span class="sh" style="color: #d14;">'''</span></span>
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<td class="new_line diff-line-num new" data-linenumber="133" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
133
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC133" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="134" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
134
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">desc</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="135" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
135
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC135" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
136
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC136" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
137
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC137" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Add options.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
138
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC138" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
139
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">add_argument</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">--sumstats</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">path</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="140" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
140
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">path to parental populations sumstats file.</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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141
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">add_argument</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">--vcf</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">path</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="142" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
142
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">path to hybrids VCF file.</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
143
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">add_argument</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">--popmap</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">path</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
144
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">path to a population map used to generate the VCF file.</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
145
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">add_argument</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">--polarize</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">store_true</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
146
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">Export a set of VCF files, one per parent population, with private alleles polarized.</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
147
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">add_argument</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">--plots</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">store_true</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
148
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">Write a file for plotting private allele frequencies along the genome.</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
149
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">add_argument</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">--smooth</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">store_true</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
150
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">Smooth private allele values in plotting files, if data are referenced aligned.</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
151
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">add_argument</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">--sigma</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">size</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
152
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">Control the smoothing. Default 75000bp, increase to smooth more, decrease to smooth less.</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
153
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">add_argument</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">-o</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">--out-path</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">prefix</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
154
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">prefix path for writing output files.</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
155
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">add_argument</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">--verbose</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">store_true</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">verbose</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
156
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">Ouput a summary of each locus.</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
157
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC157" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
158
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC158" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
159
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC159" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Parse the command line</span></span>
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<td class="new_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
160
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC160" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="161" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
161
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse_args</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
162
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC162" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="163" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
163
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
164
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">vcf_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span></span>
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<td class="new_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
165
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">popmap</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
166
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">popmap_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">popmap</span></span>
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<td class="new_line diff-line-num new" data-linenumber="167" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
167
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">popmap_used</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
168
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC168" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sumstats</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
169
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">sumstats_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sumstats</span></span>
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<td class="new_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
170
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
171
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">out_path</span></span>
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<td class="new_line diff-line-num new" data-linenumber="172" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
172
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="173" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
173
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">verbose</span></span>
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<td class="new_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
174
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC174" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">polarize</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="175" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
175
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">polarize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">polarize</span></span>
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<td class="new_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
176
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC176" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plots</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="177" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
177
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">plots</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plots</span></span>
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<td class="new_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
178
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">smooth</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="179" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
179
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">smooth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">smooth</span></span>
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<td class="new_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
180
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC180" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sigma</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
181
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">sigma</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sigma</span></span>
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<td class="new_line diff-line-num new" data-linenumber="182" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
182
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC182" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="183" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
183
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">sumstats_path</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="184" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
184
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC184" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">You must specify the path to the sumstats file.</span><span class="sh" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="185" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
185
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">print_help</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="186" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
186
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">exit</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="187" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
187
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC187" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">vcf_path</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
188
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC188" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">You must specify the path to the hybrids VCF file.</span><span class="sh" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="189" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
189
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">print_help</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="190" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
190
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">exit</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="191" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
191
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC191" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">out_path</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="192" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
192
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC192" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">You must specify a path prefix to output files.</span><span class="sh" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
193
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">print_help</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="194" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
194
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">exit</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="195" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
195
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC195" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="196" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
196
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC196" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="197" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
197
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC197" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">complement</span><span class="p">(</span><span class="n" style="color: #333;">nuc</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="198" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
198
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC198" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nuc</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">A</span><span class="sh" style="color: #d14;">'</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
199
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC199" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">T</span><span class="sh" style="color: #d14;">'</span></span>
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<td class="new_line diff-line-num new" data-linenumber="200" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
200
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC200" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">nuc</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">C</span><span class="sh" style="color: #d14;">'</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="201" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
201
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC201" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">G</span><span class="sh" style="color: #d14;">'</span></span>
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<td class="new_line diff-line-num new" data-linenumber="202" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
202
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC202" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">nuc</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">G</span><span class="sh" style="color: #d14;">'</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="203" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
203
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">C</span><span class="sh" style="color: #d14;">'</span></span>
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<td class="new_line diff-line-num new" data-linenumber="204" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
204
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">nuc</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">T</span><span class="sh" style="color: #d14;">'</span><span class="p">:</span></span>
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205
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">A</span><span class="sh" style="color: #d14;">'</span></span>
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<td class="new_line diff-line-num new" data-linenumber="206" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
206
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">nuc</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">a</span><span class="sh" style="color: #d14;">'</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="207" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
207
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">t</span><span class="sh" style="color: #d14;">'</span></span>
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<td class="new_line diff-line-num new" data-linenumber="208" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
208
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">nuc</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">c</span><span class="sh" style="color: #d14;">'</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="209" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
209
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">g</span><span class="sh" style="color: #d14;">'</span></span>
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<td class="new_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
210
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">nuc</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">g</span><span class="sh" style="color: #d14;">'</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="211" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
211
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC211" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">c</span><span class="sh" style="color: #d14;">'</span></span>
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<td class="new_line diff-line-num new" data-linenumber="212" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
212
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC212" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">nuc</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">t</span><span class="sh" style="color: #d14;">'</span><span class="p">:</span></span>
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213
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC213" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">a</span><span class="sh" style="color: #d14;">'</span></span>
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214
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC214" class="line" lang="python"></span>
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215
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC215" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="216" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
216
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC216" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_popmap_file</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">,</span> <span class="n" style="color: #333;">vcfpops_rev</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="217" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
217
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">r</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
218
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC218" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="219" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
219
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC219" class="line" lang="python"> <span class="n" style="color: #333;">lineno</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="220" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
220
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC220" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="221" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
221
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">lineno</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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222
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">strip</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="223" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
223
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC223" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="224" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
224
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC224" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">#</span><span class="sh" style="color: #d14;">"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="225" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
225
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC225" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="226" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
226
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC226" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="227" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
227
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="228" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
228
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC228" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="229" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
229
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC229" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">Error parsing popmap </span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">{}</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;"> at line {}</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">lineno</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="230" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
230
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC230" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">exit</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="231" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
231
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC231" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="232" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
232
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC232" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="233" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
233
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC233" class="line" lang="python"> <span class="n" style="color: #333;">vcfpops</span><span class="p">[</span><span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="234" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
234
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC234" class="line" lang="python"> <span class="n" style="color: #333;">vcfpops</span><span class="p">[</span><span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]].</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="235" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
235
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">vcfpops_rev</span><span class="p">[</span><span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="236" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
236
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC236" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="237" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
237
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC237" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"> Found {} samples in {} populations.</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">vcfpops_rev</span><span class="p">),</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">vcfpops</span><span class="p">)),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="238" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
238
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<td class="new_line diff-line-num new" data-linenumber="239" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
239
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC239" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
240
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC240" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="241" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
241
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC241" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_sumstats_file</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">loci</span><span class="p">,</span> <span class="n" style="color: #333;">populations_key</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="242" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
242
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC242" class="line" lang="python"> <span class="k" style="font-weight: 600;">global</span> <span class="n" style="color: #333;">ref_aligned</span><span class="p">,</span> <span class="n" style="color: #333;">ctg_limit</span><span class="p">,</span> <span class="n" style="color: #333;">smooth</span><span class="p">,</span> <span class="n" style="color: #333;">plots</span></span>
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<td class="new_line diff-line-num new" data-linenumber="243" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
243
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC243" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="244" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
244
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">r</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="245" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
245
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC245" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="246" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
246
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC246" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="247" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
247
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC247" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Parse the sumstats header and extract the population names/sample names</span></span>
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<td class="new_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
248
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC248" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="249" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
249
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC249" class="line" lang="python"> <span class="n" style="color: #333;">lineno</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="250" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
250
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC250" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="251" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
251
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">lineno</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="252" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
252
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">strip</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="253" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
253
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC253" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="254" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
254
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC254" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">#</span><span class="sh" style="color: #d14;">"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">10</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"># Locus ID</span><span class="sh" style="color: #d14;">"</span><span class="p">:</span></span>
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255
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC255" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<td class="new_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
256
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC256" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="257" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
257
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC257" class="line" lang="python"> <span class="n" style="color: #333;">parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="258" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
258
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">pop_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">:]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="259" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
259
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC259" class="line" lang="python"> <span class="n" style="color: #333;">populations_key</span><span class="p">[</span><span class="n" style="color: #333;">pop_name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">,</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="260" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
260
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC260" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="261" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
261
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC261" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
262
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC262" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Parse SNP records.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="263" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
263
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC263" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="264" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
264
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC264" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="265" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
265
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC265" class="line" lang="python"> <span class="n" style="color: #333;">lineno</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="266" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
266
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">strip</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="267" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
267
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC267" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="268" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
268
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC268" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">#</span><span class="sh" style="color: #d14;">"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="269" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
269
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC269" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="270" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
270
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC270" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="271" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
271
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC271" class="line" lang="python"> <span class="n" style="color: #333;">parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="272" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
272
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC272" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="273" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
273
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">SUMSTATS_COLS</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="274" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
274
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC274" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">Error parsing </span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">{}</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;"> on line {}, incorrect number of columns (</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">{}</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">), file not in correct format.</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>
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<td class="new_line diff-line-num new" data-linenumber="275" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
275
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">lineno</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">)),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="276" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
276
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC276" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">exit</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="277" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
277
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC277" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="278" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
278
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC278" class="line" lang="python"> <span class="n" style="color: #333;">locus_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="279" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
279
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">column</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="280" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
280
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">popul</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="281" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
281
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC281" class="line" lang="python"> <span class="n" style="color: #333;">p_allele</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="282" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
282
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC282" class="line" lang="python"> <span class="n" style="color: #333;">q_allele</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="283" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
283
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC283" class="line" lang="python"> <span class="n" style="color: #333;">all_cnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">])</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span></span>
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<td class="new_line diff-line-num new" data-linenumber="284" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
284
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC284" class="line" lang="python"> <span class="n" style="color: #333;">p_freq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">float</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="285" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
285
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">q_freq</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">p_freq</span></span>
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<td class="new_line diff-line-num new" data-linenumber="286" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
286
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">private</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">20</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">1</span><span class="sh" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="new_line diff-line-num new" data-linenumber="287" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
287
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC287" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="288" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
288
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC288" class="line" lang="python"> <span class="n" style="color: #333;">pop</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Pop</span><span class="p">(</span><span class="n" style="color: #333;">popul</span><span class="p">,</span> <span class="n" style="color: #333;">p_freq</span><span class="p">,</span> <span class="n" style="color: #333;">q_freq</span><span class="p">,</span> <span class="n" style="color: #333;">all_cnt</span><span class="p">,</span> <span class="n" style="color: #333;">private</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="289" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
289
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC289" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="290" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
290
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC290" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="291" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
291
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC291" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Have we already seen this locus and SNP?</span></span>
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<td class="new_line diff-line-num new" data-linenumber="292" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
292
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC292" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="293" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
293
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC293" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">locus_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">loci</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="294" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
294
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC294" class="line" lang="python"> <span class="n" style="color: #333;">loc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loci</span><span class="p">[</span><span class="n" style="color: #333;">locus_id</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="295" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
295
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC295" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="296" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
296
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">loc</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Locus</span><span class="p">(</span><span class="n" style="color: #333;">locus_id</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="297" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
297
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">loci</span><span class="p">[</span><span class="n" style="color: #333;">locus_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loc</span></span>
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<td class="new_line diff-line-num new" data-linenumber="298" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
298
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC298" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="299" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
299
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC299" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#if parts[1] != "un":</span></span>
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<td class="new_line diff-line-num new" data-linenumber="300" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
300
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC300" class="line" lang="python"> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">chr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="301" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
301
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC301" class="line" lang="python"> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="302" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
302
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC302" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="303" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
303
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC303" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">private</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="304" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
304
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC304" class="line" lang="python"> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">private</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="new_line diff-line-num new" data-linenumber="305" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
305
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC305" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="306" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
306
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC306" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">column</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">snps</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="307" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
307
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC307" class="line" lang="python"> <span class="n" style="color: #333;">snp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">snps</span><span class="p">[</span><span class="n" style="color: #333;">column</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
308
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC308" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
309
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC309" class="line" lang="python"> <span class="n" style="color: #333;">snp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">SNP</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="310" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
310
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC310" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="311" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
311
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC311" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">column</span></span>
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<td class="new_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
312
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC312" class="line" lang="python"> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">snps</span><span class="p">[</span><span class="n" style="color: #333;">column</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">snp</span></span>
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<td class="new_line diff-line-num new" data-linenumber="313" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
313
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC313" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="314" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
314
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">p_allele</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">-</span><span class="sh" style="color: #d14;">"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="315" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
315
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC315" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">p_allele</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p_allele</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="316" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
316
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC316" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">q_allele</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">-</span><span class="sh" style="color: #d14;">"</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="317" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
317
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC317" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">q_allele</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_allele</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="318" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
318
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC318" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">private</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="319" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
319
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC319" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">priv_pop</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="new_line diff-line-num new" data-linenumber="320" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
320
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC320" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="321" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
321
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC321" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="n" style="color: #333;">popul</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pop</span></span>
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<td class="new_line diff-line-num new" data-linenumber="322" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
322
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC322" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="323" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
323
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="324" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
324
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC324" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="325" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
325
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC325" class="line" lang="python"> <span class="n" style="color: #333;">snp_cnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="326" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
326
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC326" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">loci</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="327" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
327
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC327" class="line" lang="python"> <span class="n" style="color: #333;">loc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loci</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="328" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
328
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">snp_cnt</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">snps</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="329" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
329
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC329" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="330" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
330
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC330" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Find which allele, or alleles, was/were the private one.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="331" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
331
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC331" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># In most cases, a single allele will be private between the parent populations.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="332" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
332
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC332" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># However, there can be alternative, private alleles where each parent population</span></span>
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<td class="new_line diff-line-num new" data-linenumber="333" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
333
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC333" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># has a unique allele.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="334" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
334
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC334" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="335" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
335
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC335" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">private</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">False</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="336" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
336
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC336" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="337" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
337
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC337" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="338" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
338
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC338" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">col</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">snps</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
339
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC339" class="line" lang="python"> <span class="n" style="color: #333;">snp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">snps</span><span class="p">[</span><span class="n" style="color: #333;">col</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="340" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
340
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC340" class="line" lang="python"> <span class="n" style="color: #333;">alleles</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">p_allele</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">q_allele</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="341" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
341
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC341" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="342" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
342
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="343" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
343
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC343" class="line" lang="python"> <span class="n" style="color: #333;">pop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
344
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC344" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">p_freq</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="345" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
345
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC345" class="line" lang="python"> <span class="n" style="color: #333;">alleles</span><span class="p">[</span><span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">p_allele</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="346" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
346
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC346" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">q_freq</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="347" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
347
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC347" class="line" lang="python"> <span class="n" style="color: #333;">alleles</span><span class="p">[</span><span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">q_allele</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="348" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
348
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC348" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="349" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
349
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC349" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="350" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
350
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC350" class="line" lang="python"> <span class="n" style="color: #333;">pop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="351" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
351
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC351" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">private</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="352" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
352
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC352" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">alleles</span><span class="p">[</span><span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">p_allele</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">p_freq</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="353" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
353
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC353" class="line" lang="python"> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">priv_all</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">p_allele</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="354" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
354
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC354" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">alleles</span><span class="p">[</span><span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">q_allele</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">q_freq</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="355" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
355
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC355" class="line" lang="python"> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">priv_all</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">q_allele</span></span>
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<td class="new_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
356
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC356" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="357" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
357
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC357" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"> Read {} loci containing {} SNPs.</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">loci</span><span class="p">),</span> <span class="n" style="color: #333;">snp_cnt</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="358" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
358
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC358" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
359
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC359" class="line" lang="python"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">next</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">iter</span><span class="p">(</span><span class="n" style="color: #333;">loci</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="360" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
360
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC360" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">loci</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="nb" style="color: #0086b3;">chr</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">un</span><span class="sh" style="color: #d14;">"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">loci</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">].</span><span class="nb" style="color: #0086b3;">chr</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="361" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
361
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC361" class="line" lang="python"> <span class="n" style="color: #333;">ref_aligned</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="new_line diff-line-num new" data-linenumber="362" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
362
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC362" class="line" lang="python"> <span class="n" style="color: #333;">ctg_limit</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="363" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
363
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC363" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">smooth</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">plots</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="364" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
364
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC364" class="line" lang="python"> <span class="n" style="color: #333;">smooth</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="new_line diff-line-num new" data-linenumber="365" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
365
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC365" class="line" lang="python"> <span class="n" style="color: #333;">plots</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="new_line diff-line-num new" data-linenumber="366" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
366
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC366" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">Warning: unable to generate plots or smooth them without reference-aligned data.</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="367" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
367
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC367" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
368
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC368" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="369" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
369
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC369" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_hybrid_vcf</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">loci</span><span class="p">,</span> <span class="n" style="color: #333;">populations_key</span><span class="p">,</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">,</span> <span class="n" style="color: #333;">vcfpops_rev</span><span class="p">,</span> <span class="n" style="color: #333;">chrs_list</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="370" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
370
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC370" class="line" lang="python"> <span class="k" style="font-weight: 600;">global</span> <span class="n" style="color: #333;">ref_aligned</span></span>
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<td class="new_line diff-line-num new" data-linenumber="371" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
371
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC371" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="372" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
372
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC372" class="line" lang="python"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">r</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="373" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
373
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC373" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="374" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
374
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC374" class="line" lang="python"> <span class="n" style="color: #333;">not_found</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="375" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
375
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC375" class="line" lang="python"> <span class="n" style="color: #333;">snp_cnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="376" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
376
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC376" class="line" lang="python"> <span class="n" style="color: #333;">locus_cnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">set</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="377" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
377
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC377" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="378" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
378
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC378" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="379" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
379
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC379" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Parse the chromosome names and lengths from the VCF header, if available.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="380" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
380
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC380" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="381" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
381
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC381" class="line" lang="python"> <span class="n" style="color: #333;">lineno</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="382" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
382
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="383" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
383
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC383" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="384" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
384
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC384" class="line" lang="python"> <span class="n" style="color: #333;">lineno</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="385" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
385
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC385" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">strip</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="386" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
386
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC386" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="387" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
387
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC387" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="388" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
388
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC388" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Skip the file definition lines, but record the contig lengths.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="389" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
389
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC389" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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390
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC390" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">##contig</span><span class="sh" style="color: #d14;">"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="391" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
391
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC391" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">13</span><span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="392" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
392
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC392" class="line" lang="python"> <span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">chrlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">,</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="393" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
393
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC393" class="line" lang="python"> <span class="n" style="color: #333;">chrlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chrlen</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">:]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="394" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
394
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC394" class="line" lang="python"> <span class="n" style="color: #333;">chrs_list</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">chrlen</span><span class="p">))</span> <span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="395" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
395
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC395" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="396" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
396
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC396" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">#CHROM</span><span class="sh" style="color: #d14;">"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="397" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
397
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC397" class="line" lang="python"> <span class="n" style="color: #333;">parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="398" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
398
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC398" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<td class="new_line diff-line-num new" data-linenumber="399" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
399
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC399" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
400
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC400" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ref_aligned</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">False</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="401" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
401
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC401" class="line" lang="python"> <span class="n" style="color: #333;">chrs_list</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span> <span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">un</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="402" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
402
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC402" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="403" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
403
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC403" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="404" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
404
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC404" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># List of sample names, to be taken from the VCF header.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="405" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
405
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC405" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="406" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
406
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC406" class="line" lang="python"> <span class="n" style="color: #333;">populations_key</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="407" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
407
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC407" class="line" lang="python"> <span class="n" style="color: #333;">sample_cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="408" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
408
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC408" class="line" lang="python"> <span class="n" style="color: #333;">pop_cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="409" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
409
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC409" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
410
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC410" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">popmap_used</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="411" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
411
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC411" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="412" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
412
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC412" class="line" lang="python"> <span class="n" style="color: #333;">pop_cols</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="413" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
413
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC413" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="414" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
414
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC414" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="415" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
415
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC415" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Parse the sample names from the VCF header and record which columns the samples from</span></span>
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<td class="new_line diff-line-num new" data-linenumber="416" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
416
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC416" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># each population occur in.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="417" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
417
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC417" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="418" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
418
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC418" class="line" lang="python"> <span class="n" style="color: #333;">popmap_samples_found</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="419" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
419
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC419" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nf" style="color: #900; font-weight: 600;">range</span><span class="p">(</span><span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">)):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="420" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
420
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC420" class="line" lang="python"> <span class="n" style="color: #333;">populations_key</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="421" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
421
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC421" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="422" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
422
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC422" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">popmap_used</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vcfpops_rev</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="423" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
423
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC423" class="line" lang="python"> <span class="n" style="color: #333;">popmap_samples_found</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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424
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC424" class="line" lang="python"> <span class="n" style="color: #333;">sample_cols</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vcfpops_rev</span><span class="p">[</span><span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="425" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
425
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC425" class="line" lang="python"> <span class="n" style="color: #333;">pop_cols</span><span class="p">[</span><span class="n" style="color: #333;">vcfpops_rev</span><span class="p">[</span><span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]]].</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="426" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
426
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC426" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="427" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
427
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC427" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">popmap_used</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="428" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
428
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC428" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"> Found {} samples from population map in VCF file.</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">popmap_samples_found</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="429" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
429
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC429" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="430" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
430
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC430" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="431" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
431
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC431" class="line" lang="python"> <span class="n" style="color: #333;">lineno</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="432" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
432
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC432" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">strip</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="433" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
433
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC433" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="434" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
434
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC434" class="line" lang="python"> <span class="n" style="color: #333;">parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
435
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC435" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="436" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
436
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC436" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="437" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
437
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC437" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If referenced aligned, column 3 contains the locus ID, column of the SNP within the</span></span>
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<td class="new_line diff-line-num new" data-linenumber="438" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
438
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC438" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># locus and the strand, e.g. '152:79:-'</span></span>
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<td class="new_line diff-line-num new" data-linenumber="439" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
439
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC439" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Otherwise, if contains just the locus ID and column of the SNP.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="440" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
440
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC440" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># </span></span>
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441
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC441" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ref_aligned</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="442" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
442
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC442" class="line" lang="python"> <span class="n" style="color: #333;">locus_id</span><span class="p">,</span> <span class="n" style="color: #333;">column</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">:</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="443" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
443
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC443" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="444" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
444
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC444" class="line" lang="python"> <span class="n" style="color: #333;">locus_id</span><span class="p">,</span> <span class="n" style="color: #333;">column</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">:</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="445" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
445
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC445" class="line" lang="python"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">+</span><span class="sh" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="446" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
446
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC446" class="line" lang="python"> <span class="n" style="color: #333;">locus_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">locus_id</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="447" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
447
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC447" class="line" lang="python"> <span class="n" style="color: #333;">column</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">column</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="448" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
448
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC448" class="line" lang="python"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Strand</span><span class="p">.</span><span class="n" style="color: #333;">minus</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">-</span><span class="sh" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">Strand</span><span class="p">.</span><span class="n" style="color: #333;">plus</span></span>
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<td class="new_line diff-line-num new" data-linenumber="449" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
449
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC449" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="450" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
450
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC450" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">locus_id</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">loci</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="451" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
451
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC451" class="line" lang="python"> <span class="n" style="color: #333;">not_found</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="452" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
452
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC452" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="453" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
453
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC453" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">column</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">loci</span><span class="p">[</span><span class="n" style="color: #333;">locus_id</span><span class="p">].</span><span class="n" style="color: #333;">snps</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="454" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
454
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC454" class="line" lang="python"> <span class="n" style="color: #333;">not_found</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="455" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
455
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC455" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="456" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
456
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC456" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="457" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
457
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC457" class="line" lang="python"> <span class="n" style="color: #333;">locus_cnt</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">add</span><span class="p">(</span><span class="n" style="color: #333;">locus_id</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="458" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
458
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC458" class="line" lang="python"> <span class="n" style="color: #333;">snp_cnt</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="459" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
459
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC459" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="460" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
460
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC460" class="line" lang="python"> <span class="n" style="color: #333;">snp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loci</span><span class="p">[</span><span class="n" style="color: #333;">locus_id</span><span class="p">].</span><span class="n" style="color: #333;">snps</span><span class="p">[</span><span class="n" style="color: #333;">column</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="461" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
461
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC461" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="462" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
462
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC462" class="line" lang="python"> <span class="n" style="color: #333;">vcfpop</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Pop</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="463" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
463
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC463" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="464" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
464
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC464" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">popmap_used</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="465" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
465
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC465" class="line" lang="python"> <span class="n" style="color: #333;">indv_pops</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="466" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
466
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC466" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pop_cols</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="467" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
467
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC467" class="line" lang="python"> <span class="n" style="color: #333;">indv_pops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Pop</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="468" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
468
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC468" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="469" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
469
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC469" class="line" lang="python"> <span class="n" style="color: #333;">ref_allele</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="470" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
470
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC470" class="line" lang="python"> <span class="n" style="color: #333;">alt_allele</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="471" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
471
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC471" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="472" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
472
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC472" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Strand</span><span class="p">.</span><span class="n" style="color: #333;">minus</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="473" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
473
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC473" class="line" lang="python"> <span class="n" style="color: #333;">ref_allele</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">complement</span><span class="p">(</span><span class="n" style="color: #333;">ref_allele</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="474" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
474
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC474" class="line" lang="python"> <span class="n" style="color: #333;">alt_allele</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">complement</span><span class="p">(</span><span class="n" style="color: #333;">alt_allele</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="475" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
475
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC475" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="476" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
476
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC476" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">if </span><span class="p">((</span><span class="n" style="color: #333;">ref_allele</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">p_allele</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">ref_allele</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">q_allele</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span></span>
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<td class="new_line diff-line-num new" data-linenumber="477" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
477
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC477" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">alt_allele</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">p_allele</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">alt_allele</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">q_allele</span><span class="p">)):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="478" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
478
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC478" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">Error parsing VCF file on line {}; ref/alt alleles {}/{} do not match sumstats file ({}/{}).</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>
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<td class="new_line diff-line-num new" data-linenumber="479" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
479
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC479" class="line" lang="python"> <span class="n" style="color: #333;">lineno</span><span class="p">,</span> <span class="n" style="color: #333;">ref_allele</span><span class="p">,</span> <span class="n" style="color: #333;">alt_allele</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">p_allele</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">q_allele</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="480" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
480
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC480" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="481" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
481
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC481" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="482" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
482
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC482" class="line" lang="python"> <span class="n" style="color: #333;">genotypes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="483" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
483
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC483" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="484" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
484
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC484" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nf" style="color: #900; font-weight: 600;">range</span><span class="p">(</span><span class="n" style="color: #333;">VCF_SAMP_STRT</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">)):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="485" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
485
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC485" class="line" lang="python"> <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">,</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="486" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
486
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC486" class="line" lang="python"> <span class="n" style="color: #333;">gtype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">:</span><span class="sh" style="color: #d14;">"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="487" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
487
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC487" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="488" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
488
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC488" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">./.</span><span class="sh" style="color: #d14;">"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="489" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
489
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC489" class="line" lang="python"> <span class="n" style="color: #333;">sample_gtype</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span> <span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="490" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
490
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC490" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">gtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">0/0</span><span class="sh" style="color: #d14;">"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="491" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
491
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC491" class="line" lang="python"> <span class="n" style="color: #333;">sample_gtype</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">ref_allele</span><span class="p">,</span> <span class="n" style="color: #333;">ref_allele</span><span class="p">)</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="492" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
492
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC492" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">gtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">0/1</span><span class="sh" style="color: #d14;">"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="493" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
493
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC493" class="line" lang="python"> <span class="n" style="color: #333;">sample_gtype</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">ref_allele</span><span class="p">,</span> <span class="n" style="color: #333;">alt_allele</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="494" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
494
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC494" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">gtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">1/0</span><span class="sh" style="color: #d14;">"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="495" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
495
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC495" class="line" lang="python"> <span class="n" style="color: #333;">sample_gtype</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">ref_allele</span><span class="p">,</span> <span class="n" style="color: #333;">alt_allele</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="496" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
496
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC496" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">gtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">1/1</span><span class="sh" style="color: #d14;">"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
497
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC497" class="line" lang="python"> <span class="n" style="color: #333;">sample_gtype</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">alt_allele</span><span class="p">,</span> <span class="n" style="color: #333;">alt_allele</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="498" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
498
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC498" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="499" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
499
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC499" class="line" lang="python"> <span class="n" style="color: #333;">genotypes</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">sample_gtype</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="500" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
500
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC500" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
501
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC501" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nf" style="color: #900; font-weight: 600;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">genotypes</span><span class="p">)):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="502" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
502
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC502" class="line" lang="python"> <span class="n" style="color: #333;">gtype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genotypes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="503" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
503
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC503" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="504" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
504
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC504" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gtype</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="505" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
505
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC505" class="line" lang="python"> <span class="n" style="color: #333;">vcfpop</span><span class="p">.</span><span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="506" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
506
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC506" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gtype</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">p_allele</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="507" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
507
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC507" class="line" lang="python"> <span class="n" style="color: #333;">vcfpop</span><span class="p">.</span><span class="n" style="color: #333;">p_freq</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mf" style="color: #099;">1.0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="508" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
508
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC508" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="509" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
509
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC509" class="line" lang="python"> <span class="n" style="color: #333;">vcfpop</span><span class="p">.</span><span class="n" style="color: #333;">q_freq</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mf" style="color: #099;">1.0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="510" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
510
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC510" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gtype</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="511" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
511
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC511" class="line" lang="python"> <span class="n" style="color: #333;">vcfpop</span><span class="p">.</span><span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="512" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
512
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC512" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gtype</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">p_allele</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="513" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
513
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC513" class="line" lang="python"> <span class="n" style="color: #333;">vcfpop</span><span class="p">.</span><span class="n" style="color: #333;">p_freq</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mf" style="color: #099;">1.0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="514" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
514
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC514" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="515" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
515
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC515" class="line" lang="python"> <span class="n" style="color: #333;">vcfpop</span><span class="p">.</span><span class="n" style="color: #333;">q_freq</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mf" style="color: #099;">1.0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="516" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
516
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC516" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="517" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
517
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC517" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">popmap_used</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="518" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
518
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC518" class="line" lang="python"> <span class="n" style="color: #333;">indvpop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indv_pops</span><span class="p">[</span><span class="n" style="color: #333;">sample_cols</span><span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">VCF_SAMP_STRT</span><span class="p">]]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="519" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
519
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC519" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gtype</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="520" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
520
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC520" class="line" lang="python"> <span class="n" style="color: #333;">indvpop</span><span class="p">.</span><span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="521" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
521
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC521" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gtype</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">p_allele</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="522" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
522
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC522" class="line" lang="python"> <span class="n" style="color: #333;">indvpop</span><span class="p">.</span><span class="n" style="color: #333;">p_freq</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mf" style="color: #099;">1.0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="523" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
523
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC523" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="524" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
524
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC524" class="line" lang="python"> <span class="n" style="color: #333;">indvpop</span><span class="p">.</span><span class="n" style="color: #333;">q_freq</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mf" style="color: #099;">1.0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="525" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
525
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC525" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gtype</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="526" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
526
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC526" class="line" lang="python"> <span class="n" style="color: #333;">indvpop</span><span class="p">.</span><span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="527" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
527
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC527" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gtype</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">p_allele</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="528" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
528
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC528" class="line" lang="python"> <span class="n" style="color: #333;">indvpop</span><span class="p">.</span><span class="n" style="color: #333;">p_freq</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mf" style="color: #099;">1.0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="529" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
529
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC529" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="530" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
530
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC530" class="line" lang="python"> <span class="n" style="color: #333;">indvpop</span><span class="p">.</span><span class="n" style="color: #333;">q_freq</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mf" style="color: #099;">1.0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="531" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
531
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC531" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="532" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
532
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC532" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">vcfpop</span><span class="p">.</span><span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="533" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
533
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC533" class="line" lang="python"> <span class="n" style="color: #333;">vcfpop</span><span class="p">.</span><span class="n" style="color: #333;">p_freq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vcfpop</span><span class="p">.</span><span class="n" style="color: #333;">p_freq</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">vcfpop</span><span class="p">.</span><span class="n" style="color: #333;">cnt</span></span>
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<td class="new_line diff-line-num new" data-linenumber="534" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
534
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC534" class="line" lang="python"> <span class="n" style="color: #333;">vcfpop</span><span class="p">.</span><span class="n" style="color: #333;">q_freq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vcfpop</span><span class="p">.</span><span class="n" style="color: #333;">q_freq</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">vcfpop</span><span class="p">.</span><span class="n" style="color: #333;">cnt</span></span>
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<td class="new_line diff-line-num new" data-linenumber="535" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
535
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC535" class="line" lang="python"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="536" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
536
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC536" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">popmap_used</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="537" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
537
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC537" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">indv_pops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="538" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
538
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC538" class="line" lang="python"> <span class="n" style="color: #333;">indvpop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indv_pops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="539" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
539
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC539" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">indvpop</span><span class="p">.</span><span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="540" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
540
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC540" class="line" lang="python"> <span class="n" style="color: #333;">indvpop</span><span class="p">.</span><span class="n" style="color: #333;">p_freq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indvpop</span><span class="p">.</span><span class="n" style="color: #333;">p_freq</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">indvpop</span><span class="p">.</span><span class="n" style="color: #333;">cnt</span></span>
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<td class="new_line diff-line-num new" data-linenumber="541" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
541
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC541" class="line" lang="python"> <span class="n" style="color: #333;">indvpop</span><span class="p">.</span><span class="n" style="color: #333;">q_freq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indvpop</span><span class="p">.</span><span class="n" style="color: #333;">q_freq</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">indvpop</span><span class="p">.</span><span class="n" style="color: #333;">cnt</span></span>
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<td class="new_line diff-line-num new" data-linenumber="542" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
542
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC542" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="543" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
543
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC543" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">priv_pop</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="544" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
544
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC544" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="545" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
545
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC545" class="line" lang="python"> <span class="n" style="color: #333;">pop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="546" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
546
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC546" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">private</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="547" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
547
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC547" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">priv_all</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">p_allele</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">vcfpop</span><span class="p">.</span><span class="n" style="color: #333;">p_freq</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="548" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
548
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC548" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">priv_hyb</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="new_line diff-line-num new" data-linenumber="549" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
549
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC549" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">priv_all</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">q_allele</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">vcfpop</span><span class="p">.</span><span class="n" style="color: #333;">q_freq</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="550" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
550
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC550" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">priv_hyb</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="new_line diff-line-num new" data-linenumber="551" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
551
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC551" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="552" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
552
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC552" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="n" style="color: #333;">vcfpop</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vcfpop</span></span>
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<td class="new_line diff-line-num new" data-linenumber="553" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
553
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC553" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="554" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
554
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC554" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">popmap_used</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="555" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
555
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC555" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">indv_pops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="556" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
556
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC556" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indv_pops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span></span>
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557
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC557" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="558" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
558
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC558" class="line" lang="python"> <span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="559" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
559
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC559" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
560
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC560" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"> Read {} loci, {} snps, from {} samples.</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>
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<td class="new_line diff-line-num new" data-linenumber="561" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
561
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC561" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">locus_cnt</span><span class="p">),</span> <span class="n" style="color: #333;">snp_cnt</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">populations_key</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">])),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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562
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC562" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="563" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
563
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC563" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="564" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
564
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC564" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">order_loci</span><span class="p">(</span><span class="n" style="color: #333;">chrs_list</span><span class="p">,</span> <span class="n" style="color: #333;">loci</span><span class="p">,</span> <span class="n" style="color: #333;">ordered_loci</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="565" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
565
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC565" class="line" lang="python"> <span class="k" style="font-weight: 600;">global</span> <span class="n" style="color: #333;">ref_aligned</span></span>
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<td class="new_line diff-line-num new" data-linenumber="566" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
566
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC566" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="567" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
567
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC567" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="568" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
568
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC568" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Sort loci containing private alleles onto their respective chromosomes.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="569" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
569
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC569" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="570" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
570
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC570" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">loc_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">loci</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="571" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
571
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC571" class="line" lang="python"> <span class="n" style="color: #333;">loc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loci</span><span class="p">[</span><span class="n" style="color: #333;">loc_id</span><span class="p">]</span></span>
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572
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC572" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="573" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
573
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC573" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">chr</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="574" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
574
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC574" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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575
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC575" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="576" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
576
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC576" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">private</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">False</span><span class="p">:</span></span>
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577
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC577" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="578" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
578
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC578" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="579" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
579
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC579" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">chr</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ordered_loci</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="580" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
580
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC580" class="line" lang="python"> <span class="n" style="color: #333;">ordered_loci</span><span class="p">[</span><span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="581" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
581
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC581" class="line" lang="python"> <span class="n" style="color: #333;">ordered_loci</span><span class="p">[</span><span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">loc</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="582" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
582
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC582" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="583" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
583
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC583" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">chr</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ordered_loci</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="584" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
584
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC584" class="line" lang="python"> <span class="n" style="color: #333;">ordered_loci</span><span class="p">[</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">sort</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">attrgetter</span><span class="p">(</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">bp</span><span class="sh" style="color: #d14;">'</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="585" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
585
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC585" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="586" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
586
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC586" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="587" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
587
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC587" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Sort the chromosomes by length</span></span>
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<td class="new_line diff-line-num new" data-linenumber="588" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
588
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC588" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="589" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
589
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC589" class="line" lang="python"> <span class="n" style="color: #333;">chrs_list</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">sort</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">reverse</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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590
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC590" class="line" lang="python"> </span>
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591
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC591" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="592" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
592
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC592" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_private_allele_summary</span><span class="p">(</span><span class="n" style="color: #333;">chrs_list</span><span class="p">,</span> <span class="n" style="color: #333;">ordered_loci</span><span class="p">,</span> <span class="n" style="color: #333;">populations_key</span><span class="p">,</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">,</span> <span class="n" style="color: #333;">out_path</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="593" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
593
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC593" class="line" lang="python"> <span class="n" style="color: #333;">datestamp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">now</span><span class="p">().</span><span class="nf" style="color: #900; font-weight: 600;">strftime</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">%Y%m%d</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="594" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
594
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC594" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="595" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
595
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC595" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="596" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
596
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC596" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Open the output file.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="597" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
597
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC597" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="598" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
598
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC598" class="line" lang="python"> <span class="n" style="color: #333;">out_fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">_private_alleles.tsv</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">w</span><span class="sh" style="color: #d14;">'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="599" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
599
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC599" class="line" lang="python"> <span class="n" style="color: #333;">out_fh</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"># Generated by stacks-private-alleles, date {}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"># {}</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">datestamp</span><span class="p">,</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"> </span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">)))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="600" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
600
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC600" class="line" lang="python"> <span class="n" style="color: #333;">out_fh</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"># Chr</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">BP</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Locus</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Column</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">PrivAllele</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ParentPop</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ParentFreq</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">TotCnt</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">PrivCnt</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">VCF-Freq</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">TotCnt</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">PrivCnt</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="601" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
601
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC601" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="602" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
602
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC602" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">popmap_used</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="603" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
603
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC603" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="604" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
604
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC604" class="line" lang="python"> <span class="n" style="color: #333;">out_fh</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}-Freq</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">TotCnt</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">PrivCnt</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="605" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
605
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC605" class="line" lang="python"> <span class="n" style="color: #333;">out_fh</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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606
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC606" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Writing a summary of private alleles: </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> {}</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">_private_alleles.tsv</span><span class="sh" style="color: #d14;">"</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="607" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
607
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC607" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="608" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
608
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC608" class="line" lang="python"> <span class="n" style="color: #333;">tot_snps_per_pop</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="609" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
609
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC609" class="line" lang="python"> <span class="n" style="color: #333;">priv_pop</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="610" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
610
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC610" class="line" lang="python"> <span class="n" style="color: #333;">priv_hyb</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="611" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
611
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC611" class="line" lang="python"> <span class="n" style="color: #333;">chrno</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="612" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
612
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC612" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="613" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
613
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC613" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="614" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
614
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC614" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Iterate over chromosomes/scaffolds, longest to shortest.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="615" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
615
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC615" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="616" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
616
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC616" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">chrlen</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">chrs_list</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="617" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
617
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC617" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">chr</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ordered_loci</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="618" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
618
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC618" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="619" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
619
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC619" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">chrlen</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ctg_limit</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="620" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
620
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC620" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="621" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
621
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC621" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="622" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
622
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC622" class="line" lang="python"> <span class="n" style="color: #333;">chrno</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="623" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
623
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC623" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">chrno</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">3</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="624" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
624
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC624" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">{}: {} ({:.2f}Mbp): {} private loci</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>
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<td class="new_line diff-line-num new" data-linenumber="625" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
625
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC625" class="line" lang="python"> <span class="n" style="color: #333;">chrno</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">chrlen</span><span class="o" style="font-weight: 600;">/</span><span class="mf" style="color: #099;">1000000.0</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">ordered_loci</span><span class="p">[</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">])),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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626
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC626" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="627" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
627
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC627" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="628" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
628
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC628" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Initialize counters.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="629" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
629
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC629" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="630" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
630
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC630" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">populations_key</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="631" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
631
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC631" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="632" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
632
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC632" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="633" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
633
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC633" class="line" lang="python"> <span class="n" style="color: #333;">priv_pop</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="634" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
634
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC634" class="line" lang="python"> <span class="n" style="color: #333;">priv_hyb</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="635" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
635
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC635" class="line" lang="python"> <span class="n" style="color: #333;">tot_snps_per_pop</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="636" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
636
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC636" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="637" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
637
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC637" class="line" lang="python"> <span class="n" style="color: #333;">loc_cnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="638" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
638
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC638" class="line" lang="python"> <span class="n" style="color: #333;">snp_cnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
639
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC639" class="line" lang="python"> <span class="n" style="color: #333;">missing_hybrid_cnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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640
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC640" class="line" lang="python"></span>
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641
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC641" class="line" lang="python"> <span class="n" style="color: #333;">priv_allele_hybrid_freq</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="642" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
642
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC642" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="643" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
643
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC643" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">loc</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ordered_loci</span><span class="p">[</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">]:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="644" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
644
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC644" class="line" lang="python"> <span class="n" style="color: #333;">loc_cnt</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="645" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
645
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC645" class="line" lang="python"> <span class="n" style="color: #333;">snp_cnt</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">snps</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="646" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
646
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC646" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">snpcol</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">snps</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="647" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
647
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC647" class="line" lang="python"> <span class="n" style="color: #333;">snp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">snps</span><span class="p">[</span><span class="n" style="color: #333;">snpcol</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="648" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
648
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC648" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="649" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
649
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC649" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="650" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
650
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC650" class="line" lang="python"> <span class="n" style="color: #333;">missing_hybrid_cnt</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="651" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
651
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC651" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="652" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
652
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC652" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="653" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
653
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC653" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Record total number of SNPs found in each parent population</span></span>
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<td class="new_line diff-line-num new" data-linenumber="654" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
654
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC654" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># as well as the number of populations that have private alleles from those SNPs.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="655" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
655
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC655" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="656" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
656
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC656" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="657" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
657
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC657" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="658" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
658
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC658" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="659" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
659
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC659" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="660" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
660
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC660" class="line" lang="python"> <span class="n" style="color: #333;">tot_snps_per_pop</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
661
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC661" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="662" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
662
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC662" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">private</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="663" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
663
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC663" class="line" lang="python"> <span class="n" style="color: #333;">priv_pop</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="664" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
664
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC664" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="665" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
665
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC665" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="666" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
666
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC666" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Was this private allele found in the hybrid/vcf population? If so, print it.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="667" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
667
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC667" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="668" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
668
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC668" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">priv_hyb</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="669" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
669
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC669" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="670" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
670
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC670" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="671" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
671
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC671" class="line" lang="python"> <span class="n" style="color: #333;">pop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="672" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
672
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC672" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="673" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
673
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC673" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">private</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="674" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
674
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC674" class="line" lang="python"> <span class="n" style="color: #333;">priv_hyb</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="675" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
675
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC675" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">priv_all</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">p_allele</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="676" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
676
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC676" class="line" lang="python"> <span class="n" style="color: #333;">priv_allele_hybrid_freq</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="n" style="color: #333;">p_freq</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="677" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
677
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC677" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{:.3f}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{:.3f}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>
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<td class="new_line diff-line-num new" data-linenumber="678" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
678
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC678" class="line" lang="python"> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">,</span> <span class="n" style="color: #333;">snpcol</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="679" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
679
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC679" class="line" lang="python"> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">priv_all</span><span class="p">,</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">,</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">p_freq</span><span class="p">,</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">cnt</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
680
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC680" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">round</span><span class="p">(</span><span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">p_freq</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">cnt</span><span class="p">),</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="681" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
681
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC681" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="n" style="color: #333;">p_freq</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="n" style="color: #333;">cnt</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="682" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
682
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC682" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">round</span><span class="p">(</span><span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="n" style="color: #333;">p_freq</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="n" style="color: #333;">cnt</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="683" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
683
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC683" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">popmap_used</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="684" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
684
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC684" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="685" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
685
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC685" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="686" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
686
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC686" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{:.3f}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="687" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
687
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC687" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">p_freq</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">cnt</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="688" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
688
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC688" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">round</span><span class="p">(</span><span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">p_freq</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">cnt</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="689" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
689
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC689" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="690" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
690
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC690" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">-</span><span class="sh" style="color: #d14;">'</span><span class="p">,</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">-</span><span class="sh" style="color: #d14;">'</span><span class="p">,</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">-</span><span class="sh" style="color: #d14;">'</span><span class="p">,</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">-</span><span class="sh" style="color: #d14;">'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="691" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
691
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC691" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="692" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
692
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC692" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">priv_all</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">q_allele</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="693" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
693
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC693" class="line" lang="python"> <span class="n" style="color: #333;">priv_allele_hybrid_freq</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="n" style="color: #333;">q_freq</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="694" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
694
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC694" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{:.3f}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{:.3f}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>
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<td class="new_line diff-line-num new" data-linenumber="695" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
695
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC695" class="line" lang="python"> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">,</span> <span class="n" style="color: #333;">snpcol</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="696" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
696
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC696" class="line" lang="python"> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">priv_all</span><span class="p">,</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">,</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">q_freq</span><span class="p">,</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">cnt</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="697" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
697
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC697" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">round</span><span class="p">(</span><span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">q_freq</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">cnt</span><span class="p">),</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="698" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
698
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC698" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="n" style="color: #333;">q_freq</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="n" style="color: #333;">cnt</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="699" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
699
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC699" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">round</span><span class="p">(</span><span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="n" style="color: #333;">q_freq</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="n" style="color: #333;">cnt</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="700" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
700
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC700" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">popmap_used</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="701" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
701
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC701" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="702" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
702
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC702" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="703" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
703
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC703" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{:.3f}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>
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<td class="new_line diff-line-num new" data-linenumber="704" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
704
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC704" class="line" lang="python"> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">q_freq</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">cnt</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="705" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
705
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC705" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">round</span><span class="p">(</span><span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">q_freq</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">cnt</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="706" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
706
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC706" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="707" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
707
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC707" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">-</span><span class="sh" style="color: #d14;">'</span><span class="p">,</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">-</span><span class="sh" style="color: #d14;">'</span><span class="p">,</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">-</span><span class="sh" style="color: #d14;">'</span><span class="p">,</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">-</span><span class="sh" style="color: #d14;">'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="708" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
708
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC708" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="709" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
709
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC709" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="710" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
710
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC710" class="line" lang="python"> <span class="n" style="color: #333;">out_fh</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="711" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
711
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC711" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="712" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
712
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC712" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">chrno</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">3</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="713" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
713
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC713" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">{} loci, including {} SNPs, analyzed; in {} cases SNP present in hybrid/VCF population.</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>
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<td class="new_line diff-line-num new" data-linenumber="714" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
714
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC714" class="line" lang="python"> <span class="n" style="color: #333;">loc_cnt</span><span class="p">,</span> <span class="n" style="color: #333;">snp_cnt</span><span class="p">,</span> <span class="n" style="color: #333;">snp_cnt</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">missing_hybrid_cnt</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="715" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
715
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC715" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="716" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
716
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC716" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">priv_pop</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="717" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
717
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC717" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"> </span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">{}</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;"> had {} SNPs present; private alleles occured within {} of those SNPs ({:.2f}%)</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>
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<td class="new_line diff-line-num new" data-linenumber="718" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
718
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC718" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">tot_snps_per_pop</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">],</span> <span class="n" style="color: #333;">priv_pop</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">],</span> <span class="p">(</span><span class="n" style="color: #333;">priv_pop</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="nf" style="color: #900; font-weight: 600;">float</span><span class="p">(</span><span class="n" style="color: #333;">tot_snps_per_pop</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">])</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">100</span><span class="p">)),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="719" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
719
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC719" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"> Private allele found in {} SNPs of hybrid/VCF population ({:.2f}%)</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>
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<td class="new_line diff-line-num new" data-linenumber="720" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
720
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC720" class="line" lang="python"> <span class="n" style="color: #333;">priv_hyb</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">],</span> <span class="p">(</span><span class="n" style="color: #333;">priv_hyb</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="nf" style="color: #900; font-weight: 600;">float</span><span class="p">(</span><span class="n" style="color: #333;">tot_snps_per_pop</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">])</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">100</span><span class="p">)),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="721" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
721
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC721" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="722" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
722
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC722" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="723" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
723
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC723" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="724" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
724
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC724" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">Specify --verbose for details on more chromosomes.</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
725
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC725" class="line" lang="python"> <span class="n" style="color: #333;">out_fh</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">()</span></span>
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726
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC726" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="727" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
727
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC727" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="728" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
728
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC728" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">invert_refalt_fields</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="729" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
729
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC729" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="730" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
730
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC730" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Invert the REF and ALT alleles for this VCF line; alter the downstream genotypes to reflect this change.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="731" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
731
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC731" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="732" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
732
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC732" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># VCF is defined as: CHROM,POS,ID,REF,ALT,QUAL,FILTER,INFO,FORMAT,SAMPLEGENOTYPES...</span></span>
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<td class="new_line diff-line-num new" data-linenumber="733" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
733
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC733" class="line" lang="python"> <span class="n" style="color: #333;">invf</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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734
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC734" class="line" lang="python"> <span class="n" style="color: #333;">invf</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># CHROM,POS,ID</span></span>
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<td class="new_line diff-line-num new" data-linenumber="735" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
735
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC735" class="line" lang="python"> <span class="n" style="color: #333;">invf</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span> <span class="c1" style="color: #998; font-style: italic;"># ALT -> REF</span></span>
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<td class="new_line diff-line-num new" data-linenumber="736" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
736
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC736" class="line" lang="python"> <span class="n" style="color: #333;">invf</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="c1" style="color: #998; font-style: italic;"># REF -> ALT</span></span>
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<td class="new_line diff-line-num new" data-linenumber="737" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
737
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC737" class="line" lang="python"> <span class="n" style="color: #333;">invf</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">:</span><span class="mi" style="color: #099;">9</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># QUAL,FILTER,INFO,FORMAT</span></span>
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<td class="new_line diff-line-num new" data-linenumber="738" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
738
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC738" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="739" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
739
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC739" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sampleno</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nf" style="color: #900; font-weight: 600;">range</span><span class="p">(</span><span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="740" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
740
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC740" class="line" lang="python"> <span class="n" style="color: #333;">gt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="n" style="color: #333;">sampleno</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="741" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
741
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC741" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gt</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">0/0</span><span class="sh" style="color: #d14;">"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="742" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
742
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC742" class="line" lang="python"> <span class="n" style="color: #333;">gt</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">1/1</span><span class="sh" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gt</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">:]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="743" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
743
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC743" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">gt</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">1/1</span><span class="sh" style="color: #d14;">"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="744" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
744
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC744" class="line" lang="python"> <span class="n" style="color: #333;">gt</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">0/0</span><span class="sh" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gt</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">:]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="745" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
745
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC745" class="line" lang="python"> <span class="n" style="color: #333;">invf</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">gt</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="746" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
746
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC746" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="747" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
747
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC747" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">invf</span></span>
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748
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC748" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="749" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
749
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC749" class="line" lang="python"></span>
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750
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC750" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_polarized_vcfs</span><span class="p">(</span><span class="n" style="color: #333;">chrs_list</span><span class="p">,</span> <span class="n" style="color: #333;">loci</span><span class="p">,</span> <span class="n" style="color: #333;">populations_key</span><span class="p">,</span> <span class="n" style="color: #333;">vcf_path</span><span class="p">,</span> <span class="n" style="color: #333;">out_path</span><span class="p">):</span></span>
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751
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC751" class="line" lang="python"> <span class="n" style="color: #333;">datestamp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">now</span><span class="p">().</span><span class="nf" style="color: #900; font-weight: 600;">strftime</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">%Y%m%d</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="752" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
752
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC752" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="753" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
753
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC753" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="754" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
754
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC754" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write out a VCF file for each 'parental' population</span></span>
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<td class="new_line diff-line-num new" data-linenumber="755" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
755
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC755" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="756" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
756
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC756" class="line" lang="python"> <span class="n" style="color: #333;">vcf_fhs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="757" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
757
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC757" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="758" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
758
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC758" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pop</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">populations_key</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="759" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
759
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC759" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pop</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">:</span></span>
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760
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC760" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="761" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
761
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC761" class="line" lang="python"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">_</span><span class="sh" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pop</span> <span class="o" style="font-weight: 600;">+</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">.polarized.snps.vcf</span><span class="sh" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="762" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
762
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC762" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"> {}</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="763" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
763
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC763" class="line" lang="python"> <span class="n" style="color: #333;">vcf_fhs</span><span class="p">[</span><span class="n" style="color: #333;">pop</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">w</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="764" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
764
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC764" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="765" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
765
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC765" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="766" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
766
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC766" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Open the VCF input file again.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="767" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
767
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC767" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="768" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
768
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC768" class="line" lang="python"> <span class="n" style="color: #333;">in_fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">vcf_path</span><span class="p">,</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">r</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="769" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
769
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC769" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="770" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
770
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC770" class="line" lang="python"> <span class="n" style="color: #333;">lineno</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="771" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
771
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC771" class="line" lang="python"> <span class="n" style="color: #333;">parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="772" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
772
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC772" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="773" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
773
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC773" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write the VCF header</span></span>
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<td class="new_line diff-line-num new" data-linenumber="774" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
774
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC774" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="775" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
775
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC775" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">in_fh</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="776" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
776
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC776" class="line" lang="python"> <span class="n" style="color: #333;">lineno</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="777" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
777
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC777" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="778" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
778
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC778" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">##</span><span class="sh" style="color: #d14;">"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="779" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
779
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC779" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">10</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">##fileDate</span><span class="sh" style="color: #d14;">"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="780" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
780
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC780" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">##fileDate={}</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">datestamp</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="781" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
781
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC781" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">##source</span><span class="sh" style="color: #d14;">"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="782" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
782
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC782" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">##source={}</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">stacks-private-alleles</span><span class="se" style="color: #d14;">\"</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="783" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
783
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC783" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="784" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
784
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC784" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pop</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vcf_fhs</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
785
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC785" class="line" lang="python"> <span class="n" style="color: #333;">vcf_fhs</span><span class="p">[</span><span class="n" style="color: #333;">pop</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
786
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC786" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="787" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
787
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC787" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">#CHROM</span><span class="sh" style="color: #d14;">"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="788" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
788
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC788" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write the final line containint the column headings.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="789" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
789
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC789" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pop</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vcf_fhs</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="790" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
790
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC790" class="line" lang="python"> <span class="n" style="color: #333;">vcf_fhs</span><span class="p">[</span><span class="n" style="color: #333;">pop</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="791" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
791
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC791" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<td class="new_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
792
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC792" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="793" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
793
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC793" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">in_fh</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="794" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
794
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC794" class="line" lang="python"> <span class="n" style="color: #333;">lineno</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="795" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
795
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC795" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">strip</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="796" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
796
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC796" class="line" lang="python"> <span class="n" style="color: #333;">parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="797" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
797
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC797" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="798" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
798
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC798" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ref_aligned</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="799" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
799
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC799" class="line" lang="python"> <span class="n" style="color: #333;">locus_id</span><span class="p">,</span> <span class="n" style="color: #333;">column</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">:</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
800
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC800" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="801" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
801
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC801" class="line" lang="python"> <span class="n" style="color: #333;">locus_id</span><span class="p">,</span> <span class="n" style="color: #333;">column</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">:</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="802" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
802
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC802" class="line" lang="python"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">+</span><span class="sh" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="803" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
803
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC803" class="line" lang="python"> <span class="n" style="color: #333;">locus_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">locus_id</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="804" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
804
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC804" class="line" lang="python"> <span class="n" style="color: #333;">column</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">column</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="805" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
805
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC805" class="line" lang="python"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Strand</span><span class="p">.</span><span class="n" style="color: #333;">minus</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">-</span><span class="sh" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">Strand</span><span class="p">.</span><span class="n" style="color: #333;">plus</span></span>
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<td class="new_line diff-line-num new" data-linenumber="806" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
806
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC806" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
807
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC807" class="line" lang="python"> <span class="n" style="color: #333;">ref_all</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="808" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
808
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC808" class="line" lang="python"> <span class="n" style="color: #333;">alt_all</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="809" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
809
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC809" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="810" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
810
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC810" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># print("Looking at locus {}, snp {}, ref: {}, alt: {}".format(locus_id, column, ref_all, alt_all), file=sys.stderr)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="811" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
811
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC811" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="812" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
812
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC812" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">locus_id</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">loci</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="813" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
813
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC813" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="814" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
814
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC814" class="line" lang="python"> <span class="n" style="color: #333;">loc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loci</span><span class="p">[</span><span class="n" style="color: #333;">locus_id</span><span class="p">]</span></span>
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815
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC815" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="816" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
816
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC816" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">column</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">snps</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="817" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
817
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC817" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="818" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
818
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC818" class="line" lang="python"> <span class="n" style="color: #333;">snp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">snps</span><span class="p">[</span><span class="n" style="color: #333;">column</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="819" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
819
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC819" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="820" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
820
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC820" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">priv_hyb</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">False</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="821" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
821
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC821" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="822" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
822
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC822" class="line" lang="python"> </span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="823" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
823
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC823" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">popname</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vcf_fhs</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="824" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
824
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC824" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="825" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
825
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC825" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Does this population possess a private allele at this SNP?</span></span>
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<td class="new_line diff-line-num new" data-linenumber="826" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
826
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC826" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="827" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
827
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC827" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">popname</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="828" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
828
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC828" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="829" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
829
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC829" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="830" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
830
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC830" class="line" lang="python"> <span class="n" style="color: #333;">pop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="n" style="color: #333;">popname</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="831" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
831
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC831" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">private</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="832" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
832
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC832" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="833" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
833
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC833" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If so, check if the private allele is the REF allele; if</span></span>
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<td class="new_line diff-line-num new" data-linenumber="834" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
834
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC834" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># so, swap the REF/ALT alleles so that private alleles for this</span></span>
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<td class="new_line diff-line-num new" data-linenumber="835" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
835
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC835" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># focal population are always ALT alleles.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="836" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
836
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC836" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="837" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
837
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC837" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">priv_all</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ref_all</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="838" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
838
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC838" class="line" lang="python"> <span class="n" style="color: #333;">invparts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">invert_refalt_fields</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="839" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
839
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC839" class="line" lang="python"> <span class="n" style="color: #333;">vcf_fhs</span><span class="p">[</span><span class="n" style="color: #333;">popname</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">invparts</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="840" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
840
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC840" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="841" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
841
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC841" class="line" lang="python"> <span class="n" style="color: #333;">vcf_fhs</span><span class="p">[</span><span class="n" style="color: #333;">popname</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="842" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
842
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC842" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="843" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
843
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC843" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pop</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vcf_fhs</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="844" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
844
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC844" class="line" lang="python"> <span class="n" style="color: #333;">vcf_fhs</span><span class="p">[</span><span class="n" style="color: #333;">pop</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="845" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
845
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC845" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="846" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
846
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC846" class="line" lang="python"> <span class="n" style="color: #333;">in_fh</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="847" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
847
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC847" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="848" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
848
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC848" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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849
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC849" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="850" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
850
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC850" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="851" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
851
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC851" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">calc_weights</span><span class="p">(</span><span class="n" style="color: #333;">sigma</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="852" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
852
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC852" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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853
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC853" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Calculate weights for window smoothing operations.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="854" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
854
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC854" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="855" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
855
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC855" class="line" lang="python"> <span class="n" style="color: #333;">limit</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">sigma</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="856" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
856
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC856" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="857" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
857
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC857" class="line" lang="python"> <span class="n" style="color: #333;">weights</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mf" style="color: #099;">0.0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">limit</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="858" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
858
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC858" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nf" style="color: #900; font-weight: 600;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">limit</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="859" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
859
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC859" class="line" lang="python"> <span class="n" style="color: #333;">weights</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">math</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">exp</span><span class="p">((</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">math</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">pow</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">))</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">math</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">pow</span><span class="p">(</span><span class="n" style="color: #333;">sigma</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="860" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
860
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC860" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="861" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
861
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC861" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">weights</span></span>
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<td class="new_line diff-line-num new" data-linenumber="862" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
862
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC862" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="863" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
863
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC863" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="864" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
864
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC864" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">determine_window_limits</span><span class="p">(</span><span class="n" style="color: #333;">sites</span><span class="p">,</span> <span class="n" style="color: #333;">limit</span><span class="p">,</span> <span class="n" style="color: #333;">center_bp</span><span class="p">,</span> <span class="n" style="color: #333;">pos_l</span><span class="p">,</span> <span class="n" style="color: #333;">pos_u</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="865" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
865
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC865" class="line" lang="python"> <span class="n" style="color: #333;">limit_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">center_bp</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">limit</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">center_bp</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">limit</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="866" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
866
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC866" class="line" lang="python"> <span class="n" style="color: #333;">limit_u</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">center_bp</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">limit</span></span>
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<td class="new_line diff-line-num new" data-linenumber="867" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
867
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC867" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="868" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
868
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC868" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">pos_l</span> <span class="o" style="font-weight: 600;"><</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">sites</span><span class="p">):</span></span>
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869
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC869" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sites</span><span class="p">[</span><span class="n" style="color: #333;">pos_l</span><span class="p">].</span><span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">limit_l</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="870" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
870
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC870" class="line" lang="python"> <span class="n" style="color: #333;">pos_l</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="871" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
871
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC871" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="872" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
872
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC872" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<td class="new_line diff-line-num new" data-linenumber="873" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
873
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC873" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="874" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
874
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC874" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">pos_u</span> <span class="o" style="font-weight: 600;"><</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">sites</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="875" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
875
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC875" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sites</span><span class="p">[</span><span class="n" style="color: #333;">pos_u</span><span class="p">].</span><span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">limit_u</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="876" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
876
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC876" class="line" lang="python"> <span class="n" style="color: #333;">pos_u</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="877" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
877
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC877" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="878" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
878
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC878" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<td class="new_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
879
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC879" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="880" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
880
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC880" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pos_l</span><span class="p">,</span> <span class="n" style="color: #333;">pos_u</span></span>
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<td class="new_line diff-line-num new" data-linenumber="881" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
881
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC881" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="882" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
882
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC882" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="883" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
883
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC883" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">smooth_chromosome</span><span class="p">(</span><span class="n" style="color: #333;">sites</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="884" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
884
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC884" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="885" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
885
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC885" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># To generate smooth genome-wide distributions of Fst, we calculate a kernel-smoothing</span></span>
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<td class="new_line diff-line-num new" data-linenumber="886" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
886
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC886" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># moving average of Fst values along each ordered chromosome.</span></span>
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887
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC887" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="888" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
888
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC888" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># For each genomic region centered on a nucleotide position c, the contribution of the population</span></span>
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<td class="new_line diff-line-num new" data-linenumber="889" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
889
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC889" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># genetic statistic at position p to the region average was weighted by the Gaussian function:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="890" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
890
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC890" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># exp( (-1 * (p - c)^2) / (2 * sigma^2))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="891" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
891
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC891" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="892" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
892
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC892" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># In addition, we weight each position according to (n_k - 1), where n_k is the number of alleles</span></span>
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<td class="new_line diff-line-num new" data-linenumber="893" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
893
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC893" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># sampled at that location.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="894" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
894
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC894" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="895" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
895
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC895" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># By default, sigma = 150Kb, for computational efficiency, only calculate average out to 3sigma.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="896" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
896
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC896" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="897" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
897
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC897" class="line" lang="python"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="898" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
898
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC898" class="line" lang="python"> <span class="n" style="color: #333;">pos_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="899" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
899
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC899" class="line" lang="python"> <span class="n" style="color: #333;">pos_u</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="900" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
900
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC900" class="line" lang="python"> <span class="nb" style="color: #0086b3;">sum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="901" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
901
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC901" class="line" lang="python"> <span class="n" style="color: #333;">final_weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="902" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
902
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC902" class="line" lang="python"> <span class="n" style="color: #333;">allele_cnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="903" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
903
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC903" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="904" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
904
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC904" class="line" lang="python"> <span class="n" style="color: #333;">weights</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">calc_weights</span><span class="p">(</span><span class="n" style="color: #333;">sigma</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="905" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
905
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC905" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="906" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
906
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC906" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pos_c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nf" style="color: #900; font-weight: 600;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">sites</span><span class="p">)):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="907" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
907
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC907" class="line" lang="python"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sites</span><span class="p">[</span><span class="n" style="color: #333;">pos_c</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="908" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
908
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC908" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="909" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
909
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC909" class="line" lang="python"> <span class="nb" style="color: #0086b3;">sum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="910" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
910
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC910" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="911" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
911
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC911" class="line" lang="python"> <span class="n" style="color: #333;">pos_l</span><span class="p">,</span> <span class="n" style="color: #333;">pos_u</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">determine_window_limits</span><span class="p">(</span><span class="n" style="color: #333;">sites</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sigma</span><span class="p">),</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">pos_l</span><span class="p">,</span> <span class="n" style="color: #333;">pos_u</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="912" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
912
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC912" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="913" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
913
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC913" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># print("c.bp: {}, pos_c: {}, pos_l: {}, pos_u: {}; sites len: {}".format(c.bp, pos_c, pos_l, pos_u, len(sites)), file=sys.stderr)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="914" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
914
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC914" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pos_p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nf" style="color: #900; font-weight: 600;">range</span><span class="p">(</span><span class="n" style="color: #333;">pos_l</span><span class="p">,</span> <span class="n" style="color: #333;">pos_u</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="915" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
915
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC915" class="line" lang="python"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sites</span><span class="p">[</span><span class="n" style="color: #333;">pos_p</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="916" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
916
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC916" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="917" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
917
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC917" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bp</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="918" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
918
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC918" class="line" lang="python"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bp</span></span>
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<td class="new_line diff-line-num new" data-linenumber="919" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
919
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC919" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="920" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
920
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC920" class="line" lang="python"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">bp</span></span>
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<td class="new_line diff-line-num new" data-linenumber="921" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
921
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC921" class="line" lang="python"></span>
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922
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC922" class="line" lang="python"> <span class="n" style="color: #333;">final_weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">1.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">weights</span><span class="p">[</span><span class="n" style="color: #333;">dist</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="923" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
923
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC923" class="line" lang="python"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">smoothed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">smoothed</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">stat</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">final_weight</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="924" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
924
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC924" class="line" lang="python"> <span class="nb" style="color: #0086b3;">sum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">final_weight</span></span>
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<td class="new_line diff-line-num new" data-linenumber="925" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
925
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC925" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="926" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
926
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC926" class="line" lang="python"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">smoothed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">smoothed</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="927" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
927
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC927" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="928" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
928
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC928" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<td class="new_line diff-line-num new" data-linenumber="929" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
929
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC929" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="930" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
930
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC930" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="931" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
931
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC931" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_plot_values</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="n" style="color: #333;">pop_1</span><span class="p">,</span> <span class="n" style="color: #333;">pop_2</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="932" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
932
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC932" class="line" lang="python"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="933" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
933
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC933" class="line" lang="python"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="934" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
934
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC934" class="line" lang="python"> <span class="n" style="color: #333;">p1_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">pop_1</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="935" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
935
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC935" class="line" lang="python"> <span class="n" style="color: #333;">p2_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">pop_2</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="936" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
936
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC936" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="937" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
937
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC937" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">p1_len</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">p2_len</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="938" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
938
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC938" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="939" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
939
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC939" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">p2_len</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="940" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
940
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC940" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">p1_len</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">pop_1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">pop_2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">bp</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="941" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
941
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC941" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">smooth</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="942" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
942
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC942" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{:.3f}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{:.5f}</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">pop_1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">pop_1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">pop_1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">pop</span><span class="p">,</span> <span class="n" style="color: #333;">pop_1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">stat</span><span class="p">,</span> <span class="n" style="color: #333;">pop_1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">smoothed</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
943
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC943" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="944" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
944
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC944" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{:.3f}</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">pop_1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">pop_1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">pop_1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">pop</span><span class="p">,</span> <span class="n" style="color: #333;">pop_1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">stat</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="945" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
945
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC945" class="line" lang="python"> <span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+</span> <span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="946" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
946
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC946" class="line" lang="python"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="947" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
947
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC947" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="948" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
948
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC948" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">p1_len</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="949" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
949
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC949" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">smooth</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="950" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
950
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC950" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{:.3f}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{:.5f}</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">pop_1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">pop_1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">pop_1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">pop</span><span class="p">,</span> <span class="n" style="color: #333;">pop_1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">stat</span><span class="p">,</span> <span class="n" style="color: #333;">pop_1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">smoothed</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="951" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
951
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC951" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="952" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
952
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC952" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{:.3f}</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">pop_1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">pop_1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">pop_1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">pop</span><span class="p">,</span> <span class="n" style="color: #333;">pop_1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">stat</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="953" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
953
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC953" class="line" lang="python"> <span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+</span> <span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="954" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
954
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC954" class="line" lang="python"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="955" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
955
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC955" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="956" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
956
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC956" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">p1_len</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="957" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
957
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC957" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">p2_len</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">pop_2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pop_1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">bp</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="958" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
958
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC958" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">smooth</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="959" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
959
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC959" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{:.3f}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{:.5f}</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">pop_2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">pop_2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">pop_2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">pop</span><span class="p">,</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pop_2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">stat</span><span class="p">),</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pop_2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">smoothed</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="960" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
960
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC960" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="961" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
961
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC961" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{:.3f}</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">pop_2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">pop_2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">pop_2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">pop</span><span class="p">,</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pop_2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">stat</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="962" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
962
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC962" class="line" lang="python"> <span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+</span> <span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="963" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
963
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC963" class="line" lang="python"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="964" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
964
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC964" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="965" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
965
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC965" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">p2_len</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="966" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
966
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC966" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">smooth</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="967" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
967
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC967" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{:.3f}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{:.5f}</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">pop_2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">pop_2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">pop_2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">pop</span><span class="p">,</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pop_2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">stat</span><span class="p">),</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pop_2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">smoothed</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="968" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
968
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC968" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="969" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
969
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC969" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{:.3f}</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">pop_2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">pop_2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">pop_2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">pop</span><span class="p">,</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pop_2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">stat</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="970" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
970
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC970" class="line" lang="python"> <span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+</span> <span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="971" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
971
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC971" class="line" lang="python"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="972" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
972
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC972" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="973" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
973
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC973" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="974" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
974
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC974" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_plots</span><span class="p">(</span><span class="n" style="color: #333;">chrs_list</span><span class="p">,</span> <span class="n" style="color: #333;">ordered_loci</span><span class="p">,</span> <span class="n" style="color: #333;">populations_key</span><span class="p">,</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">,</span> <span class="n" style="color: #333;">out_path</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
975
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC975" class="line" lang="python"> <span class="n" style="color: #333;">datestamp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">now</span><span class="p">().</span><span class="nf" style="color: #900; font-weight: 600;">strftime</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">%Y%m%d</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="976" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
976
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC976" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="977" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
977
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC977" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="978" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
978
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC978" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If requested, write a file to plot private allele frequencies in the VCF population.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="979" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
979
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC979" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The y-axis scales from 1 to -1, the x-axis is the genome coordinates</span></span>
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<td class="new_line diff-line-num new" data-linenumber="980" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
980
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC980" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The first population is positive on the y-axis, the second negative;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="981" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
981
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC981" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The frequency of the private allele in the VCF population is the y value.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="982" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
982
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC982" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="983" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
983
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC983" class="line" lang="python"> <span class="n" style="color: #333;">plot_pops</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">list</span><span class="p">(</span><span class="n" style="color: #333;">populations_key</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="984" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
984
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC984" class="line" lang="python"> <span class="n" style="color: #333;">plot_fhs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="985" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
985
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC985" class="line" lang="python"> <span class="n" style="color: #333;">plot_fhs</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">_plot_by_chromosome-all.tsv</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">w</span><span class="sh" style="color: #d14;">'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="986" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
986
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC986" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"> {}</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">_plot_by_chromosome-all.tsv</span><span class="sh" style="color: #d14;">"</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="987" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
987
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC987" class="line" lang="python"> <span class="n" style="color: #333;">plot_fhs</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"># Generated by stacks-private-alleles, {}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"># {}</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">datestamp</span><span class="p">,</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"> </span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">)))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="988" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
988
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC988" class="line" lang="python"> <span class="n" style="color: #333;">plot_fhs</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"># Population </span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">{}</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">: positive values</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"># Population </span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">{}</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">: negative values</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">plot_pops</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">plot_pops</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="989" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
989
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC989" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">smooth</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="990" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
990
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC990" class="line" lang="python"> <span class="n" style="color: #333;">plot_fhs</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"># Chr</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">BP</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Population</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">VCF-PrivateAlleleFreq</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">VCF-Smoothed</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="991" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
991
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC991" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="992" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
992
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC992" class="line" lang="python"> <span class="n" style="color: #333;">plot_fhs</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"># Chr</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">BP</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Population</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">VCF-PrivateAlleleFreq</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="993" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
993
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC993" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="994" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
994
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC994" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">popmap_used</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="995" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
995
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC995" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="996" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
996
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC996" class="line" lang="python"> <span class="n" style="color: #333;">plot_fhs</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">_plot_by_chromosome-</span><span class="sh" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">+</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">.tsv</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">w</span><span class="sh" style="color: #d14;">'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="997" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
997
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC997" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"> {}</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">_plot_by_chromosome-</span><span class="sh" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">+</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">.tsv</span><span class="sh" style="color: #d14;">"</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="998" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
998
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC998" class="line" lang="python"> <span class="n" style="color: #333;">plot_fhs</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"># Generated by stacks-private-alleles, date {}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"># {}</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">datestamp</span><span class="p">,</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"> </span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">)))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="999" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
999
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC999" class="line" lang="python"> <span class="n" style="color: #333;">plot_fhs</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"># Population </span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">{}</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">: positive values</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"># Population </span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">{}</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">: negative values</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">plot_pops</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">plot_pops</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1000" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1000
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1000" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">smooth</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1001" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1001
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1001" class="line" lang="python"> <span class="n" style="color: #333;">plot_fhs</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"># Chr</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">BP</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Population</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}-PrivateAlleleFreq</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}-Smoothed</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span><span class="n" style="color: #333;">p</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1002" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1002
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1002" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1003" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1003
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1003" class="line" lang="python"> <span class="n" style="color: #333;">plot_fhs</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"># Chr</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">BP</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Population</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}-PrivateAlleleFreq</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1004" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1004
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1004" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="1005" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1005
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1005" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">smooth</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1006" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1006
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1006" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;"> Smoothing values</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #d14;">''</span><span class="p">,</span> <span class="n" style="color: #333;">flush</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1007" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1007
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1007" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="1008" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1008
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1008" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1009" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1009
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1009" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Iterate over chromosomes/scaffolds, longest to shortest.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1010" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1010
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1010" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1011" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1011
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1011" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">chrlen</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">chrs_list</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1012" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1012
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1012" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">chr</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ordered_loci</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1013" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1013
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1013" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1014" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1014
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1014" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">chrlen</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ctg_limit</span><span class="p">:</span></span>
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1015
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1015" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1016" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1016
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1016" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="1017" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1017
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1017" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1018" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1018
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1018" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Create arrays to hold SmoothStat objects to do the plot smoothing.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1019" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1019
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1019" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1020" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1020
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1020" class="line" lang="python"> <span class="n" style="color: #333;">pop_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1021" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1021
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1021" class="line" lang="python"> <span class="n" style="color: #333;">pop_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1022" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1022
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1022" class="line" lang="python"> <span class="n" style="color: #333;">pop_1_vcfpops</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1023" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1023
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1023" class="line" lang="python"> <span class="n" style="color: #333;">pop_2_vcfpops</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1024" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1024
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1024" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">popmap_used</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1025" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1025
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1025" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1026" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1026
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1026" class="line" lang="python"> <span class="n" style="color: #333;">pop_1_vcfpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1027" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1027
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1027" class="line" lang="python"> <span class="n" style="color: #333;">pop_2_vcfpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1028" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1028
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1028" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="1029" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1029
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1029" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">loc</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ordered_loci</span><span class="p">[</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">]:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1030" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1030
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1030" class="line" lang="python"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1031" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1031
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1031" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">snpcol</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">snps</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1032" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1032
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1032" class="line" lang="python"> <span class="n" style="color: #333;">snp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">snps</span><span class="p">[</span><span class="n" style="color: #333;">snpcol</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1033" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1033
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1033" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="1034" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1034
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1034" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1035" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1035
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1035" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Was this private allele found in the hybrid/vcf population? If so, print it.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1036" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1036
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1036" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1037" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1037
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1037" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">priv_hyb</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1038" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1038
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1038" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="1039" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1039
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1039" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1040" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1040
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1040" class="line" lang="python"> <span class="n" style="color: #333;">pop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1041" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1041
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1041" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="1042" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1042
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1042" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">private</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1043" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1043
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1043" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="1044" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1044
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1044" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">priv_all</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">p_allele</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1045" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1045
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1045" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">pop</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">plot_pops</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1046" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1046
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1046" class="line" lang="python"> <span class="n" style="color: #333;">pop_1</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="nc" style="color: #458; font-weight: 600;">SmoothStat</span><span class="p">(</span><span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">,</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="n" style="color: #333;">cnt</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="n" style="color: #333;">p_freq</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1047" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1047
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1047" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">popmap_used</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1048" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1048
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1048" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1049" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1049
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1049" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1050" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1050
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1050" class="line" lang="python"> <span class="n" style="color: #333;">pop_1_vcfpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="nc" style="color: #458; font-weight: 600;">SmoothStat</span><span class="p">(</span><span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">,</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">cnt</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">p_freq</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1051" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1051
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1051" class="line" lang="python"> </span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1052" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1052
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1052" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">pop</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">plot_pops</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1053" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1053
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1053" class="line" lang="python"> <span class="n" style="color: #333;">pop_2</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="nc" style="color: #458; font-weight: 600;">SmoothStat</span><span class="p">(</span><span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">,</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="n" style="color: #333;">cnt</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="n" style="color: #333;">p_freq</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1054" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1054
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1054" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">popmap_used</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1055" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1055
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1055" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1056" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1056
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1056" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1057" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1057
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1057" class="line" lang="python"> <span class="n" style="color: #333;">pop_2_vcfpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="nc" style="color: #458; font-weight: 600;">SmoothStat</span><span class="p">(</span><span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">,</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">cnt</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">p_freq</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1058" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1058
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1058" class="line" lang="python"> </span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1059" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1059
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1059" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">priv_all</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">q_allele</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1060" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1060
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1060" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">pop</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">plot_pops</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1061" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1061
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1061" class="line" lang="python"> <span class="n" style="color: #333;">pop_1</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="nc" style="color: #458; font-weight: 600;">SmoothStat</span><span class="p">(</span><span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">,</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="n" style="color: #333;">cnt</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="n" style="color: #333;">q_freq</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1062" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1062
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1062" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">popmap_used</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1063" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1063
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1063" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1064" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1064
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1064" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1065" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1065
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1065" class="line" lang="python"> <span class="n" style="color: #333;">pop_1_vcfpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="nc" style="color: #458; font-weight: 600;">SmoothStat</span><span class="p">(</span><span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">,</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">cnt</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">q_freq</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1066" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1066
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1066" class="line" lang="python"> </span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1067" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1067
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1067" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">pop</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">plot_pops</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1068" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1068
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1068" class="line" lang="python"> <span class="n" style="color: #333;">pop_2</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="nc" style="color: #458; font-weight: 600;">SmoothStat</span><span class="p">(</span><span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">,</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="n" style="color: #333;">cnt</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">pops</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">].</span><span class="n" style="color: #333;">q_freq</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1069" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1069
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1069" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">popmap_used</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1070" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1070
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1070" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1071" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1071
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1071" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1072" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1072
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1072" class="line" lang="python"> <span class="n" style="color: #333;">pop_2_vcfpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="nc" style="color: #458; font-weight: 600;">SmoothStat</span><span class="p">(</span><span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">,</span> <span class="n" style="color: #333;">pop</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">cnt</span><span class="p">,</span> <span class="n" style="color: #333;">snp</span><span class="p">.</span><span class="n" style="color: #333;">indvpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">q_freq</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1073" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1073
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1073" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="1074" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1074
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1074" class="line" lang="python"> <span class="n" style="color: #333;">pop_1</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">sort</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">attrgetter</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">bp</span><span class="sh" style="color: #d14;">"</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1075" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1075
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1075" class="line" lang="python"> <span class="n" style="color: #333;">pop_2</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">sort</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">attrgetter</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">bp</span><span class="sh" style="color: #d14;">"</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1076" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1076
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1076" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">popmap_used</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1077" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1077
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1077" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1078" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1078
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1078" class="line" lang="python"> <span class="n" style="color: #333;">pop_1_vcfpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">sort</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">attrgetter</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">bp</span><span class="sh" style="color: #d14;">"</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1079" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1079
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1079" class="line" lang="python"> <span class="n" style="color: #333;">pop_2_vcfpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">sort</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">attrgetter</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">bp</span><span class="sh" style="color: #d14;">"</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1080" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1080
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1080" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="1081" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1081
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1081" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1082" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1082
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1082" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Smooth the values.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1083" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1083
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1083" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1084" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1084
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1084" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">smooth</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1085" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1085
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1085" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">smooth_chromosome</span><span class="p">(</span><span class="n" style="color: #333;">pop_1</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1086" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1086
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1086" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">smooth_chromosome</span><span class="p">(</span><span class="n" style="color: #333;">pop_2</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1087" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1087
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1087" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">popmap_used</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1088" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1088
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1088" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1089" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1089
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1089" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">smooth_chromosome</span><span class="p">(</span><span class="n" style="color: #333;">pop_1_vcfpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1090" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1090
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1090" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">smooth_chromosome</span><span class="p">(</span><span class="n" style="color: #333;">pop_2_vcfpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1091" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1091
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1091" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">.</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #d14;">''</span><span class="p">,</span> <span class="n" style="color: #333;">flush</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1092" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1092
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1092" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="1093" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1093
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1093" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1094" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1094
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1094" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write the values.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1095" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1095
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1095" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1096" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1096
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1096" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">write_plot_values</span><span class="p">(</span><span class="n" style="color: #333;">plot_fhs</span><span class="p">[</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">vcf</span><span class="sh" style="color: #d14;">'</span><span class="p">],</span> <span class="n" style="color: #333;">pop_1</span><span class="p">,</span> <span class="n" style="color: #333;">pop_2</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1097" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1097
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1097" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">popmap_used</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1098" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1098
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1098" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1099" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1099
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1099" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">write_plot_values</span><span class="p">(</span><span class="n" style="color: #333;">plot_fhs</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">],</span> <span class="n" style="color: #333;">pop_1_vcfpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">],</span> <span class="n" style="color: #333;">pop_2_vcfpops</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1100" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1100
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1100" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="1101" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1101
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1101" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">plot_fhs</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1102" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1102
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1102" class="line" lang="python"> <span class="n" style="color: #333;">plot_fhs</span><span class="p">[</span><span class="n" style="color: #333;">f</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1103" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1103
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1103" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">smooth</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1104" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1104
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1104" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1105" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1105
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1105" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="1106" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1106
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1106" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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1107
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1107" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="1108" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1108
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1108" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="1109" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1109
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1109" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">():</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1110" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1110
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1110" class="line" lang="python"> <span class="n" style="color: #333;">loci</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1111" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1111
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1111" class="line" lang="python"> <span class="n" style="color: #333;">ordered_loci</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1112" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1112
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1112" class="line" lang="python"> <span class="n" style="color: #333;">chrs_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1113" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1113
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1113" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1114" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1114
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1114" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># List of populations, and ordered sample names for each.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1115" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1115
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1115" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1116" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1116
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1116" class="line" lang="python"> <span class="n" style="color: #333;">populations_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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1117
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1117" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="1118" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1118
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1118" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">parse_command_line</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1119" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1119
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1119" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="1120" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1120
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1120" class="line" lang="python"> <span class="n" style="color: #333;">vcfpops</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1121" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1121
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1121" class="line" lang="python"> <span class="n" style="color: #333;">vcfpops_rev</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1122" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1122
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1122" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">popmap_used</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1123" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1123
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1123" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">Parsing population map: </span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">{}</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">...</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">popmap_path</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1124" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1124
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1124" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">parse_popmap_file</span><span class="p">(</span><span class="n" style="color: #333;">popmap_path</span><span class="p">,</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">,</span> <span class="n" style="color: #333;">vcfpops_rev</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1125" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1125
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1125" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="1126" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1126
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1126" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">Parsing sumstats file: </span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">{}</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">...</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">sumstats_path</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1127" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1127
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1127" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">parse_sumstats_file</span><span class="p">(</span><span class="n" style="color: #333;">sumstats_path</span><span class="p">,</span> <span class="n" style="color: #333;">loci</span><span class="p">,</span> <span class="n" style="color: #333;">populations_key</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1128" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1128
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1128" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="1129" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1129
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1129" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">Parsing VCF file: </span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">{}</span><span class="sh" style="color: #d14;">'</span><span class="s" style="color: #d14;">...</span><span class="sh" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">vcf_path</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1130" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1130
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1130" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">parse_hybrid_vcf</span><span class="p">(</span><span class="n" style="color: #333;">vcf_path</span><span class="p">,</span> <span class="n" style="color: #333;">loci</span><span class="p">,</span> <span class="n" style="color: #333;">populations_key</span><span class="p">,</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">,</span> <span class="n" style="color: #333;">vcfpops_rev</span><span class="p">,</span> <span class="n" style="color: #333;">chrs_list</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1131" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1131
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1131" class="line" lang="python"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1132" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1132
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1132" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">order_loci</span><span class="p">(</span><span class="n" style="color: #333;">chrs_list</span><span class="p">,</span> <span class="n" style="color: #333;">loci</span><span class="p">,</span> <span class="n" style="color: #333;">ordered_loci</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1133" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1133
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1133" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="1134" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1134
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1134" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">write_private_allele_summary</span><span class="p">(</span><span class="n" style="color: #333;">chrs_list</span><span class="p">,</span> <span class="n" style="color: #333;">ordered_loci</span><span class="p">,</span> <span class="n" style="color: #333;">populations_key</span><span class="p">,</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">,</span> <span class="n" style="color: #333;">out_path</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1135" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1135
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1135" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="1136" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1136
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1136" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">polarize</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1137" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1137
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1137" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Writing polarized VCF files:</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1138" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1138
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1138" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">write_polarized_vcfs</span><span class="p">(</span><span class="n" style="color: #333;">chrs_list</span><span class="p">,</span> <span class="n" style="color: #333;">loci</span><span class="p">,</span> <span class="n" style="color: #333;">populations_key</span><span class="p">,</span> <span class="n" style="color: #333;">vcf_path</span><span class="p">,</span> <span class="n" style="color: #333;">out_path</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1139" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1139
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1139" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">done.</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1140" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1140
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1140" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="1141" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1141
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1141" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">plots</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1142" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1142
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1142" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Generating plotting files:</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1143" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1143
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1143" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">write_plots</span><span class="p">(</span><span class="n" style="color: #333;">chrs_list</span><span class="p">,</span> <span class="n" style="color: #333;">ordered_loci</span><span class="p">,</span> <span class="n" style="color: #333;">populations_key</span><span class="p">,</span> <span class="n" style="color: #333;">vcfpops</span><span class="p">,</span> <span class="n" style="color: #333;">out_path</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1144" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1144
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1144" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">done.</span><span class="sh" style="color: #d14;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1145" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1145
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1145" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="1146" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1146
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1146" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># #</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1147" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1147
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1147" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#------------------------------------------------------------------------------#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1148" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1148
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1148" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># #</span></span>
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1149
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1149" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #d14;">"</span><span class="s" style="color: #d14;">__main__</span><span class="sh" style="color: #d14;">"</span><span class="p">:</span></span>
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1150
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1150" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">()</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#119d50f2f2d1e3f64b65bbd89f3cafcfb13ca0d4"><strong style="font-weight: 600;">src/Seq.h</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="148" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -148,12 +148,12 @@ void Seq::reserve(size_t n, bool with_qual) {</td>
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<td class="old_line diff-line-num" data-linenumber="148" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
148
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<td class="new_line diff-line-num" data-linenumber="148" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
148
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">[</span><span class="n" style="color: #333;">capacity</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="149" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
149
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<td class="new_line diff-line-num" data-linenumber="149" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
149
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC149" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
150
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<td class="new_line diff-line-num" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
150
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC150" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">with_qual</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
151
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<td class="new_line diff-line-num old" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">qual</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
151
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">[]</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">qual</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="152" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
152
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<td class="new_line diff-line-num" data-linenumber="152" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
152
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">[</span><span class="n" style="color: #333;">capacity</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="153" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
153
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<td class="new_line diff-line-num" data-linenumber="153" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
153
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC153" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="154" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
154
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<td class="new_line diff-line-num" data-linenumber="154" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
154
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC154" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="155" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
155
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<td class="new_line diff-line-num" data-linenumber="155" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
155
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC155" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Delete it to keep the capacity predictable.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="156" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
156
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<td class="new_line diff-line-num old" data-linenumber="156" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC156" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">qual</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
156
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC156" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">[]</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">qual</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="157" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
157
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<td class="new_line diff-line-num" data-linenumber="157" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
157
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC157" class="line" lang="cpp"> <span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="158" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
158
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<td class="new_line diff-line-num" data-linenumber="158" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
158
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC158" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="159" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
159
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<td class="new_line diff-line-num" data-linenumber="159" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
159
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC159" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#85c0ee6f77dd1ab892cf45bfd301d678f6ebec1f"><strong style="font-weight: 600;">src/clean.cc</strong></a>
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1
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-</span></span>
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2
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2
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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3
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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2011-202<span class="idiff left right deletion" style="background-color: #fac5cd;">1</span>, Julian Catchen <jcatchen@illinois.edu></span></span>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2011-202<span class="idiff left right addition" style="background-color: #c7f0d2;">4</span>, Julian Catchen <jcatchen@illinois.edu></span></span>
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4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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5
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// This file is part of Stacks.</span></span>
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6
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6
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="107" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="107" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -107,11 +107,16 @@ parse_input_record(Seq *s, RawRead *r)</td>
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<td class="old_line diff-line-num" data-linenumber="107" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
107
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<td class="new_line diff-line-num" data-linenumber="107" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
107
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">lim</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
108
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<td class="new_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
108
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC108" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="109" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
109
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<td class="new_line diff-line-num" data-linenumber="109" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
109
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC109" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Count the number of colons to differentiate Illumina version.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="110" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
110
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<td class="new_line diff-line-num old" data-linenumber="110" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC110" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// CASAVA 1.8+ has a FASTQ header like this:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="110" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
110
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC110" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
111
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC111" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Illumina's BCL Convert program or CASAVA 1.8+ has a FASTQ header like this:</span></span>
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<td class="old_line diff-line-num" data-linenumber="111" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
111
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<td class="new_line diff-line-num" data-linenumber="112" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
112
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC112" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// @HWI-ST0747:155:C01WHABXX:8:1101:6455:26332 1:N:0:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="112" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
113
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC113" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// </span></span>
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<td class="old_line diff-line-num" data-linenumber="112" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
112
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<td class="new_line diff-line-num" data-linenumber="114" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
114
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC114" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Or, with the embedded barcode:</span></span>
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<td class="old_line diff-line-num" data-linenumber="113" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
113
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<td class="new_line diff-line-num" data-linenumber="115" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
115
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC115" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// @HWI-ST1233:67:D12GNACXX:7:2307:14604:78978 1:N:0:ATCACG</span></span>
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<td class="old_line diff-line-num old" data-linenumber="114" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
114
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<td class="new_line diff-line-num old" data-linenumber="116" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC114" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="116" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
116
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC116" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// </span></span>
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<td class="old_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="117" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
117
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC117" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Or, with a UMI (unique molecular identifier -- for PCR duplicate control):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
118
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC118" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// @LH00346:7:22CH5TLT3:5:1101:1407:1032:rTACCCAGT 1:N:0:ACATTGCG</span></span>
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<td class="old_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
119
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC119" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// -the 'r' in the UMI field indicates it is reverse complemented.</span></span>
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115
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<td class="new_line diff-line-num" data-linenumber="120" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
120
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC120" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="116" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
116
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<td class="new_line diff-line-num" data-linenumber="121" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
121
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC121" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Or, parse FASTQ header from previous versions that looks like this:</span></span>
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117
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<td class="new_line diff-line-num" data-linenumber="122" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
122
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC122" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// @HWI-ST0747_0141:4:1101:1240:2199#0/1</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="126" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="131" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -126,16 +131,16 @@ parse_input_record(Seq *s, RawRead *r)</td>
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<td class="old_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
126
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<td class="new_line diff-line-num" data-linenumber="131" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
131
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC131" class="line" lang="cpp"> <span class="n" style="color: #333;">hash_cnt</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'#'</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="127" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
127
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<td class="new_line diff-line-num" data-linenumber="132" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
132
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC132" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="128" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
128
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<td class="new_line diff-line-num" data-linenumber="133" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
133
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC133" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="129" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
129
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<td class="new_line diff-line-num old" data-linenumber="134" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC129" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">colon_cnt</span> <span class="o" style="font-weight: 600;"><span class="idiff left deletion" style="background-color: #fac5cd;">==</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="mi" style="color: #099;"><span class="idiff right deletion" style="background-color: #fac5cd;">9</span></span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">hash_cnt</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="134" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
134
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC134" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">(</span>(</span><span class="n" style="color: #333;">colon_cnt</span> <span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">>=</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="mi" style="color: #099;"><span class="idiff addition" style="background-color: #c7f0d2;">9</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">&&</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">colon_cnt</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;"><=</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="mi" style="color: #099;"><span class="idiff addition" style="background-color: #c7f0d2;">10</span></span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">)</span></span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">hash_cnt</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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130
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<td class="new_line diff-line-num" data-linenumber="135" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
135
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fastq_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">illv2_fastq</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="131" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
131
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<td class="new_line diff-line-num" data-linenumber="136" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
136
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC136" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num old" data-linenumber="132" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
132
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<td class="new_line diff-line-num old" data-linenumber="137" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC132" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// According to Illumina manual, "CASAVA v1.8 User Guide" page 41:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="133" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
137
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC137" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right addition" style="background-color: #c7f0d2;">Colon_cnt == 9; </span>According to Illumina manual, "CASAVA v1.8 User Guide" page 41:</span></span>
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138
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC138" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// @<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:<x-pos>:<y-pos> <read>:<is filtered>:<control number>:<index sequence></span></span>
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<td class="old_line diff-line-num" data-linenumber="134" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
134
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<td class="new_line diff-line-num" data-linenumber="139" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
139
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC139" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="135" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
135
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<td class="new_line diff-line-num" data-linenumber="140" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
140
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC140" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">;</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">':'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="p">;</span> <span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="136" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
136
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<td class="new_line diff-line-num" data-linenumber="141" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
141
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC141" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="137" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
137
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<td class="new_line diff-line-num" data-linenumber="142" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
142
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC142" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="138" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
138
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<td class="new_line diff-line-num old" data-linenumber="143" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">strcpy</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">(</span></span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine</span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff right deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
143
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC143" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine</span><span class="p"><span class="idiff left right addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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139
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<td class="new_line diff-line-num" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
144
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC144" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">':'</span><span class="p">;</span></span>
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145
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC145" class="line" lang="cpp"> <span class="p">}</span></span>
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146
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC146" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="172" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="177" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -172,12 +177,28 @@ parse_input_record(Seq *s, RawRead *r)</td>
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<td class="old_line diff-line-num" data-linenumber="172" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
172
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<td class="new_line diff-line-num" data-linenumber="177" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
177
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC177" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">':'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="173" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
173
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<td class="new_line diff-line-num" data-linenumber="178" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
178
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC178" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="174" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
174
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<td class="new_line diff-line-num" data-linenumber="179" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
179
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC179" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="175" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
175
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<td class="new_line diff-line-num old" data-linenumber="180" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC175" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">;</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="p">;</span> <span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="176" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
176
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<td class="new_line diff-line-num old" data-linenumber="180" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC176" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="177" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
177
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<td class="new_line diff-line-num old" data-linenumber="180" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC177" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="178" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
178
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<td class="new_line diff-line-num old" data-linenumber="180" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC178" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atoi</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="179" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
179
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<td class="new_line diff-line-num old" data-linenumber="180" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC179" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">' '</span><span class="p">;</span></span>
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180
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<td class="new_line diff-line-num old" data-linenumber="180" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC180" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
180
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC180" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">;</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="p">;</span> <span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
181
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC181" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="182" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
182
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC182" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="183" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
183
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC183" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atoi</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="184" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
184
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC184" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="185" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
185
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC185" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="186" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
186
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC186" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">colon_cnt</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="187" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
187
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC187" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
188
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC188" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// According to Illumina's BCL Convert program an extra field occurs containing the UMI:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="189" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
189
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC189" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// @<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:<x-pos>:<y-pos>:<UMI> <read>:<is filtered>:<control number>:<index sequence></span></span>
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<td class="new_line diff-line-num new" data-linenumber="190" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
190
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC190" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="new_line diff-line-num new" data-linenumber="191" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
191
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC191" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">';'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="192" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
192
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC192" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fastq_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">illv3_fastq</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
193
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC193" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" data-linenumber="194" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
194
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC194" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">;</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">':'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="p">;</span> <span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="195" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
195
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC195" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="196" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
196
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC196" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="197" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
197
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC197" class="line" lang="cpp"> <span class="n" style="color: #333;">strncpy</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">umi</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">id_len</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="198" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
198
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC198" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
199
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC199" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="200" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
200
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC200" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="201" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
201
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC201" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">' '</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
181
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<td class="new_line diff-line-num" data-linenumber="202" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
202
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC202" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="182" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
182
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<td class="new_line diff-line-num" data-linenumber="203" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
203
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC203" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">;</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">':'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="p">;</span> <span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="183" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
183
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<td class="new_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
204
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC204" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="270" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="291" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -270,7 +291,7 @@ parse_input_record(Seq *s, RawRead *r)</td>
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<td class="old_line diff-line-num" data-linenumber="270" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
270
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<td class="new_line diff-line-num" data-linenumber="291" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
291
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC291" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">;</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">':'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="p">;</span> <span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="271" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
271
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<td class="new_line diff-line-num" data-linenumber="292" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
292
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC292" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="272" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
272
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<td class="new_line diff-line-num" data-linenumber="293" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
293
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC293" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="273" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
273
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<td class="new_line diff-line-num old" data-linenumber="294" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC273" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">strcpy</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">(</span></span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine</span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff right deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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294
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC294" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine</span><span class="p"><span class="idiff left right addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<td class="new_line diff-line-num" data-linenumber="295" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
295
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC295" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">':'</span><span class="p">;</span></span>
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296
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC296" class="line" lang="cpp"> <span class="p">}</span></span>
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297
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC297" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="315" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="336" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -315,8 +336,16 @@ parse_input_record(Seq *s, RawRead *r)</td>
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315
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<td class="new_line diff-line-num" data-linenumber="336" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
336
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC336" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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316
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<td class="new_line diff-line-num" data-linenumber="337" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
337
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC337" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fastq_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">generic_fastq</span><span class="p">;</span></span>
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317
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338
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC338" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="318" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
318
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<td class="new_line diff-line-num old" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC318" class="line" lang="cpp"> <span class="n" style="color: #333;">strncpy</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">id_len</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="319" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
319
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<td class="new_line diff-line-num old" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC319" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine</span><span class="p">[</span><span class="n" style="color: #333;">id_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
339
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC339" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="new_line diff-line-num new" data-linenumber="340" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
340
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC340" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check if the header already contains a "/1" or "/2" notation at the end,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="341" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
341
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC341" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// from previous parsing of the file (e.g. Sequence Read Archve data). Remove</span></span>
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<td class="new_line diff-line-num new" data-linenumber="342" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
342
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC342" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// if present.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="343" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
343
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC343" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="new_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
344
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC344" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="345" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
345
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC345" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'/'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'1'</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'2'</span><span class="p">))</span></span>
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346
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC346" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="347" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
347
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC347" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="320" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="348" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
348
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC348" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="320" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
320
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<td class="new_line diff-line-num" data-linenumber="349" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
349
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC349" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="321" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
321
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<td class="new_line diff-line-num" data-linenumber="350" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
350
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC350" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="322" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
322
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<td class="new_line diff-line-num" data-linenumber="351" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
351
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC351" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="451" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="480" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -451,6 +480,14 @@ check_quality_scores(RawRead *href, int qual_offset, int score_limit, int len_li</td>
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451
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<td class="new_line diff-line-num" data-linenumber="480" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
480
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC480" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// | | | | |</span></span>
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<td class="old_line diff-line-num" data-linenumber="452" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
452
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<td class="new_line diff-line-num" data-linenumber="481" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
481
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC481" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 64 74 84 94 104</span></span>
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<td class="old_line diff-line-num" data-linenumber="453" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
453
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<td class="new_line diff-line-num" data-linenumber="482" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
482
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC482" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 0 10(90%) 20(99%) 30(99.9%) 40(99.99%)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="454" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="483" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
483
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC483" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num new" data-linenumber="454" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="484" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
484
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC484" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Illumina 1.8+ encodes phred scores between ASCII values 33 (0 quality) and 74 (41 quality)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="485" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
485
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC485" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="new_line diff-line-num new" data-linenumber="486" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
486
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC486" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJK</span></span>
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<td class="old_line diff-line-num new" data-linenumber="454" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="487" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
487
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC487" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// | | | | |</span></span>
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<td class="new_line diff-line-num new" data-linenumber="488" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
488
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC488" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 33 43 53 63 73</span></span>
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<td class="new_line diff-line-num new" data-linenumber="489" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
489
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC489" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 0 10(90%) 20(99%) 30(99.9%) 40(99.99%)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="490" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
490
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC490" class="line" lang="cpp"></span>
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454
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<td class="new_line diff-line-num" data-linenumber="491" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
491
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC491" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC492" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="456" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="493" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
493
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC493" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Drop sequence if the average phred quality score drops below a threshold within a sliding window.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="459" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="496" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -459,12 +496,9 @@ check_quality_scores(RawRead *href, int qual_offset, int score_limit, int len_li</td>
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459
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496
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC496" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="460" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
460
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<td class="new_line diff-line-num" data-linenumber="497" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
497
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC497" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Convert the encoded quality scores to their integer values</span></span>
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461
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<td class="new_line diff-line-num" data-linenumber="498" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
498
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC498" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num old" data-linenumber="462" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
462
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<td class="new_line diff-line-num old" data-linenumber="499" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC462" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// cerr << "Integer scores: ";</span></span>
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<td class="old_line diff-line-num" data-linenumber="463" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
463
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<td class="new_line diff-line-num" data-linenumber="499" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
499
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC499" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="464" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
464
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<td class="new_line diff-line-num" data-linenumber="500" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
500
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC500" class="line" lang="cpp"> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">int_scores</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">phred</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">qual_offset</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="465" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
465
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<td class="new_line diff-line-num old" data-linenumber="501" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC465" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// cerr << href->int_scores[j] << " ";</span></span>
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466
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<td class="new_line diff-line-num" data-linenumber="501" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
501
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC501" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="467" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
467
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<td class="new_line diff-line-num old" data-linenumber="502" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC467" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// cerr << "\n";</span></span>
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468
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502
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC502" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="469" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
469
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<td class="new_line diff-line-num" data-linenumber="503" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
503
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC503" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="470" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
470
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<td class="new_line diff-line-num" data-linenumber="504" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
504
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC504" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mean</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="530" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="564" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -530,6 +564,71 @@ check_quality_scores(RawRead *href, int qual_offset, int score_limit, int len_li</td>
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<td class="old_line diff-line-num" data-linenumber="530" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
530
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<td class="new_line diff-line-num" data-linenumber="564" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
564
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC564" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="531" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
531
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<td class="new_line diff-line-num" data-linenumber="565" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
565
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC565" class="line" lang="cpp"><span class="p">}</span></span>
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532
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566
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC566" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" data-linenumber="567" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
567
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC567" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span></span>
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<td class="new_line diff-line-num new" data-linenumber="568" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
568
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC568" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">check_poly_g_run</span><span class="p">(</span><span class="n" style="color: #333;">RawRead</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">href</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len_limit</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="569" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
569
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC569" class="line" lang="cpp"><span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="570" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
570
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC570" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num new" data-linenumber="533" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="571" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
571
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC571" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Search for a run of G nucleotides at the 3' end of the read. In Illumina machines with</span></span>
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<td class="new_line diff-line-num new" data-linenumber="572" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
572
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC572" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// two-color chemistry, no color signal is interpreted as a 'G'. However, when sequencing of</span></span>
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<td class="new_line diff-line-num new" data-linenumber="573" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
573
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC573" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// a cluster has failed, and no signal is returned, that is also interpreted as a G and</span></span>
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<td class="new_line diff-line-num new" data-linenumber="574" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
574
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC574" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// will receive a very high quality score. If we see a run of these Gs at the end of the</span></span>
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<td class="new_line diff-line-num new" data-linenumber="575" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
575
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC575" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// sequence, drop the seqeunce.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="576" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
576
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC576" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="new_line diff-line-num new" data-linenumber="577" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
577
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC577" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">run_limit</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="578" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
578
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC578" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">polyg_phred_lim</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">35</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="579" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
579
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC579" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">exception_lim</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="580" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
580
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC580" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="new_line diff-line-num new" data-linenumber="581" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
581
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC581" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Set a stop index to the first element of the sequence, not including any barcode.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="582" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
582
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC582" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="new_line diff-line-num new" data-linenumber="583" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
583
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC583" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">offset</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="584" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
584
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC584" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" data-linenumber="585" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
585
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC585" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="new_line diff-line-num new" data-linenumber="586" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
586
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC586" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// We will look for a run of a certain length (run_len) while allowing for a small number</span></span>
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<td class="new_line diff-line-num new" data-linenumber="587" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
587
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC587" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// of exceptions to the run, either with a different base or a lowerer phred score.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="588" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
588
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC588" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">run_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="589" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
589
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC589" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">exception_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="590" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
590
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC590" class="line" lang="cpp"> </span>
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<td class="new_line diff-line-num new" data-linenumber="591" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
591
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC591" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="new_line diff-line-num new" data-linenumber="592" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
592
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC592" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Set j to be the last element in the sequence.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="593" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
593
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC593" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="new_line diff-line-num new" data-linenumber="594" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
594
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC594" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="595" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
595
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC595" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" data-linenumber="596" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
596
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC596" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// cerr << "Start: " << j << "; Stop: " << stop << "\n";</span></span>
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<td class="new_line diff-line-num new" data-linenumber="597" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
597
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC597" class="line" lang="cpp"> </span>
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<td class="new_line diff-line-num new" data-linenumber="598" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
598
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC598" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">stop</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="599" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
599
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC599" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" data-linenumber="600" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
600
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC600" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// cerr << " Col: " << j << "; Nuc: " << href->seq[j] << "; Phred: " << href->phred[j] << "; Int: " << href->int_scores[j] << "\n";</span></span>
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<td class="new_line diff-line-num new" data-linenumber="601" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
601
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC601" class="line" lang="cpp"> </span>
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602
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC602" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'G'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">int_scores</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">polyg_phred_lim</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="603" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
603
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC603" class="line" lang="cpp"> <span class="n" style="color: #333;">run_len</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="604" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
604
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC604" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="new_line diff-line-num new" data-linenumber="605" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
605
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC605" class="line" lang="cpp"> <span class="n" style="color: #333;">exception_len</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="606" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
606
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC606" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="533" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="607" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
607
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC607" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exception_len</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">exception_lim</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="533" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="608" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
608
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC608" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// cerr << "Returning 1; run_len: " << run_len << "; exception_len: " << exception_len << "\n";</span></span>
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<td class="old_line diff-line-num new" data-linenumber="533" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="609" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
609
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC609" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// cerr << " " << href->seq << "\n " << href->phred << "\n";</span></span>
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<td class="new_line diff-line-num new" data-linenumber="610" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
610
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC610" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="611" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
611
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC611" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="612" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
612
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC612" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num new" data-linenumber="533" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="613" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
613
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC613" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">run_len</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">run_limit</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="533" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="614" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
614
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC614" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// cerr << "Returning -1; run_len: " << run_len << "; exception_len: " << exception_len << "\n";</span></span>
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<td class="old_line diff-line-num new" data-linenumber="533" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="615" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
615
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC615" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// cerr << " " << href->seq << "\n " << href->phred << "\n";</span></span>
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<td class="old_line diff-line-num new" data-linenumber="533" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="616" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
616
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC616" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">len_limit</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="617" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
617
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC617" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="618" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
618
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC618" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="619" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
619
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC619" class="line" lang="cpp"> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC620" class="line" lang="cpp"> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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621
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC621" class="line" lang="cpp"> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">phred</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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622
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC622" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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623
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624
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626
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627
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628
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC628" class="line" lang="cpp"></span>
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629
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC629" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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630
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC630" class="line" lang="cpp"><span class="p">}</span></span>
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631
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC631" class="line" lang="cpp"></span>
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533
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<td class="new_line diff-line-num" data-linenumber="632" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
632
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC632" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span></span>
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534
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<td class="new_line diff-line-num" data-linenumber="633" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
633
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC633" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">correct_barcode</span><span class="p">(</span><span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bcs</span><span class="p">,</span> <span class="n" style="color: #333;">RawRead</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">href</span><span class="p">,</span> <span class="n" style="color: #333;">seqt</span> <span class="n" style="color: #333;">type</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">num_errs</span><span class="p">)</span></span>
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535
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634
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC634" class="line" lang="cpp"><span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="619" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="718" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -619,8 +718,9 @@ filter_adapter_seq(RawRead *href, char *adapter, int adp_len, AdapterHash &adp_k</td>
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619
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<td class="new_line diff-line-num" data-linenumber="718" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
718
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC718" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmer_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">distance</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len_limit</span><span class="p">)</span></span>
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620
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719
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC719" class="line" lang="cpp"><span class="p">{</span></span>
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621
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720
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC720" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">hits</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="622" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
622
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<td class="new_line diff-line-num old" data-linenumber="721" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC622" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">num_kmers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmer_size</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="623" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
623
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<td class="new_line diff-line-num old" data-linenumber="721" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC623" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="624" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="721" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
721
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC721" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">query_stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">inline_bc_len</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="624" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="722" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
722
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC722" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">num_kmers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">query_stop</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmer_size</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="624" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="723" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
723
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC723" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">query_stop</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="624" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
624
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<td class="new_line diff-line-num" data-linenumber="724" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
724
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC724" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">kmer</span><span class="p">;</span></span>
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625
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725
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC725" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="626" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
626
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<td class="new_line diff-line-num" data-linenumber="726" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
726
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC726" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="651" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="751" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -651,13 +751,17 @@ filter_adapter_seq(RawRead *href, char *adapter, int adp_len, AdapterHash &adp_k</td>
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<td class="old_line diff-line-num" data-linenumber="651" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
651
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<td class="new_line diff-line-num" data-linenumber="751" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
751
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC751" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="652" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
652
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<td class="new_line diff-line-num" data-linenumber="752" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
752
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC752" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// cerr << "Starting comparison at i: "<< i << "; j: " << j << "\n";</span></span>
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<td class="old_line diff-line-num" data-linenumber="653" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
653
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<td class="new_line diff-line-num" data-linenumber="753" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
753
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC753" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="654" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
654
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<td class="new_line diff-line-num old" data-linenumber="754" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC654" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;"><span class="idiff left right deletion" style="background-color: #fac5cd;">0</span></span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="655" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="754" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
754
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC754" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;"><span class="idiff left right addition" style="background-color: #c7f0d2;">query_stop</span></span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="655" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
655
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<td class="new_line diff-line-num" data-linenumber="755" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
755
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC755" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">])</span></span>
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<td class="old_line diff-line-num" data-linenumber="656" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
656
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<td class="new_line diff-line-num" data-linenumber="756" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
756
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC756" class="line" lang="cpp"> <span class="n" style="color: #333;">mismatches</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC757" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC758" class="line" lang="cpp"> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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759
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC759" class="line" lang="cpp"> <span class="p">}</span></span>
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660
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC660" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" data-linenumber="760" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
760
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC760" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="761" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
761
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC761" class="line" lang="cpp"> <span class="n" style="color: #333;">mismatches</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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762
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC762" class="line" lang="cpp"> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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763
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC763" class="line" lang="cpp"> <span class="p">}</span></span>
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764
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC764" class="line" lang="cpp"> </span>
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661
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<td class="new_line diff-line-num" data-linenumber="765" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
765
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC765" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mismatches</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">distance</span><span class="p">)</span></span>
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662
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766
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC766" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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663
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767
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC767" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#1644bd85290d6144938b4b136f22f9635a67964e"><strong style="font-weight: 600;">src/clean.h</strong></a>
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1
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-</span></span>
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2
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2
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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3
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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2011-202<span class="idiff left right deletion" style="background-color: #fac5cd;">3</span>, Julian Catchen <jcatchen@uoregon.edu></span></span>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2011-202<span class="idiff left right addition" style="background-color: #c7f0d2;">4</span>, Julian Catchen <jcatchen@uoregon.edu></span></span>
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4
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4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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5
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// This file is part of Stacks.</span></span>
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6
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6
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="30" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -30,14 +30,18 @@</td>
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<td class="old_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include</span> <span class="cpf">"input.h"</span></span>
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<td class="old_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
31
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<td class="new_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
31
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC31" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include</span> <span class="cpf">"kmers.h"</span></span>
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<td class="old_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
32
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<td class="new_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
32
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC32" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
33
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<td class="new_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC33" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">fastqt</span> <span class="p">{</span><span class="n" style="color: #333;">generic_fastq</span><span class="p">,</span> <span class="n" style="color: #333;">illv1_fastq</span><span class="p">,</span> <span class="n" style="color: #333;">illv2_fastq</span><span class="p">};</span></span>
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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
33
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC33" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">fastqt</span> <span class="p">{</span><span class="n" style="color: #333;">generic_fastq</span><span class="p">,</span> <span class="n" style="color: #333;">illv1_fastq</span><span class="p">,</span> <span class="n" style="color: #333;">illv2_fastq</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff right addition" style="background-color: #c7f0d2;">illv3_fastq</span></span><span class="p">};</span></span>
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<td class="old_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
34
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<td class="new_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC34" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
35
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC35" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">barcodet</span> <span class="p">{</span><span class="n" style="color: #333;">null_null</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
36
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">null_inline</span><span class="p">,</span> <span class="n" style="color: #333;">null_index</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
37
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<td class="new_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
37
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">inline_null</span><span class="p">,</span> <span class="n" style="color: #333;">index_null</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
38
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<td class="new_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
38
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC38" class="line" lang="cpp"> <span class="n" style="color: #333;">inline_inline</span><span class="p">,</span> <span class="n" style="color: #333;">index_index</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
39
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">inline_index</span><span class="p">,</span> <span class="n" style="color: #333;">index_inline</span><span class="p">};</span></span>
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<td class="old_line diff-line-num old" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
40
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<td class="new_line diff-line-num old" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC40" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">seqt</span> <span class="p">{</span><span class="n" style="color: #333;">single_end</span><span class="p">,</span> <span class="n" style="color: #333;">paired_end</span><span class="p">};</span></span>
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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
40
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC40" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
41
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC41" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">seqt</span> <span class="p">{</span><span class="n" style="color: #333;">single_end</span><span class="p">,</span> <span class="n" style="color: #333;">paired_end</span><span class="p">};</span></span>
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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
42
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC42" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
43
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC43" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">machinet</span> <span class="p">{</span><span class="n" style="color: #333;">genome_analyzer_iix</span><span class="p">,</span> <span class="n" style="color: #333;">miseq</span><span class="p">,</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">hiseq</span><span class="p">,</span> <span class="n" style="color: #333;">nextseq</span><span class="p">,</span> <span class="n" style="color: #333;">novaseq</span><span class="p">,</span> <span class="n" style="color: #333;">miniseq</span><span class="p">,</span> <span class="n" style="color: #333;">unknown</span><span class="p">};</span></span>
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41
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<td class="new_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
45
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC45" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
42
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<td class="new_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
46
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC46" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">unordered_map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">hash</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">AdapterHash</span><span class="p">;</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC47" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="143" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="147" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -143,34 +147,37 @@ public:</td>
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<td class="old_line diff-line-num" data-linenumber="143" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
143
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<td class="new_line diff-line-num" data-linenumber="147" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
147
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC147" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
144
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<td class="new_line diff-line-num" data-linenumber="148" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
148
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC148" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">RawRead</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="145" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
145
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<td class="new_line diff-line-num" data-linenumber="149" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
149
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC149" class="line" lang="cpp"><span class="nl">public:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="146" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
146
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">fastqt</span> <span class="n" style="color: #333;">fastq_type</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="147" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
147
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC147" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">inline_bc</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="148" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
148
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC148" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">index_bc</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="149" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
149
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC149" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">se_bc</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
150
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC150" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pe_bc</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
151
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC151" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">machine</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="152" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
152
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC152" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">run</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="153" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
153
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC153" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lane</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="154" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
154
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC154" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tile</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="155" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
155
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC155" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>
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156
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC156" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="157" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
157
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC157" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="158" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
158
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC158" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">read</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="159" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
159
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC159" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="160" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
160
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC160" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">phred</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="161" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
161
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC161" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">int_scores</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="162" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
162
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC162" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">filter</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
163
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC163" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">inline_bc_len</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="164" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
164
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC164" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">retain</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="165" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
165
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="166" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
166
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="167" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
167
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC167" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">win_len</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="168" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
168
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC168" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">stop_pos</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="169" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
169
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC169" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
150
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC150" class="line" lang="cpp"> <span class="n" style="color: #333;">fastqt</span> <span class="n" style="color: #333;">fastq_type</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
151
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC151" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">inline_bc</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
152
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC152" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">index_bc</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
153
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC153" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">se_bc</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
154
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC154" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pe_bc</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
155
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC155" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_machine</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
156
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">machinet</span> <span class="n" style="color: #333;">machine_type</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
157
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC157" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">umi</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
158
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC158" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">run</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
159
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC159" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lane</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
160
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC160" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tile</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="161" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
161
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC161" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
162
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC162" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="163" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
163
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC163" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
164
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC164" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">read</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
165
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC165" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
166
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC166" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">phred</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="167" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
167
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC167" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">int_scores</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
168
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC168" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">filter</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
169
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC169" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">inline_bc_len</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
170
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC170" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">retain</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
171
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC171" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="172" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
172
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC172" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="173" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
173
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC173" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">win_len</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
174
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC174" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">stop_pos</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="175" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
175
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC175" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
170
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<td class="new_line diff-line-num" data-linenumber="176" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
176
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC176" class="line" lang="cpp"> <span class="n" style="color: #333;">RawRead</span><span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">buf_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">barcode_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">win_size</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="171" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
171
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<td class="new_line diff-line-num" data-linenumber="177" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
177
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC177" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">inline_bc</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">[</span><span class="n" style="color: #333;">id_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="172" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
172
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<td class="new_line diff-line-num" data-linenumber="178" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
178
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC178" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">index_bc</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">[</span><span class="n" style="color: #333;">id_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="old_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
173
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<td class="new_line diff-line-num old" data-linenumber="179" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC173" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">[</span><span class="n" style="color: #333;">id_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="old_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="179" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
179
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC179" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_machine</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">[</span><span class="n" style="color: #333;">id_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="old_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
180
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC180" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">[</span><span class="n" style="color: #333;">id_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="174" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
174
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<td class="new_line diff-line-num" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
181
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC181" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">[</span><span class="n" style="color: #333;">buf_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="175" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
175
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<td class="new_line diff-line-num" data-linenumber="182" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
182
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC182" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">phred</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">[</span><span class="n" style="color: #333;">buf_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="176" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
176
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<td class="new_line diff-line-num" data-linenumber="183" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
183
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC183" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">int_scores</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">[</span><span class="n" style="color: #333;">buf_len</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="189" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="196" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -189,10 +196,18 @@ public:</td>
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<td class="old_line diff-line-num" data-linenumber="189" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
189
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<td class="new_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
196
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC196" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="190" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
190
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<td class="new_line diff-line-num" data-linenumber="197" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
197
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC197" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">inline_bc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="191" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
191
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<td class="new_line diff-line-num" data-linenumber="198" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
198
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC198" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">index_bc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="192" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
192
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<td class="new_line diff-line-num old" data-linenumber="199" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC192" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
199
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC199" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_machine</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="200" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
200
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC200" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">umi</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="193" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
193
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<td class="new_line diff-line-num" data-linenumber="201" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
201
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC201" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="194" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
194
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<td class="new_line diff-line-num" data-linenumber="202" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
202
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC202" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">phred</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
195
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<td class="new_line diff-line-num" data-linenumber="203" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
203
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC203" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="196" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="204" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
204
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC204" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">inline_bc</span><span class="p">[</span><span class="n" style="color: #333;">id_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="196" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="205" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
205
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC205" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">index_bc</span><span class="p">[</span><span class="n" style="color: #333;">id_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="196" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="206" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
206
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC206" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_machine</span><span class="p">[</span><span class="n" style="color: #333;">id_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="196" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="207" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
207
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC207" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">umi</span><span class="p">[</span><span class="n" style="color: #333;">id_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="196" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="208" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
208
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC208" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="196" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="209" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
209
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC209" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">detect_machine_type</span><span class="p">();</span></span>
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<td class="old_line diff-line-num new" data-linenumber="196" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
210
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC210" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
196
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<td class="new_line diff-line-num" data-linenumber="211" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
211
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC211" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">set_len</span><span class="p">(</span><span class="n" style="color: #333;">buf_len</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="197" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
197
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<td class="new_line diff-line-num" data-linenumber="212" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
212
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC212" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="198" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
198
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<td class="new_line diff-line-num" data-linenumber="213" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
213
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC213" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">se_bc</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="241" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="256" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -241,7 +256,8 @@ public:</td>
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<td class="old_line diff-line-num" data-linenumber="241" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
241
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<td class="new_line diff-line-num" data-linenumber="256" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
256
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC256" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">RawRead</span><span class="p">()</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="242" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
242
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<td class="new_line diff-line-num" data-linenumber="257" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
257
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC257" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="p">[]</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">inline_bc</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="243" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
243
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<td class="new_line diff-line-num" data-linenumber="258" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
258
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC258" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="p">[]</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">index_bc</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="244" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
244
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<td class="new_line diff-line-num old" data-linenumber="259" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC244" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="p">[]</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="245" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="259" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
259
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC259" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="p">[]</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_machine</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="245" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="260" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
260
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC260" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="p">[]</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">umi</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="245" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
245
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<td class="new_line diff-line-num" data-linenumber="261" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
261
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC261" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="p">[]</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="246" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
246
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<td class="new_line diff-line-num" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
262
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC262" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="p">[]</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">phred</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="247" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
247
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<td class="new_line diff-line-num" data-linenumber="263" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
263
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC263" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="p">[]</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">int_scores</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="259" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="275" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -259,6 +275,63 @@ public:</td>
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<td class="old_line diff-line-num" data-linenumber="259" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
259
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<td class="new_line diff-line-num" data-linenumber="275" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
275
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC275" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="260" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
260
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<td class="new_line diff-line-num" data-linenumber="276" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
276
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC276" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="261" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
261
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<td class="new_line diff-line-num" data-linenumber="277" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
277
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC277" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="278" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
278
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC278" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">detect_machine_type</span><span class="p">()</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="279" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
279
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC279" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="280" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
280
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC280" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_machine</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="281" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
281
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC281" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="282" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
282
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'A'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="283" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
283
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC283" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'A'</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="284" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
284
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC284" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextseq</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="285" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
285
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC285" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="286" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
286
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC286" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">novaseq</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="287" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
287
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC287" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="288" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
288
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC288" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="289" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
289
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC289" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'V'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="290" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
290
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC290" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextseq</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="291" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
291
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC291" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="292" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
292
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC292" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'C'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="293" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
293
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC293" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'D'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="294" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
294
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC294" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'J'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="295" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
295
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC295" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'K'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="296" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
296
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC296" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hiseq</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="297" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
297
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC297" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="298" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
298
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC298" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'H'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="299" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
299
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC299" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'W'</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="300" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
300
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC300" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">novaseq</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="301" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
301
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC301" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="s" style="color: #d14;">"HWI-M"</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="302" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
302
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC302" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">miseq</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="303" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
303
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC303" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="s" style="color: #d14;">"HWUSI"</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="304" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
304
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC304" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genome_analyzer_iix</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="305" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
305
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC305" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="s" style="color: #d14;">"HWI-C"</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="306" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
306
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC306" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hiseq</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="307" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
307
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC307" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="s" style="color: #d14;">"HWI-D"</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
308
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC308" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hiseq</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
309
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC309" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="310" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
310
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC310" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'M'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="311" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
311
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC311" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
312
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC312" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">miniseq</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="313" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
313
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC313" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="314" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
314
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC314" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">miseq</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="315" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
315
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC315" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="316" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
316
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC316" class="line" lang="cpp"> <span class="nl">default:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="317" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
317
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC317" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unknown</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="318" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
318
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC318" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="319" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
319
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC319" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="320" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
320
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC320" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="321" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
321
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC321" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="322" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
322
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC322" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="323" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
323
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC323" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">machine</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="324" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
324
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC324" class="line" lang="cpp"> <span class="n" style="color: #333;">strncpy</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_machine</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">id_len</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="325" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
325
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC325" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">detect_machine_type</span><span class="p">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="326" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
326
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC326" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="327" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
327
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC327" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">machine</span><span class="p">()</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="328" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
328
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC328" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_machine</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="329" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
329
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC329" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="330" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
330
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC330" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">check_poly_g</span><span class="p">()</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="331" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
331
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC331" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">machinet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">novaseq</span> <span class="o" style="font-weight: 600;">||</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">machinet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">nextseq</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="332" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
332
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC332" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="333" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
333
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC333" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="334" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
334
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC334" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
262
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<td class="new_line diff-line-num" data-linenumber="335" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
335
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC335" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">set_len</span><span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">buf_len</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="263" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
263
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<td class="new_line diff-line-num" data-linenumber="336" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
336
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC336" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">buf_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="264" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
264
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<td class="new_line diff-line-num" data-linenumber="337" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
337
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC337" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="333" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="406" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -333,6 +406,7 @@ int filter_adapter_seq(RawRead *, char *, int, AdapterHash &, int, int, int);</td>
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<td class="old_line diff-line-num" data-linenumber="333" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
333
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<td class="new_line diff-line-num" data-linenumber="406" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
406
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC406" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">init_adapter_seq</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;">AdapterHash</span> <span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="334" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
334
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<td class="new_line diff-line-num" data-linenumber="407" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
407
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC407" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="335" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
335
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<td class="new_line diff-line-num" data-linenumber="408" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
408
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC408" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">check_quality_scores</span><span class="p">(</span><span class="n" style="color: #333;">RawRead</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="336" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="409" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
409
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC409" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">check_poly_g_run</span><span class="p">(</span><span class="n" style="color: #333;">RawRead</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="336" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
336
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<td class="new_line diff-line-num" data-linenumber="410" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
410
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC410" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="337" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
337
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<td class="new_line diff-line-num" data-linenumber="411" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
411
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC411" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="338" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
338
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<td class="new_line diff-line-num" data-linenumber="412" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
412
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC412" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Templated function to process barcodes.</span></span>
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<li id="2f7325ed14b982f91f8a457bac8ca0389322f5a3">
<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#2f7325ed14b982f91f8a457bac8ca0389322f5a3"><strong style="font-weight: 600;">src/clone_filter.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -31,11 +31,13 @@</td>
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<td class="old_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
31
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<td class="new_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
31
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC31" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
32
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<td class="new_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
32
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC32" class="line" lang="cpp"><span class="n" style="color: #333;">FileT</span> <span class="n" style="color: #333;">in_file_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FileT</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unknown</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
33
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<td class="new_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
33
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC33" class="line" lang="cpp"><span class="n" style="color: #333;">FileT</span> <span class="n" style="color: #333;">out_file_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FileT</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unknown</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
34
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC34" class="line" lang="cpp"><span class="n" style="color: #333;">InputT</span> <span class="n" style="color: #333;">in_path_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">InputT</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">files</span><span class="p">;</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC35" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">in_file</span><span class="p">;</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC36" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">in_file_p1</span><span class="p">;</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC37" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">in_file_p2</span><span class="p">;</span></span>
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<td class="new_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
38
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC38" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">in_path_1</span><span class="p">;</span></span>
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38
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<td class="new_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
39
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC39" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">in_path_2</span><span class="p">;</span></span>
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40
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC40" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">out_basename</span><span class="p">;</span></span>
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39
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<td class="new_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
41
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC41" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">out_path</span><span class="p">;</span></span>
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42
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC42" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">discards</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC43" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">interleaved</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#03f856e8b44c3c125706ba7e7a8c138a914e7063"><strong style="font-weight: 600;">src/constants.h</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="177" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="177" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -177,6 +177,14 @@ enum class FileT {unknown,</td>
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177
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177
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC177" class="line" lang="cpp"> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="n" style="color: #333;">gzvcf</span></span>
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<td class="old_line diff-line-num" data-linenumber="178" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
178
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178
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC178" class="line" lang="cpp"><span class="p">};</span></span>
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179
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179
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC179" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
180
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC180" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
181
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC181" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Supported file types</span></span>
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<td class="new_line diff-line-num new" data-linenumber="182" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
182
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC182" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="new_line diff-line-num new" data-linenumber="183" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
183
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC183" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">InputT</span> <span class="p">{</span><span class="n" style="color: #333;">unknown</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="184" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
184
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC184" class="line" lang="cpp"> <span class="n" style="color: #333;">directory</span><span class="p">,</span></span>
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185
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<td class="new_line diff-line-num new" data-linenumber="186" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
186
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC186" class="line" lang="cpp"><span class="p">};</span></span>
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<td class="new_line diff-line-num new" data-linenumber="187" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
187
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC187" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="180" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
180
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<td class="new_line diff-line-num" data-linenumber="188" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
188
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC188" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">stacks_handle_exceptions</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
181
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<td class="new_line diff-line-num" data-linenumber="189" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
189
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC189" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="182" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
182
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<td class="new_line diff-line-num" data-linenumber="190" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
190
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC190" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="nf" style="color: #900; font-weight: 600;">remove_suffix</span><span class="p">(</span><span class="n" style="color: #333;">FileT</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#9b5186210cef02bd7aa4ac577214b1ba3b2fa6a8"><strong style="font-weight: 600;">src/cstacks.cc</strong></a>
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1
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1
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-</span></span>
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2
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2
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3
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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2010-202<span class="idiff left right deletion" style="background-color: #fac5cd;">3</span>, Julian Catchen <jcatchen@illinois.edu></span></span>
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<td class="old_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2010-202<span class="idiff left right addition" style="background-color: #c7f0d2;">4</span>, Julian Catchen <jcatchen@illinois.edu></span></span>
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4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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5
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// This file is part of Stacks.</span></span>
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6
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6
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1869" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1869" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1869,24 +1869,24 @@ int parse_command_line(int argc, char* argv[]) {</td>
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<td class="old_line diff-line-num" data-linenumber="1869" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1869
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<td class="new_line diff-line-num" data-linenumber="1869" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1869
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1869" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">option</span> <span class="n" style="color: #333;">long_options</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1870" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1870
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<td class="new_line diff-line-num" data-linenumber="1870" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1870
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1870" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"help"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'h'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="1871" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1871
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<td class="new_line diff-line-num" data-linenumber="1871" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1871
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1871" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"version"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">1000</span><span class="p">},</span></span>
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1872
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<td class="new_line diff-line-num old" data-linenumber="1872" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1872" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"uniq-haplotypes"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'u'</span><span class="p">},</span><span class="idiff left deletion" style="background-color: #fac5cd;"> </span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"uniq_haplotypes"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">no_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'u'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">},</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="1873" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1873
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<td class="new_line diff-line-num old" data-linenumber="1872" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1873" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"report-mmatches"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'R'</span><span class="p">},</span><span class="idiff left deletion" style="background-color: #fac5cd;"> </span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"report_mmatches"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">no_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'R'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">},</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="1874" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1874
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<td class="new_line diff-line-num old" data-linenumber="1872" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1874" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"disable-gapped"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'G'</span><span class="p">},</span><span class="idiff left deletion" style="background-color: #fac5cd;"> </span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"disable_gapped"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">no_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'G'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">},</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="1875" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1875
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<td class="new_line diff-line-num old" data-linenumber="1872" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1875" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"max-gaps"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'X'</span><span class="p">},</span><span class="idiff left deletion" style="background-color: #fac5cd;"> </span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"max_gaps"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">required_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'X'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">},</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="1876" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1876
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<td class="new_line diff-line-num old" data-linenumber="1872" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1876" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"min-aln-len"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'x'</span><span class="p">},</span> <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"min_aln_len"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">required_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'x'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">},</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="1877" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1877
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<td class="new_line diff-line-num old" data-linenumber="1872" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1877" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"ctag-dist"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'n'</span><span class="p">},</span> <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"ctag_dist"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">required_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'n'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">},</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="1878" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1878
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<td class="new_line diff-line-num old" data-linenumber="1872" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1878" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"k-len"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'k'</span><span class="p">},</span> <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"k_len"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">required_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'k'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">},</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="1879" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1879
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<td class="new_line diff-line-num old" data-linenumber="1872" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1879" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"in-path"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'P'</span><span class="p">},</span> <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"in_path"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">required_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'P'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">},</span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="1880" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1872" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1872
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1872" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"uniq-haplotypes"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'u'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1880" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1873" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1873
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1873" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"report-mmatches"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'R'</span><span class="p">},</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1874" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1874
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1874" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"disable-gapped"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'G'</span><span class="p">},</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1875" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1875
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1875" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"max-gaps"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'X'</span><span class="p">},</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1876" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1876
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1876" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"min-aln-len"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'x'</span><span class="p">},</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="1877" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1877
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1877" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"ctag-dist"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'n'</span><span class="p">},</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="1878" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1878
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1878" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"k-len"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'k'</span><span class="p">},</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="1879" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1879
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1879" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"in-path"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'P'</span><span class="p">},</span> </span>
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1880
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<td class="new_line diff-line-num" data-linenumber="1880" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1880
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1880" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"popmap"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'M'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="1881" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1881
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<td class="new_line diff-line-num" data-linenumber="1881" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1881
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1881" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"catalog"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'c'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="1882" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1882
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<td class="new_line diff-line-num" data-linenumber="1882" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1882
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1882" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sample"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'s'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1883" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1883
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<td class="new_line diff-line-num old" data-linenumber="1883" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1883" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"out-path"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">},</span> <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"out_path"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">required_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'o'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">},</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="1884" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1884
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<td class="new_line diff-line-num old" data-linenumber="1883" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1884" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"threads"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'<span class="idiff left right deletion" style="background-color: #fac5cd;">p</span>'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1885" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1883" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1883
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1883" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"out-path"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">},</span> </span>
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<td class="old_line diff-line-num new" data-linenumber="1885" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1884" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1884
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1884" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"threads"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'<span class="idiff left addition" style="background-color: #c7f0d2;">t</span>'</span><span class="p">},</span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span></span>
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1885
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<td class="new_line diff-line-num" data-linenumber="1885" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1885
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1885" class="line" lang="cpp"> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1886" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1886
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<td class="new_line diff-line-num" data-linenumber="1886" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1886
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1886" class="line" lang="cpp"> <span class="p">};</span></span>
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1887
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1887
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1887" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="1888" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1888
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<td class="new_line diff-line-num" data-linenumber="1888" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1888
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1888" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">option_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1889" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1889
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<td class="new_line diff-line-num old" data-linenumber="1889" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1889" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt_long</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"hvuRGX:x:o:s:c:p:n:k:P:M:"</span><span class="p">,</span> <span class="n" style="color: #333;">long_options</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">option_index</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1890" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1889" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1889
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1889" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt_long</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"hvuRGX:x:o:s:c:p:<span class="idiff left right addition" style="background-color: #c7f0d2;">t:</span>n:k:P:M:"</span><span class="p">,</span> <span class="n" style="color: #333;">long_options</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">option_index</span><span class="p">);</span></span>
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1890
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<td class="new_line diff-line-num" data-linenumber="1890" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1890
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1890" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="1891" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1891
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<td class="new_line diff-line-num" data-linenumber="1891" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1891
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1891" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Detect the end of the options.</span></span>
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<td class="old_line diff-line-num" data-linenumber="1892" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1892
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<td class="new_line diff-line-num" data-linenumber="1892" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1892
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1892" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1931" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1931" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1931,6 +1931,7 @@ int parse_command_line(int argc, char* argv[]) {</td>
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1931
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<td class="new_line diff-line-num" data-linenumber="1931" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1931
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1931" class="line" lang="cpp"> <span class="n" style="color: #333;">version</span><span class="p">();</span></span>
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<td class="old_line diff-line-num" data-linenumber="1932" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1932
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<td class="new_line diff-line-num" data-linenumber="1932" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1932
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1932" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1933" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1933
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<td class="new_line diff-line-num" data-linenumber="1933" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1933
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1933" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'p'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1934" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1934" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1934
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1934" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'t'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="1934" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1934
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<td class="new_line diff-line-num" data-linenumber="1935" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1935
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1935" class="line" lang="cpp"> <span class="n" style="color: #333;">num_threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">is_integer</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1935" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1935
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<td class="new_line diff-line-num" data-linenumber="1936" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1936
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1936" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1936" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1936
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<td class="new_line diff-line-num" data-linenumber="1937" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1937
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1937" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'P'</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2005" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2006" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2005,13 +2006,13 @@ void version() {</td>
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2005
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<td class="new_line diff-line-num" data-linenumber="2006" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2006
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2006" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="2006" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2006
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<td class="new_line diff-line-num" data-linenumber="2007" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2007
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2007" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">help</span><span class="p">()</span> <span class="p">{</span></span>
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2007
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<td class="new_line diff-line-num" data-linenumber="2008" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2008
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2008" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"cstacks "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2008" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2008
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<td class="new_line diff-line-num old" data-linenumber="2009" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2008" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"cstacks -P in_dir -M popmap [-n num_mismatches] [-<span class="idiff left right deletion" style="background-color: #fac5cd;">p</span> num_threads]"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2009" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2009
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<td class="new_line diff-line-num old" data-linenumber="2009" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2009" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"cstacks -s sample1_path [-s sample2_path ...] -o path [-n num_mismatches] [-<span class="idiff left right deletion" style="background-color: #fac5cd;">p</span> num_threads]"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2010" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2009" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2009
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2009" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"cstacks -P in_dir -M popmap [-n num_mismatches] [-<span class="idiff left right addition" style="background-color: #c7f0d2;">t</span> num_threads]"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2010" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2010" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2010
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2010" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"cstacks -s sample1_path [-s sample2_path ...] -o path [-n num_mismatches] [-<span class="idiff left right addition" style="background-color: #c7f0d2;">t</span> num_threads]"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2010" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2010
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<td class="new_line diff-line-num" data-linenumber="2011" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2011
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2011" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2011" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2011
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<td class="new_line diff-line-num" data-linenumber="2012" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2012
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2012" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -P,--in-path: path to the directory containing Stacks files.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2012" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2012
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<td class="new_line diff-line-num" data-linenumber="2013" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2013
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2013" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -M,--popmap: path to a population map file.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2013" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2013
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<td class="new_line diff-line-num" data-linenumber="2014" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2014
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2014" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -n: number of mismatches allowed between sample loci when build the catalog (default 1; suggested: set to ustacks -M)."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2014" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2014
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<td class="new_line diff-line-num old" data-linenumber="2015" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2014" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -<span class="idiff left right deletion" style="background-color: #fac5cd;">p</span>,--threads: enable parallel execution with num_threads threads.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2015" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2015" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2015
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2015" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -<span class="idiff left right addition" style="background-color: #c7f0d2;">t</span>,--threads: enable parallel execution with num_threads threads.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2015" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2015
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<td class="new_line diff-line-num" data-linenumber="2016" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2016
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2016" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -s: sample prefix from which to load loci into the catalog."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2016" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2016
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<td class="new_line diff-line-num" data-linenumber="2017" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2017
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2017" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -o,--outpath: output path to write results."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2017" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2017
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<td class="new_line diff-line-num" data-linenumber="2018" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2018
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2018" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -c,--catalog <path>: add to an existing catalog.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#930a2c5c4679e2fa7738631bb355df01e13be529"><strong style="font-weight: 600;">src/file_io.cc</strong></a>
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1
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<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-</span></span>
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2
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2
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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3
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2012-202<span class="idiff left right deletion" style="background-color: #fac5cd;">1</span>, Julian Catchen <jcatchen@illinois.edu></span></span>
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3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2012-202<span class="idiff left right addition" style="background-color: #c7f0d2;">4</span>, Julian Catchen <jcatchen@illinois.edu></span></span>
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4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// This file is part of Stacks.</span></span>
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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6
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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -21,10 +21,6 @@</td>
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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
21
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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
21
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC21" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
22
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<td class="new_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
22
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC22" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// file_io.cc -- common routines for opening groups of files and processing barcode lists.</span></span>
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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
23
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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
23
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC23" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
24
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<td class="new_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC24" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Julian Catchen</span></span>
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<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
25
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<td class="new_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC25" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// jcatchen@uoregon.edu</span></span>
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<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
26
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<td class="new_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC26" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// University of Oregon</span></span>
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<td class="old_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
27
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<td class="new_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC27" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC24" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include</span> <span class="cpf">"file_io.h"</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC26" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="56" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="52" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -56,8 +52,10 @@ open_files(vector<pair<string, string> > &files,</td>
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<td class="old_line diff-line-num" data-linenumber="56" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC52" class="line" lang="cpp"> <span class="n" style="color: #333;">BarcodePair</span> <span class="n" style="color: #333;">bc</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="57" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
53
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC53" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="58" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
54
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC54" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If the size of the barcodes vector is 0, then no barcodes</span></span>
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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC59" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// were submitted. In this case, we want to open output files</span></span>
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<td class="old_line diff-line-num old" data-linenumber="60" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
60
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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC60" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// of the same name as input files, but in out_path.</span></span>
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<td class="old_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
55
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC55" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// were submitted. In this case, we want to either:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
56
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC56" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 1. open output files using out_basename, if supplied by the user, or</span></span>
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<td class="old_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
57
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC57" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 2. open output files of the same name as input files,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
58
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC58" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// in both cases opening the files in out_path.</span></span>
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<td class="old_line diff-line-num" data-linenumber="61" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
61
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<td class="new_line diff-line-num" data-linenumber="59" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
59
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC59" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="62" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
62
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<td class="new_line diff-line-num" data-linenumber="60" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
60
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC60" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">barcodes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">merge</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="p">{</span></span>
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63
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<td class="new_line diff-line-num" data-linenumber="61" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
61
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC61" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="67" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -69,22 +67,26 @@ open_files(vector<pair<string, string> > &files,</td>
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<td class="old_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
69
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<td class="new_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
67
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC67" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">paired</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
70
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<td class="new_line diff-line-num" data-linenumber="68" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
68
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">pe</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="71" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
71
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<td class="new_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
69
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC69" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="72" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
72
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<td class="new_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
73
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<td class="new_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC73" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
74
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<td class="new_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC74" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num old" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
75
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<td class="new_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC75" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check that the file has a proper suffix for the output type.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
76
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<td class="new_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC76" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
77
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<td class="new_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC77" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="78" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
78
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<td class="new_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC78" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".bam"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="79" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
79
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<td class="new_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC79" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="80" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
80
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<td class="new_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC80" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="81" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
81
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<td class="new_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="82" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
82
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<td class="new_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC82" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="83" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
83
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<td class="new_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC83" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
70
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC70" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_basename</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
71
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">out_basename</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
72
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC72" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num" data-linenumber="84" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
84
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<td class="new_line diff-line-num" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
73
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC73" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="85" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
85
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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
74
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
75
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC75" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
76
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC76" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check that the file has a proper suffix for the output type.</span></span>
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<td class="old_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
77
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC77" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
78
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC78" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
79
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC79" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".bam"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
80
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
81
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC81" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="82" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
82
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC82" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
83
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC83" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
84
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC84" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
85
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC85" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
86
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
87
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC87" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
86
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<td class="new_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
88
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC88" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="87" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
87
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<td class="new_line diff-line-num old" data-linenumber="89" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC87" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
89
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC89" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
88
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<td class="new_line diff-line-num" data-linenumber="90" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
90
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC90" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stat</span><span class="p">((</span><span class="n" style="color: #333;">in_path_1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sb_1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="89" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
89
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<td class="new_line diff-line-num" data-linenumber="91" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
91
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Unable to stat input file '"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">in_path_1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="90" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
90
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<td class="new_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
92
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC92" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="107" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="109" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -107,19 +109,25 @@ open_files(vector<pair<string, string> > &files,</td>
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<td class="old_line diff-line-num" data-linenumber="107" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
107
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<td class="new_line diff-line-num" data-linenumber="109" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
109
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC109" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
108
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<td class="new_line diff-line-num" data-linenumber="110" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
110
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">paired</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="109" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
109
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<td class="new_line diff-line-num" data-linenumber="111" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
111
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC111" class="line" lang="cpp"> <span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">interleaved</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="110" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
110
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<td class="new_line diff-line-num old" data-linenumber="112" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">file</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="111" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
111
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<td class="new_line diff-line-num" data-linenumber="112" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
112
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC112" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="112" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
112
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<td class="new_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
113
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<td class="new_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC113" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".bam"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="114" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
114
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<td class="new_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC114" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="115" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
115
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<td class="new_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC115" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="116" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
116
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<td class="new_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC116" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="117" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
117
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<td class="new_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC117" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
118
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<td class="new_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC118" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
113
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC113" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_basename</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
114
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC114" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">out_basename</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
115
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC115" class="line" lang="cpp"> </span>
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119
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<td class="new_line diff-line-num" data-linenumber="116" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
116
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC116" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="120" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
120
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<td class="new_line diff-line-num old" data-linenumber="117" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC120" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="117" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
117
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC117" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">file</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
118
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC118" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
119
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
120
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".bam"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
121
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
122
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC122" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
123
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="124" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
124
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
125
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
126
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC126" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
127
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
128
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC128" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="121" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
121
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<td class="new_line diff-line-num" data-linenumber="129" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
129
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC129" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
122
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<td class="new_line diff-line-num old" data-linenumber="130" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC122" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
130
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC130" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num" data-linenumber="123" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
123
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<td class="new_line diff-line-num" data-linenumber="131" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
131
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC131" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stat</span><span class="p">((</span><span class="n" style="color: #333;">in_path_2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">file</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sb_1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
124
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<td class="new_line diff-line-num" data-linenumber="132" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
132
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC132" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Unable to stat input file '"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">in_path_2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
125
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<td class="new_line diff-line-num" data-linenumber="133" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
133
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC133" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="140" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="148" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -140,17 +148,22 @@ open_files(vector<pair<string, string> > &files,</td>
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<td class="old_line diff-line-num" data-linenumber="140" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
140
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<td class="new_line diff-line-num" data-linenumber="148" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
148
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="141" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
141
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<td class="new_line diff-line-num" data-linenumber="149" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
149
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC149" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="142" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
142
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<td class="new_line diff-line-num" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
150
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC150" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="143" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
143
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<td class="new_line diff-line-num old" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC143" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
144
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<td class="new_line diff-line-num old" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC144" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="145" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
145
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<td class="new_line diff-line-num old" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC145" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="146" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
146
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<td class="new_line diff-line-num old" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
151
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_basename</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
152
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">out_basename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
153
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC153" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
154
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC154" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
155
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC155" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">;</span></span>
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147
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<td class="new_line diff-line-num" data-linenumber="156" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
156
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="148" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
148
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<td class="new_line diff-line-num old" data-linenumber="157" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="149" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
149
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<td class="new_line diff-line-num old" data-linenumber="157" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC149" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".bam"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
150
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<td class="new_line diff-line-num old" data-linenumber="157" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC150" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
157
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC157" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
158
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC158" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
159
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC159" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
160
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC160" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="161" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
161
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC161" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".bam"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
162
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="163" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
163
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC163" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
164
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC164" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
151
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<td class="new_line diff-line-num" data-linenumber="165" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
165
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC165" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="152" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
152
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<td class="new_line diff-line-num old" data-linenumber="166" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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153
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<td class="new_line diff-line-num old" data-linenumber="166" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC153" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
166
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC166" class="line" lang="cpp"> </span>
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154
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<td class="new_line diff-line-num" data-linenumber="167" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
167
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC167" class="line" lang="cpp"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">ofstream</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">ifstream</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="155" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
155
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<td class="new_line diff-line-num" data-linenumber="168" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
168
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC168" class="line" lang="cpp"> <span class="n" style="color: #333;">rem_1_fhs</span><span class="p">[</span><span class="n" style="color: #333;">bc</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fh</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="156" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
156
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<td class="new_line diff-line-num" data-linenumber="169" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
169
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC169" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="159" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="172" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -159,17 +172,22 @@ open_files(vector<pair<string, string> > &files,</td>
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<td class="old_line diff-line-num" data-linenumber="159" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
159
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<td class="new_line diff-line-num" data-linenumber="172" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
172
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC172" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="160" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
160
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<td class="new_line diff-line-num" data-linenumber="173" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
173
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC173" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="161" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
161
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<td class="new_line diff-line-num" data-linenumber="174" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
174
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC174" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="162" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
162
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<td class="new_line diff-line-num old" data-linenumber="175" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
163
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<td class="new_line diff-line-num old" data-linenumber="175" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC163" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="164" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
164
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<td class="new_line diff-line-num old" data-linenumber="175" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC164" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="165" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
165
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<td class="new_line diff-line-num old" data-linenumber="175" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="175" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
175
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC175" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_basename</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
176
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC176" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">out_basename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="177" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
177
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC177" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
178
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC178" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="179" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
179
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC179" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="166" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
166
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<td class="new_line diff-line-num" data-linenumber="180" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
180
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC180" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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167
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<td class="new_line diff-line-num old" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC167" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="168" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
168
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<td class="new_line diff-line-num old" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC168" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".bam"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="169" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
169
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<td class="new_line diff-line-num old" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC169" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
181
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC181" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="182" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
182
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC182" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="183" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
183
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC183" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="184" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
184
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC184" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="185" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
185
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC185" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".bam"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="186" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
186
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC186" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="187" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
187
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC187" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
188
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC188" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
170
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<td class="new_line diff-line-num" data-linenumber="189" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
189
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC189" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="171" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
171
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<td class="new_line diff-line-num old" data-linenumber="190" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC171" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="172" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
172
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<td class="new_line diff-line-num old" data-linenumber="190" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC172" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="173" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="190" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
190
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC190" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num" data-linenumber="173" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
173
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<td class="new_line diff-line-num" data-linenumber="191" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
191
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC191" class="line" lang="cpp"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">ofstream</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">ifstream</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="174" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
174
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<td class="new_line diff-line-num" data-linenumber="192" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
192
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC192" class="line" lang="cpp"> <span class="n" style="color: #333;">rem_2_fhs</span><span class="p">[</span><span class="n" style="color: #333;">bc</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fh</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="175" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
175
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<td class="new_line diff-line-num" data-linenumber="193" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
193
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC193" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="184" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="202" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -184,7 +202,12 @@ open_files(vector<pair<string, string> > &files,</td>
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<td class="old_line diff-line-num" data-linenumber="184" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
184
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<td class="new_line diff-line-num" data-linenumber="202" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
202
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC202" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="185" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
185
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<td class="new_line diff-line-num" data-linenumber="203" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
203
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC203" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">barcodes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">merge</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="186" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
186
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<td class="new_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
204
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC204" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="187" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
187
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<td class="new_line diff-line-num old" data-linenumber="205" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC187" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_unbarcoded"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="205" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
205
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC205" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_basename</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="206" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
206
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC206" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">out_basename</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="207" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
207
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC207" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="208" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
208
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC208" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="209" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
209
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC209" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_unbarcoded"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
210
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC210" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="188" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
188
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<td class="new_line diff-line-num" data-linenumber="211" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
211
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">ofstream</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">ifstream</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="189" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
189
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<td class="new_line diff-line-num" data-linenumber="212" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
212
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC212" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="190" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
190
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<td class="new_line diff-line-num" data-linenumber="213" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
213
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC213" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fail</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="200" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="223" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -200,7 +223,12 @@ open_files(vector<pair<string, string> > &files,</td>
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<td class="old_line diff-line-num" data-linenumber="200" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
200
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<td class="new_line diff-line-num" data-linenumber="223" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
223
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC223" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="201" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
201
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224
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC224" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="202" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
202
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<td class="new_line diff-line-num" data-linenumber="225" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
225
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC225" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">paired</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="203" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
203
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<td class="new_line diff-line-num old" data-linenumber="226" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC203" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_unbarcoded"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="204" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="226" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
226
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC226" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_basename</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="204" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="227" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
227
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC227" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">out_basename</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="204" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="228" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
228
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC228" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num new" data-linenumber="204" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="229" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
229
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC229" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="204" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="230" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
230
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC230" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_unbarcoded"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="231" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
231
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC231" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
204
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<td class="new_line diff-line-num" data-linenumber="232" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
232
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC232" class="line" lang="cpp"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">ofstream</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">ifstream</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="205" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
205
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<td class="new_line diff-line-num" data-linenumber="233" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
233
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC233" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="206" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
206
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<td class="new_line diff-line-num" data-linenumber="234" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
234
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC234" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fail</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="214" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="242" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -214,7 +242,12 @@ open_files(vector<pair<string, string> > &files,</td>
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<td class="old_line diff-line-num" data-linenumber="214" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
214
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<td class="new_line diff-line-num" data-linenumber="242" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
242
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC242" class="line" lang="cpp"> <span class="n" style="color: #333;">pair_2_fhs</span><span class="p">[</span><span class="n" style="color: #333;">bc</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fh</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="215" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
215
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<td class="new_line diff-line-num" data-linenumber="243" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
243
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC243" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="216" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
216
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<td class="new_line diff-line-num" data-linenumber="244" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
244
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC244" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="217" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
217
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<td class="new_line diff-line-num old" data-linenumber="245" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC217" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_unbarcoded.rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="245" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
245
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC245" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_basename</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="246" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
246
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC246" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">out_basename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="247" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
247
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC247" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
248
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC248" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="249" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
249
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC249" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_unbarcoded.rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="250" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
250
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC250" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="218" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
218
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<td class="new_line diff-line-num" data-linenumber="251" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
251
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC251" class="line" lang="cpp"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">ofstream</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">ifstream</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="219" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
219
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<td class="new_line diff-line-num" data-linenumber="252" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
252
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC252" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="220" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
220
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<td class="new_line diff-line-num" data-linenumber="253" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
253
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC253" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fail</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="228" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="261" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -228,7 +261,12 @@ open_files(vector<pair<string, string> > &files,</td>
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<td class="old_line diff-line-num" data-linenumber="228" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
228
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<td class="new_line diff-line-num" data-linenumber="261" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
261
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC261" class="line" lang="cpp"> <span class="n" style="color: #333;">rem_1_fhs</span><span class="p">[</span><span class="n" style="color: #333;">bc</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fh</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="229" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
229
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<td class="new_line diff-line-num" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
262
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC262" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="230" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
230
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<td class="new_line diff-line-num" data-linenumber="263" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
263
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC263" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="231" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
231
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<td class="new_line diff-line-num old" data-linenumber="264" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC231" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_unbarcoded.rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="232" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="264" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
264
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC264" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_basename</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="232" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="265" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
265
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC265" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">out_basename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="266" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
266
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC266" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num new" data-linenumber="232" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="267" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
267
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC267" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="268" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
268
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC268" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_unbarcoded.rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="232" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="269" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
269
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC269" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="232" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
232
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<td class="new_line diff-line-num" data-linenumber="270" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
270
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC270" class="line" lang="cpp"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">ofstream</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">ifstream</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="233" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
233
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<td class="new_line diff-line-num" data-linenumber="271" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
271
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC271" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="234" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
234
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<td class="new_line diff-line-num" data-linenumber="272" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
272
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC272" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fail</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="334" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="372" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -334,8 +372,10 @@ open_files(vector<pair<string, string> > &files,</td>
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<td class="old_line diff-line-num" data-linenumber="334" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
334
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<td class="new_line diff-line-num" data-linenumber="372" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
372
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC372" class="line" lang="cpp"> <span class="n" style="color: #333;">BarcodePair</span> <span class="n" style="color: #333;">bc</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="335" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
335
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<td class="new_line diff-line-num" data-linenumber="373" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
373
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC373" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="336" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
336
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<td class="new_line diff-line-num" data-linenumber="374" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
374
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC374" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If the size of the barcodes vector is 0, then no barcodes</span></span>
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<td class="old_line diff-line-num old" data-linenumber="337" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
337
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<td class="new_line diff-line-num old" data-linenumber="375" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC337" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// were submitted. In this case, we want to open output files</span></span>
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<td class="old_line diff-line-num old" data-linenumber="338" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
338
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<td class="new_line diff-line-num old" data-linenumber="375" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC338" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// of the same name as input files, but in out_path.</span></span>
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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="375" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
375
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC375" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// were submitted. In this case, we want to either:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="376" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
376
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC376" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 1. open output files using out_basename, if supplied by the user, or</span></span>
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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="377" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
377
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC377" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 2. open output files of the same name as input files,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="378" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
378
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC378" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// in both cases opening the files in out_path.</span></span>
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<td class="old_line diff-line-num" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
339
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<td class="new_line diff-line-num" data-linenumber="379" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
379
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC379" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="340" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
340
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<td class="new_line diff-line-num" data-linenumber="380" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
380
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC380" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">barcodes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">merge</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="p">{</span></span>
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341
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<td class="new_line diff-line-num" data-linenumber="381" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
381
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC381" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="347" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="387" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -347,20 +387,24 @@ open_files(vector<pair<string, string> > &files,</td>
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347
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<td class="new_line diff-line-num" data-linenumber="387" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
387
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC387" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">paired</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="348" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
348
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<td class="new_line diff-line-num" data-linenumber="388" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
388
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC388" class="line" lang="cpp"> <span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">pe</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="349" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
349
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<td class="new_line diff-line-num" data-linenumber="389" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
389
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC389" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="350" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
350
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<td class="new_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC350" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="351" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
351
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<td class="new_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC351" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="352" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
352
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<td class="new_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC352" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num old" data-linenumber="353" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
353
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<td class="new_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC353" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check that the file has a proper suffix for the output type.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="354" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
354
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<td class="new_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC354" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num old" data-linenumber="355" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
355
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<td class="new_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC355" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="356" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
356
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<td class="new_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC356" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".bam"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="357" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
357
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<td class="new_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC357" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="358" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
358
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<td class="new_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC358" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
359
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<td class="new_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC359" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="360" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
360
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<td class="new_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC360" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="361" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
361
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<td class="new_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC361" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="362" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="390" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
390
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC390" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_basename</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="362" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="391" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
391
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC391" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">out_basename</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="362" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="392" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
392
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC392" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num" data-linenumber="362" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
362
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<td class="new_line diff-line-num" data-linenumber="393" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
393
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC393" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="363" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
363
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<td class="new_line diff-line-num old" data-linenumber="394" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC363" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="364" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="394" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
394
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC394" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="364" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="395" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
395
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC395" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num new" data-linenumber="364" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="396" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
396
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC396" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check that the file has a proper suffix for the output type.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="397" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
397
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC397" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num new" data-linenumber="364" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="398" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
398
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC398" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="364" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="399" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
399
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC399" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".bam"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="364" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
400
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC400" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="364" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="401" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
401
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC401" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="402" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
402
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC402" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="403" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
403
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC403" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="364" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="404" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
404
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC404" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="364" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="405" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
405
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC405" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="406" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
406
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC406" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="407" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
407
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC407" class="line" lang="cpp"> <span class="p">}</span></span>
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364
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<td class="new_line diff-line-num" data-linenumber="408" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
408
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC408" class="line" lang="cpp"> <span class="p">}</span></span>
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365
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409
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC409" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="366" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
366
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<td class="new_line diff-line-num" data-linenumber="410" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
410
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC410" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stat</span><span class="p">((</span><span class="n" style="color: #333;">in_path_1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sb_1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="385" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="429" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -385,18 +429,24 @@ open_files(vector<pair<string, string> > &files,</td>
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<td class="old_line diff-line-num" data-linenumber="385" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
385
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<td class="new_line diff-line-num" data-linenumber="429" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
429
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC429" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="386" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
386
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<td class="new_line diff-line-num" data-linenumber="430" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
430
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC430" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="387" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
387
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<td class="new_line diff-line-num" data-linenumber="431" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
431
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC431" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">paired</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="388" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
388
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<td class="new_line diff-line-num old" data-linenumber="432" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC388" class="line" lang="cpp"> <span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">interleaved</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="389" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
389
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<td class="new_line diff-line-num old" data-linenumber="432" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC389" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">file</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="390" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
390
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<td class="new_line diff-line-num" data-linenumber="432" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
432
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC432" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="391" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
391
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<td class="new_line diff-line-num old" data-linenumber="433" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC391" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="392" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
392
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<td class="new_line diff-line-num old" data-linenumber="433" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC392" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".bam"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="393" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
393
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<td class="new_line diff-line-num old" data-linenumber="433" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC393" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="394" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
394
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<td class="new_line diff-line-num old" data-linenumber="433" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC394" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="395" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
395
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<td class="new_line diff-line-num old" data-linenumber="433" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC395" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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396
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<td class="new_line diff-line-num old" data-linenumber="433" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC396" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="397" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
397
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<td class="new_line diff-line-num old" data-linenumber="433" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC397" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="398" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="433" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
433
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC433" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_basename</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="398" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="434" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
434
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC434" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">out_basename</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="398" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
435
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC435" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num" data-linenumber="398" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
398
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<td class="new_line diff-line-num" data-linenumber="436" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
436
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC436" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="399" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
399
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<td class="new_line diff-line-num old" data-linenumber="437" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC399" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="437" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
437
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC437" class="line" lang="cpp"> <span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">interleaved</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="438" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
438
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC438" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">file</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="439" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
439
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC439" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="440" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
440
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC440" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="441" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
441
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC441" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".bam"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="442" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
442
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC442" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="443" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
443
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC443" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="444" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
444
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC444" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="445" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
445
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC445" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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446
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC446" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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447
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC447" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="448" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
448
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC448" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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449
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC449" class="line" lang="cpp"> <span class="p">}</span></span>
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450
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC450" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="401" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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451
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452
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC452" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stat</span><span class="p">((</span><span class="n" style="color: #333;">in_path_2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">file</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sb_1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="420" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
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<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -420,17 +470,22 @@ open_files(vector<pair<string, string> > &files,</td>
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470
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC470" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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471
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC471" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="422" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
422
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<td class="new_line diff-line-num" data-linenumber="472" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
472
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC472" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="423" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
423
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<td class="new_line diff-line-num old" data-linenumber="473" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC423" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="424" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
424
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<td class="new_line diff-line-num old" data-linenumber="473" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC424" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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425
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<td class="new_line diff-line-num old" data-linenumber="473" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC425" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="426" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
426
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<td class="new_line diff-line-num old" data-linenumber="473" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC426" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="473" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
473
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC473" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_basename</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="474" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
474
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC474" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">out_basename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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475
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC475" class="line" lang="cpp"> </span>
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<td class="new_line diff-line-num new" data-linenumber="476" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
476
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC476" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="477" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
477
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC477" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="427" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
427
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<td class="new_line diff-line-num" data-linenumber="478" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
478
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC478" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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428
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<td class="new_line diff-line-num old" data-linenumber="479" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC428" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="429" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
429
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<td class="new_line diff-line-num old" data-linenumber="479" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC429" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".bam"</span><span class="p">)</span> <span class="p">{</span></span>
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430
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<td class="new_line diff-line-num old" data-linenumber="479" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC430" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="479" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
479
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC479" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="480" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
480
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC480" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="481" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
481
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC481" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="482" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
482
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC482" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="431" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="483" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
483
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC483" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".bam"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="484" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
484
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC484" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="485" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
485
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC485" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="486" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
486
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC486" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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431
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<td class="new_line diff-line-num" data-linenumber="487" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
487
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC487" class="line" lang="cpp"> <span class="p">}</span></span>
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432
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<td class="new_line diff-line-num old" data-linenumber="488" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC432" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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433
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC433" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" data-linenumber="488" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
488
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC488" class="line" lang="cpp"> </span>
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434
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<td class="new_line diff-line-num" data-linenumber="489" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
489
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC489" class="line" lang="cpp"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">gzFile</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="435" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
435
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<td class="new_line diff-line-num" data-linenumber="490" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
490
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC490" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzopen</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="s" style="color: #d14;">"wb"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="436" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
436
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<td class="new_line diff-line-num" data-linenumber="491" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
491
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC491" class="line" lang="cpp"> <span class="n" style="color: #333;">rem_1_fhs</span><span class="p">[</span><span class="n" style="color: #333;">bc</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fh</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="440" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="495" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -440,17 +495,22 @@ open_files(vector<pair<string, string> > &files,</td>
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440
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<td class="new_line diff-line-num" data-linenumber="495" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
495
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC495" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="new_line diff-line-num" data-linenumber="496" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
496
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC496" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="442" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
442
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<td class="new_line diff-line-num" data-linenumber="497" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
497
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC497" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="443" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
443
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<td class="new_line diff-line-num old" data-linenumber="498" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC443" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="444" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
444
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<td class="new_line diff-line-num old" data-linenumber="498" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC444" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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445
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<td class="new_line diff-line-num old" data-linenumber="498" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC445" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="446" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
446
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<td class="new_line diff-line-num old" data-linenumber="498" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC446" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="498" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
498
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC498" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_basename</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="499" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
499
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC499" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">out_basename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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500
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC500" class="line" lang="cpp"> </span>
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501
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC501" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="502" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
502
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC502" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="447" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
447
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<td class="new_line diff-line-num" data-linenumber="503" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
503
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC503" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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448
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<td class="new_line diff-line-num old" data-linenumber="504" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC448" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="449" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
449
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<td class="new_line diff-line-num old" data-linenumber="504" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC449" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".bam"</span><span class="p">)</span> <span class="p">{</span></span>
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450
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<td class="new_line diff-line-num old" data-linenumber="504" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC450" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="451" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="504" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
504
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC504" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="505" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
505
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC505" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="506" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
506
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC506" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="507" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
507
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC507" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="451" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="508" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
508
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC508" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".bam"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="509" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
509
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC509" class="line" lang="cpp"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filepath</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="510" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
510
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC510" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="511" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
511
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC511" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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451
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<td class="new_line diff-line-num" data-linenumber="512" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
512
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC512" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="452" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
452
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<td class="new_line diff-line-num old" data-linenumber="513" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC452" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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453
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC453" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="454" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="513" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
513
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC513" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num" data-linenumber="454" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
454
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<td class="new_line diff-line-num" data-linenumber="514" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
514
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC514" class="line" lang="cpp"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">gzFile</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="455" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
455
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<td class="new_line diff-line-num" data-linenumber="515" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
515
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC515" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzopen</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="s" style="color: #d14;">"wb"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="456" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
456
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<td class="new_line diff-line-num" data-linenumber="516" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
516
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC516" class="line" lang="cpp"> <span class="n" style="color: #333;">rem_2_fhs</span><span class="p">[</span><span class="n" style="color: #333;">bc</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fh</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="463" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="523" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -463,9 +523,14 @@ open_files(vector<pair<string, string> > &files,</td>
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463
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<td class="new_line diff-line-num" data-linenumber="523" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
523
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC523" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="464" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
464
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<td class="new_line diff-line-num" data-linenumber="524" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
524
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC524" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="465" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
465
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<td class="new_line diff-line-num" data-linenumber="525" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
525
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC525" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="526" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
526
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC526" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="466" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
466
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<td class="new_line diff-line-num" data-linenumber="527" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
527
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC527" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">barcodes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">merge</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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467
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<td class="new_line diff-line-num" data-linenumber="528" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
528
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC528" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="468" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
468
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<td class="new_line diff-line-num old" data-linenumber="529" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC468" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_unbarcoded"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="529" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
529
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC529" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_basename</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="530" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
530
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC530" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">out_basename</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="531" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
531
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC531" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="532" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
532
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC532" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_unbarcoded"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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533
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC533" class="line" lang="cpp"> <span class="p">}</span></span>
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469
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<td class="new_line diff-line-num" data-linenumber="534" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
534
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC534" class="line" lang="cpp"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">gzFile</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="470" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
470
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535
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC535" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzopen</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="s" style="color: #d14;">"wb"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="471" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
471
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536
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC536" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="482" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="547" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -482,7 +547,11 @@ open_files(vector<pair<string, string> > &files,</td>
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482
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<td class="new_line diff-line-num" data-linenumber="547" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
547
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC547" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="483" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
483
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<td class="new_line diff-line-num" data-linenumber="548" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
548
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC548" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="484" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
484
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<td class="new_line diff-line-num" data-linenumber="549" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
549
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC549" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">paired</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="485" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
485
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<td class="new_line diff-line-num old" data-linenumber="550" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC485" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_unbarcoded"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="486" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="550" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
550
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC550" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_basename</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="486" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="551" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
551
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC551" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">out_basename</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="486" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="552" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
552
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC552" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="486" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="553" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
553
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC553" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_unbarcoded"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="486" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="554" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
554
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC554" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="486" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
486
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<td class="new_line diff-line-num" data-linenumber="555" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
555
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC555" class="line" lang="cpp"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">gzFile</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="487" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
487
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<td class="new_line diff-line-num" data-linenumber="556" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
556
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC556" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzopen</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="s" style="color: #d14;">"wb"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="488" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
488
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557
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC557" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="497" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="566" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -497,7 +566,11 @@ open_files(vector<pair<string, string> > &files,</td>
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<td class="old_line diff-line-num" data-linenumber="497" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
497
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<td class="new_line diff-line-num" data-linenumber="566" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
566
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC566" class="line" lang="cpp"> <span class="n" style="color: #333;">pair_2_fhs</span><span class="p">[</span><span class="n" style="color: #333;">bc</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fh</span><span class="p">;</span></span>
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498
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567
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC567" class="line" lang="cpp"> <span class="p">}</span></span>
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499
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568
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC568" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="500" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
500
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<td class="new_line diff-line-num old" data-linenumber="569" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC500" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_unbarcoded.rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="569" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
569
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC569" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_basename</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="570" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
570
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC570" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">out_basename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="571" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
571
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC571" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="572" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
572
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC572" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_unbarcoded.rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_1</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="573" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
573
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC573" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="501" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
501
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<td class="new_line diff-line-num" data-linenumber="574" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
574
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC574" class="line" lang="cpp"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">gzFile</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="502" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
502
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<td class="new_line diff-line-num" data-linenumber="575" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
575
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC575" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzopen</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="s" style="color: #d14;">"wb"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="503" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
503
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<td class="new_line diff-line-num" data-linenumber="576" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
576
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC576" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="512" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="585" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -512,7 +585,11 @@ open_files(vector<pair<string, string> > &files,</td>
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<td class="old_line diff-line-num" data-linenumber="512" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
512
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<td class="new_line diff-line-num" data-linenumber="585" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
585
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC585" class="line" lang="cpp"> <span class="n" style="color: #333;">rem_1_fhs</span><span class="p">[</span><span class="n" style="color: #333;">bc</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fh</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="513" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
513
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<td class="new_line diff-line-num" data-linenumber="586" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
586
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC586" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="514" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
514
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<td class="new_line diff-line-num" data-linenumber="587" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
587
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC587" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="515" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
515
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<td class="new_line diff-line-num old" data-linenumber="588" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC515" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_unbarcoded.rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="516" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="588" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
588
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC588" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_basename</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="516" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="589" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
589
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC589" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">out_basename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="590" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
590
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC590" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="591" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
591
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC591" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_unbarcoded.rem"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_2</span><span class="p">;</span></span>
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592
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC592" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="516" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
516
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<td class="new_line diff-line-num" data-linenumber="593" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
593
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC593" class="line" lang="cpp"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">gzFile</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="517" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
517
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<td class="new_line diff-line-num" data-linenumber="594" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
594
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC594" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzopen</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="s" style="color: #d14;">"wb"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="518" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
518
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595
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC595" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="909" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="986" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -909,10 +986,10 @@ load_barcodes(string barcode_file, vector<BarcodePair> &barcodes,</td>
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<td class="old_line diff-line-num" data-linenumber="909" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
909
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<td class="new_line diff-line-num" data-linenumber="986" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
986
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC986" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span></span>
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<td class="old_line diff-line-num" data-linenumber="910" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
910
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<td class="new_line diff-line-num" data-linenumber="987" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
987
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC987" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">build_file_list</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">files</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="911" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
911
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<td class="new_line diff-line-num" data-linenumber="988" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
988
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC988" class="line" lang="cpp"><span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="912" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
912
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<td class="new_line diff-line-num old" data-linenumber="989" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC912" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right deletion" style="background-color: #fac5cd;">//</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="913" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
913
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<td class="new_line diff-line-num old" data-linenumber="989" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC913" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right deletion" style="background-color: #fac5cd;">// Scan a directory for a list of files.</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="914" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
914
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<td class="new_line diff-line-num old" data-linenumber="989" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC914" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num old" data-linenumber="915" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
915
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<td class="new_line diff-line-num old" data-linenumber="989" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC915" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left deletion" style="background-color: #fac5cd;">if</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">in_path_1</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">length</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">()</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">></span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="mi" style="color: #099;"><span class="idiff deletion" style="background-color: #fac5cd;">0</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">)</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">{</span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="916" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="989" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
989
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC989" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">if</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">in_path_type</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">==</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">InputT</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">::</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">directory</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">)</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">{</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="990" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
990
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC990" class="line" lang="cpp"> <span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition" style="background-color: #c7f0d2;">//</span></span></span>
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991
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC991" class="line" lang="cpp"><span class="idiff left addition" style="background-color: #c7f0d2;"> </span> <span class="c1" style="color: #998; font-style: italic;">//<span class="idiff right addition" style="background-color: #c7f0d2;"> Scan a directory for a list of files.</span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="916" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="992" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
992
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC992" class="line" lang="cpp"> <span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition" style="background-color: #c7f0d2;">//</span></span></span>
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<td class="old_line diff-line-num" data-linenumber="916" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
916
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<td class="new_line diff-line-num" data-linenumber="993" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
993
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC993" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="n" style="color: #333;">paired_file</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="917" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
917
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<td class="new_line diff-line-num" data-linenumber="994" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
994
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC994" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="918" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
918
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<td class="new_line diff-line-num" data-linenumber="995" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
995
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC995" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">dirent</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">direntry</span><span class="p">;</span></span>
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<li id="11bb84c7517c5dd061e913712c92d72cd6a698db">
<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#11bb84c7517c5dd061e913712c92d72cd6a698db"><strong style="font-weight: 600;">src/file_io.h</strong></a>
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1
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<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-</span></span>
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<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2
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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3
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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2012, Julian Catchen <jcatchen@<span class="idiff left right deletion" style="background-color: #fac5cd;">uoregon</span>.edu></span></span>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2012<span class="idiff left addition" style="background-color: #c7f0d2;">-2024</span>, Julian Catchen <jcatchen@<span class="idiff right addition" style="background-color: #c7f0d2;">illinois</span>.edu></span></span>
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4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// This file is part of Stacks.</span></span>
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6
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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -46,11 +46,13 @@</td>
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<td class="old_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
46
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<td class="new_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
46
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC46" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
47
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<td class="new_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
47
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC47" class="line" lang="cpp"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">FileT</span> <span class="n" style="color: #333;">in_file_type</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
48
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<td class="new_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
48
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC48" class="line" lang="cpp"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">FileT</span> <span class="n" style="color: #333;">out_file_type</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
49
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC49" class="line" lang="cpp"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">InputT</span> <span class="n" style="color: #333;">in_path_type</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
49
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<td class="new_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
50
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC50" class="line" lang="cpp"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">barcodet</span> <span class="n" style="color: #333;">barcode_type</span><span class="p">;</span></span>
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50
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<td class="new_line diff-line-num" data-linenumber="51" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
51
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC51" class="line" lang="cpp"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">paired</span><span class="p">;</span></span>
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51
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<td class="new_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
52
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC52" class="line" lang="cpp"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">interleaved</span><span class="p">;</span></span>
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52
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<td class="new_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
53
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC53" class="line" lang="cpp"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">merge</span><span class="p">;</span></span>
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53
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<td class="new_line diff-line-num" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
54
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC54" class="line" lang="cpp"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">out_path</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
55
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC55" class="line" lang="cpp"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">out_basename</span><span class="p">;</span></span>
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54
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<td class="new_line diff-line-num" data-linenumber="56" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
56
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC56" class="line" lang="cpp"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">in_file</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
55
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<td class="new_line diff-line-num" data-linenumber="57" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
57
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC57" class="line" lang="cpp"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">in_file_p1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="56" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
56
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<td class="new_line diff-line-num" data-linenumber="58" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
58
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC58" class="line" lang="cpp"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">in_file_p2</span><span class="p">;</span></span>
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<li id="5d057fdf8543f341f83844acdc94851f57407d44">
<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#5d057fdf8543f341f83844acdc94851f57407d44"><strong style="font-weight: 600;">src/populations.cc</strong></a>
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1
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<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-</span></span>
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2
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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3
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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2012-202<span class="idiff left right deletion" style="background-color: #fac5cd;">3</span>, Julian Catchen <jcatchen@illinois.edu></span></span>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2012-202<span class="idiff left right addition" style="background-color: #c7f0d2;">4</span>, Julian Catchen <jcatchen@illinois.edu></span></span>
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4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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5
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// This file is part of Stacks.</span></span>
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6
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6
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -43,10 +43,13 @@ string bl_file;</td>
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<td class="old_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
43
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<td class="new_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
43
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC43" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">wl_file</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
44
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<td class="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
44
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC44" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bs_wl_file</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
45
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<td class="new_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
45
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC45" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">enz</span><span class="p">;</span></span>
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<td class="new_line diff-line-num old" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC46" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sigma</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">150000.0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
47
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<td class="new_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
46
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC46" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">min_samples_overall</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
48
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<td class="new_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
47
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC47" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">min_samples_per_pop</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
49
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<td class="new_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
48
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC48" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_populations</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
49
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC49" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">min_gt_depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
50
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC50" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minor_allele_freq</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
51
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC51" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">minor_allele_cnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
52
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC52" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">max_obs_het</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span><span class="p">;</span></span>
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50
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<td class="new_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
53
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC53" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">filter_haplotype_wise</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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51
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<td class="new_line diff-line-num" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
54
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC54" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">batch_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10000</span><span class="p">;</span></span>
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<td class="new_line diff-line-num" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
55
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC55" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">calc_fstats</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -70,12 +73,9 @@ bool mapping_cross = false;</td>
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<td class="old_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
70
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<td class="new_line diff-line-num" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
73
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC73" class="line" lang="cpp"><span class="n" style="color: #333;">CrossT</span> <span class="n" style="color: #333;">mapcross_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CrossT</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unk</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="71" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
71
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<td class="new_line diff-line-num" data-linenumber="74" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
74
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC74" class="line" lang="cpp"><span class="n" style="color: #333;">FormatT</span> <span class="n" style="color: #333;">mapcross_format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FormatT</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unk</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="72" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
72
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<td class="new_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
75
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC75" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
73
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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC73" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">min_gt_depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="74" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
74
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<td class="new_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
76
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC76" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">merge_prune_lim</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span><span class="p">;</span></span>
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75
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC75" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minor_allele_freq</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
76
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC76" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">minor_allele_cnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
77
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC77" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">max_obs_het</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="78" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
78
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<td class="new_line diff-line-num" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
77
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC77" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p_value_cutoff</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.05</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
78
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC78" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sigma</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">150000.0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="79" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
79
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<td class="new_line diff-line-num" data-linenumber="79" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
79
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC79" class="line" lang="cpp"><span class="n" style="color: #333;">corr_type</span> <span class="n" style="color: #333;">fst_correction</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">no_correction</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="80" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
80
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<td class="new_line diff-line-num" data-linenumber="80" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
80
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC80" class="line" lang="cpp"><span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">debug_flags</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="81" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
81
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<td class="new_line diff-line-num" data-linenumber="81" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
81
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC81" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="305" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="305" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -305,6 +305,10 @@ try {</td>
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<td class="old_line diff-line-num" data-linenumber="305" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
305
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<td class="new_line diff-line-num" data-linenumber="305" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
305
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC305" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="306" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
306
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<td class="new_line diff-line-num" data-linenumber="306" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
306
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC306" class="line" lang="cpp"> <span class="n" style="color: #333;">Timer</span> <span class="n" style="color: #333;">timer</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="307" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
307
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<td class="new_line diff-line-num" data-linenumber="307" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
307
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC307" class="line" lang="cpp"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">BEGIN batch_progress</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
308
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC308" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
309
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC309" class="line" lang="cpp"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"# List of individual sites filtered.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="310" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
310
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC310" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"action</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">locus</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">chr</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">bp</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">col</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">reason</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">[sample]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="311" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
311
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC311" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
308
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<td class="new_line diff-line-num" data-linenumber="312" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
312
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC312" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="309" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
309
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<td class="new_line diff-line-num" data-linenumber="313" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
313
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC313" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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310
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<td class="new_line diff-line-num" data-linenumber="314" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
314
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC314" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Read the next set of loci to process.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="322" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="326" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -322,7 +326,7 @@ try {</td>
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322
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<td class="new_line diff-line-num" data-linenumber="326" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
326
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC326" class="line" lang="cpp"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">bloc</span><span class="p">.</span><span class="n" style="color: #333;">chr</span><span class="p">();</span></span>
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<td class="old_line diff-line-num" data-linenumber="323" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
323
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<td class="new_line diff-line-num" data-linenumber="327" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
327
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC327" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="324" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
324
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<td class="new_line diff-line-num" data-linenumber="328" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
328
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC328" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Batch "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">bloc</span><span class="p">.</span><span class="n" style="color: #333;">next_batch_number</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">flush</span><span class="p">;</span></span>
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325
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<td class="new_line diff-line-num old" data-linenumber="329" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC325" class="line" lang="cpp"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Batch "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">bloc</span><span class="p">.</span><span class="n" style="color: #333;">next_batch_number</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="329" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
329
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC329" class="line" lang="cpp"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"<span class="idiff left right addition" style="background-color: #c7f0d2;"># </span>Batch "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">bloc</span><span class="p">.</span><span class="n" style="color: #333;">next_batch_number</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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326
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<td class="new_line diff-line-num" data-linenumber="330" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
330
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC330" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="327" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
327
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<td class="new_line diff-line-num" data-linenumber="331" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
331
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC331" class="line" lang="cpp"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">": analyzed "</span></span>
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328
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<td class="new_line diff-line-num" data-linenumber="332" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
332
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC332" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">batch_total</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" loci; filtered "</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="427" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="431" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -427,6 +431,8 @@ try {</td>
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<td class="old_line diff-line-num" data-linenumber="427" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
427
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<td class="new_line diff-line-num" data-linenumber="431" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
431
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC431" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">n_sites</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" genomic sites, of which "</span></span>
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<td class="old_line diff-line-num" data-linenumber="428" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
428
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<td class="new_line diff-line-num" data-linenumber="432" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
432
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC432" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">n_multiloci_sites</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" were covered by multiple loci ("</span></span>
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<td class="old_line diff-line-num" data-linenumber="429" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
429
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<td class="new_line diff-line-num" data-linenumber="433" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
433
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC433" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">as_percentage</span><span class="p">(</span><span class="n" style="color: #333;">n_multiloci_sites</span><span class="p">,</span> <span class="n" style="color: #333;">n_sites</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">").</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="434" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
434
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC434" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">min_gt_depth</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
435
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC435" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Filtered "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">filtered_genotypes</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" genotypes that fell below the minimum genotype depth threshold.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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430
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436
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC436" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">total_sites</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="431" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
431
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<td class="new_line diff-line-num" data-linenumber="437" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
437
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC437" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Error: All data has been filtered out.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="432" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
432
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<td class="new_line diff-line-num" data-linenumber="438" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
438
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC438" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">exception</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1266" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1272" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1266,7 +1272,7 @@ LocusFilter::apply_filters_stacks(LocBin& loc, ostream& log_fh, const MetaPopInf</td>
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<td class="old_line diff-line-num" data-linenumber="1266" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1266
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<td class="new_line diff-line-num" data-linenumber="1272" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1272
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1272" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="1267" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1267
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<td class="new_line diff-line-num" data-linenumber="1273" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1273
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1273" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Filter genotypes for depth.</span></span>
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<td class="old_line diff-line-num" data-linenumber="1268" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1268
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<td class="new_line diff-line-num" data-linenumber="1274" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1274
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1274" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1269" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1269
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<td class="new_line diff-line-num old" data-linenumber="1275" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1269" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gt_depth_filter</span><span class="p">(</span><span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">cloc</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1270" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1275" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1275
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1275" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gt_depth_filter</span><span class="p">(</span><span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">cloc</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff right addition" style="background-color: #c7f0d2;">log_fh</span></span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1270" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1270
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<td class="new_line diff-line-num" data-linenumber="1276" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1276
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1276" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="1271" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1271
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<td class="new_line diff-line-num" data-linenumber="1277" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1277
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1277" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="1272" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1272
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<td class="new_line diff-line-num" data-linenumber="1278" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1278
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1278" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Identify individual SNPs that are below the -r threshold or the minor allele</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1358" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1364" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1358,26 +1364,45 @@ LocusFilter::filter(const MetaPopInfo *mpopi, Datum **d, CSLocus *cloc)</td>
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<td class="old_line diff-line-num" data-linenumber="1358" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1358
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<td class="new_line diff-line-num" data-linenumber="1364" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1364
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1364" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1359" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1359
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<td class="new_line diff-line-num" data-linenumber="1365" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1365
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1365" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="1360" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1360
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<td class="new_line diff-line-num" data-linenumber="1366" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1366
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1366" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1361" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1361
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<td class="new_line diff-line-num old" data-linenumber="1367" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1361" class="line" lang="cpp"><span class="n" style="color: #333;">LocusFilter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">gt_depth_filter</span><span class="p">(</span><span class="n" style="color: #333;">Datum</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CSLocus</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cloc</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1362" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1367" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1367
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1367" class="line" lang="cpp"><span class="n" style="color: #333;">LocusFilter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">gt_depth_filter</span><span class="p">(</span><span class="n" style="color: #333;">Datum</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CSLocus</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cloc</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">ostream</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">&</span></span><span class="n" style="color: #333;"><span class="idiff right addition" style="background-color: #c7f0d2;">log_fh</span></span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="1362" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1362
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<td class="new_line diff-line-num" data-linenumber="1368" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1368
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1368" class="line" lang="cpp"><span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1363" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1363
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<td class="new_line diff-line-num" data-linenumber="1369" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1369
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1369" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">min_gt_depth</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="1364" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1364
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<td class="new_line diff-line-num" data-linenumber="1370" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1370
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1370" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1365" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1365
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<td class="new_line diff-line-num" data-linenumber="1371" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1371
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1371" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cloc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">snps</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span></span>
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<td class="old_line diff-line-num" data-linenumber="1366" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1366
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<td class="new_line diff-line-num" data-linenumber="1372" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1372
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1372" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1367" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1367
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<td class="new_line diff-line-num old" data-linenumber="1373" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1367" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">spl</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">spl</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_sample_cnt</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">spl</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1368" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1368
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<td class="new_line diff-line-num old" data-linenumber="1373" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1368" class="line" lang="cpp"> <span class="n" style="color: #333;">Datum</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">spl</span><span class="p">];</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1369" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1373" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1373
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1373" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="1369" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1374" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1374
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1374" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_sample_cnt</span><span class="p">;</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1369" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1375" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1375
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1375" class="line" lang="cpp"> <span class="n" style="color: #333;">Datum</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">];</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1369" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1376" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1376
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1376" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="1369" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1377" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1377
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1377" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1369" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1378" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1378
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1378" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num" data-linenumber="1369" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1369
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<td class="new_line diff-line-num" data-linenumber="1379" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1379
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1379" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">obshap</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1370" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1370
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<td class="new_line diff-line-num old" data-linenumber="1380" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1370" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">obshap</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cloc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">snps</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1371" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1371
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<td class="new_line diff-line-num old" data-linenumber="1380" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1371" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">obshap</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cloc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">snps</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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1372
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<td class="new_line diff-line-num old" data-linenumber="1380" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1372" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">snp</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">snp</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">cloc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">snps</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">snp</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1380" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1380
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1380" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">obshap</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cloc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">snps</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1373" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1381" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1381
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1381" class="line" lang="cpp"> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">obshap</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cloc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">snps</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1373" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1382" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1382
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1382" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num new" data-linenumber="1373" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1383" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1383
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1383" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">snp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">snp</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">cloc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">snps</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">snp</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1373" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1373
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<td class="new_line diff-line-num" data-linenumber="1384" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1384
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1384" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cloc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">snps</span><span class="p">[</span><span class="n" style="color: #333;">snp</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">col</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1374" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1385" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1385
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1385" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num" data-linenumber="1374" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1374
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<td class="new_line diff-line-num" data-linenumber="1386" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1386
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1386" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">model</span><span class="p">[</span><span class="n" style="color: #333;">col</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'U'</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="1375" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1375
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<td class="new_line diff-line-num" data-linenumber="1387" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1387
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1387" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1376" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1388" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1388
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1388" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="1376" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1376
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<td class="new_line diff-line-num" data-linenumber="1389" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1389
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1389" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check this genotype's depth.</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1377" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1390" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1390
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1390" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="1377" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1377
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<td class="new_line diff-line-num" data-linenumber="1391" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1391
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1391" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">snpdata</span><span class="p">[</span><span class="n" style="color: #333;">snp</span><span class="p">].</span><span class="n" style="color: #333;">tot_depth</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_gt_depth</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1378" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1378
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<td class="new_line diff-line-num" data-linenumber="1392" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1392
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1392" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">model</span><span class="p">[</span><span class="n" style="color: #333;">col</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'U'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1379" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1379
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<td class="new_line diff-line-num old" data-linenumber="1393" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1379" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1393" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1393
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1393" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_filtered_genotypes</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1380" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1394" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1394
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1394" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="1380" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1380
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<td class="new_line diff-line-num" data-linenumber="1395" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1395
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1395" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">obshap</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">snp</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1381" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1396" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1396
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1396" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="1381" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1397" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1397
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1397" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1381" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1398" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1398
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1398" class="line" lang="cpp"> <span class="n" style="color: #333;">log_fh</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"pruned_polymorphic_site</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1381" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1399" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1399
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1399" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cloc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1400" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1400
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1400" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cloc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">chr</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1381" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1401" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1401
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1401" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cloc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sort_bp</span><span class="p">(</span><span class="n" style="color: #333;">col</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1402" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1402
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1402" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1381" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1403" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1403
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1403" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"genotype_depth"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1404" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1404
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1404" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">mpopi</span><span class="p">.</span><span class="n" style="color: #333;">samples</span><span class="p">()[</span><span class="n" style="color: #333;">s</span><span class="p">].</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1405" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1405
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1405" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1381" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1381
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<td class="new_line diff-line-num" data-linenumber="1406" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1406
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1406" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1382" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1382
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<td class="new_line diff-line-num" data-linenumber="1407" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1407
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1407" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1383" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1383
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<td class="new_line diff-line-num" data-linenumber="1408" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1408
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1408" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1403" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1428" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1403,10 +1428,11 @@ LocusFilter::init(MetaPopInfo *mpopi)</td>
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1403
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<td class="new_line diff-line-num" data-linenumber="1428" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1428
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1428" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="p">[</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_sample_cnt</span><span class="p">];</span></span>
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1404
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<td class="new_line diff-line-num" data-linenumber="1429" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1429
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1429" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_pop_tot</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="p">[</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_pop_cnt</span><span class="p">];</span></span>
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1405
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<td class="new_line diff-line-num" data-linenumber="1430" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1430
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1430" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="1406" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1406
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<td class="new_line diff-line-num old" data-linenumber="1431" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1406" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_filtered_loci</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1407" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1407
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<td class="new_line diff-line-num old" data-linenumber="1431" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1407" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_total_loci</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1408" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1408
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<td class="new_line diff-line-num old" data-linenumber="1431" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1408" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_filtered_sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1409" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1409
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<td class="new_line diff-line-num old" data-linenumber="1431" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1409" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_total_sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1410" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1431" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1431
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1431" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_filtered_loci</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1410" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1432" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1432
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1432" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_total_loci</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1410" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1433" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1433
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1433" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_filtered_sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1434" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1434
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1434" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_filtered_genotypes</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1435" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1435
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1435" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_total_sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1410
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<td class="new_line diff-line-num" data-linenumber="1436" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1436
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1436" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="1411" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1411
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<td class="new_line diff-line-num" data-linenumber="1437" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1437
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1437" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">pop_sthg</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1412
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1438
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1438" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3704" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3730" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -3704,8 +3730,9 @@ output_parameters(ostream &fh)</td>
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<td class="old_line diff-line-num" data-linenumber="3704" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3704
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<td class="new_line diff-line-num" data-linenumber="3730" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3730
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3730" class="line" lang="cpp"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"populations parameters selected:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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3705
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<td class="new_line diff-line-num" data-linenumber="3731" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3731
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3731" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">input_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">InputMode</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vcf</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="3706" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3706
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<td class="new_line diff-line-num" data-linenumber="3732" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3732
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3732" class="line" lang="cpp"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Input mode: VCF</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3707" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3707
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<td class="new_line diff-line-num old" data-linenumber="3733" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3707" class="line" lang="cpp"> <span class="n" style="color: #333;">fh</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3708" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3708
</td>
<td class="new_line diff-line-num old" data-linenumber="3733" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3708" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Percent samples limit per population: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">min_samples_per_pop</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3709" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3733" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3733
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3733" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">min_gt_depth</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3709" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3734" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3734
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3734" class="line" lang="cpp"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Minimum read depth to include genotype: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">min_gt_depth</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3709" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="3735" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3735
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3735" class="line" lang="cpp"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Percent samples limit per population: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">min_samples_per_pop</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="3709" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3709
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<td class="new_line diff-line-num" data-linenumber="3736" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3736
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3736" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Locus Population limit: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">min_populations</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="3710" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3710
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<td class="new_line diff-line-num" data-linenumber="3737" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3737
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3737" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Percent samples overall: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">min_samples_overall</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="3711" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3711
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<td class="new_line diff-line-num" data-linenumber="3738" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3738
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3738" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Minor allele frequency cutoff: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">minor_allele_freq</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3785" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3812" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -3785,7 +3812,7 @@ parse_command_line(int argc, char* argv[])</td>
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<td class="old_line diff-line-num" data-linenumber="3785" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3785
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<td class="new_line diff-line-num" data-linenumber="3812" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3812
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3812" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"whitelist"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'W'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="3786" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3786
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<td class="new_line diff-line-num" data-linenumber="3813" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3813
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3813" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"blacklist"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'B'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="3787" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3787
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<td class="new_line diff-line-num" data-linenumber="3814" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3814
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3814" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"batch-size"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">1999</span><span class="p">},</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3788" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3788
</td>
<td class="new_line diff-line-num old" data-linenumber="3815" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3788" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"<span class="idiff left right deletion" style="background-color: #fac5cd;">dbg-</span>min-gt-depth"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">2001</span><span class="p">},</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3789" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3815" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3815
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3815" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"min-gt-depth"</span><span class="p">,</span> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">2001</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="3789" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3789
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<td class="new_line diff-line-num" data-linenumber="3816" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3816
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3816" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"write-single-snp"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'I'</span><span class="p">},</span> </span>
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<td class="old_line diff-line-num" data-linenumber="3790" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3790
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<td class="new_line diff-line-num" data-linenumber="3817" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3817
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3817" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"write-random-snp"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'j'</span><span class="p">},</span> </span>
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<td class="old_line diff-line-num" data-linenumber="3791" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3791
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<td class="new_line diff-line-num" data-linenumber="3818" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3818
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3818" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"no-hap-exports"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">1012</span><span class="p">},</span> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3851" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3878" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -3851,7 +3878,7 @@ parse_command_line(int argc, char* argv[])</td>
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<td class="old_line diff-line-num" data-linenumber="3851" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3851
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<td class="new_line diff-line-num" data-linenumber="3878" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3878
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3878" class="line" lang="cpp"> <span class="n" style="color: #333;">batch_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">is_integer</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="3852" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3852
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<td class="new_line diff-line-num" data-linenumber="3879" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3879
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3879" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="3853" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3853
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<td class="new_line diff-line-num" data-linenumber="3880" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3880
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3880" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">2001</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3854" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3854
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<td class="new_line diff-line-num old" data-linenumber="3881" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3854" class="line" lang="cpp"> <span class="n" style="color: #333;">min_gt_depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right deletion" style="background-color: #fac5cd;">stol</span></span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3855" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3881" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3881
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3881" class="line" lang="cpp"> <span class="n" style="color: #333;">min_gt_depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right addition" style="background-color: #c7f0d2;">is_integer</span></span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="3855" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3855
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<td class="new_line diff-line-num" data-linenumber="3882" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3882
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3882" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="3856" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3856
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<td class="new_line diff-line-num" data-linenumber="3883" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3883
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3883" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'O'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="3857" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3857
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<td class="new_line diff-line-num" data-linenumber="3884" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3884
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3884" class="line" lang="cpp"> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4277" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4304" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -4277,6 +4304,7 @@ void help() {</td>
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<td class="old_line diff-line-num" data-linenumber="4277" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4277
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<td class="new_line diff-line-num" data-linenumber="4304" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4304
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4304" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --min-maf [float]: specify a minimum minor allele frequency required to process a SNP (0 < min_maf < 0.5; applied to the metapopulation).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="4278" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4278
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<td class="new_line diff-line-num" data-linenumber="4305" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4305
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4305" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --min-mac [int]: specify a minimum minor allele count required to process a SNP (applied to the metapopulation).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="4279" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4279
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<td class="new_line diff-line-num" data-linenumber="4306" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4306
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4306" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --max-obs-het [float]: specify a maximum observed heterozygosity required to process a SNP (applied ot the metapopulation).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="4280" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="4307" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
4307
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4307" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --min-gt-depth [int]: specify a minimum number of reads to include a called SNP (otherwise marked as missing data).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="4280" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4280
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<td class="new_line diff-line-num" data-linenumber="4308" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4308
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4308" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4281
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<td class="new_line diff-line-num" data-linenumber="4309" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4309
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4309" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --write-single-snp: restrict data analysis to only the first SNP per locus (implies --no-haps).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="4282" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4282
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<td class="new_line diff-line-num" data-linenumber="4310" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4310
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4310" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --write-random-snp: restrict data analysis to one random SNP per locus (implies --no-haps).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4342" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4370" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -4342,7 +4370,6 @@ void help() {</td>
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4342
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<td class="new_line diff-line-num" data-linenumber="4370" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4370
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4370" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG</span></span>
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4343
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<td class="new_line diff-line-num" data-linenumber="4371" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4371
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4371" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="4344" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4344
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<td class="new_line diff-line-num" data-linenumber="4372" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4372
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4372" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"DEBUG:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="4345" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
4345
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<td class="new_line diff-line-num old" data-linenumber="4373" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4345" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --dbg-min-gt-depth</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="4346" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4346
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<td class="new_line diff-line-num" data-linenumber="4373" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4373
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4373" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --genepop-haps-3digits: Use 3-digit alleles in the genepop haps output (default is 2-digit).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="4347" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4347
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<td class="new_line diff-line-num" data-linenumber="4374" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4374
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4374" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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4348
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<td class="new_line diff-line-num" data-linenumber="4375" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4375
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4375" class="line" lang="cpp"> <span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#e4426463c64a505bc8fcb199c701d8e0003a4ab4"><strong style="font-weight: 600;">src/populations.h</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="223" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="223" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -223,6 +223,7 @@ public:</td>
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<td class="old_line diff-line-num" data-linenumber="223" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
223
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<td class="new_line diff-line-num" data-linenumber="223" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
223
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC223" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_batch_total_loci</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="224" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
224
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<td class="new_line diff-line-num" data-linenumber="224" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
224
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC224" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_batch_seen_loci</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="225" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
225
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<td class="new_line diff-line-num" data-linenumber="225" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
225
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC225" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_filtered_sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="226" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="226" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
226
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC226" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_filtered_genotypes</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="226" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
226
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<td class="new_line diff-line-num" data-linenumber="227" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
227
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC227" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_total_sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="227" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
227
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<td class="new_line diff-line-num" data-linenumber="228" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
228
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC228" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_variant_sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="228" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
228
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<td class="new_line diff-line-num" data-linenumber="229" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
229
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC229" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="256" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -255,7 +256,7 @@ public:</td>
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<td class="old_line diff-line-num" data-linenumber="255" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
255
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<td class="new_line diff-line-num" data-linenumber="256" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
256
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC256" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">filter_snps</span><span class="p">(</span><span class="n" style="color: #333;">LocBin</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">loc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">MetaPopInfo</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">mpopi</span><span class="p">,</span> <span class="n" style="color: #333;">ostream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">log_fh</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="256" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
256
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<td class="new_line diff-line-num" data-linenumber="257" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
257
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC257" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">filter_haps</span><span class="p">(</span><span class="n" style="color: #333;">LocBin</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">loc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">MetaPopInfo</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">mpopi</span><span class="p">,</span> <span class="n" style="color: #333;">ostream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">log_fh</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="257" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
257
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<td class="new_line diff-line-num" data-linenumber="258" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
258
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC258" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">filter_fixed_sites</span><span class="p">(</span><span class="n" style="color: #333;">LocBin</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">loc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">MetaPopInfo</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">mpopi</span><span class="p">,</span> <span class="n" style="color: #333;">ostream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">log_fh</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="258" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
258
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<td class="new_line diff-line-num old" data-linenumber="259" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC258" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">gt_depth_filter</span><span class="p">(</span><span class="n" style="color: #333;">Datum</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CSLocus</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cloc</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="259" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="259" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
259
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC259" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">gt_depth_filter</span><span class="p">(</span><span class="n" style="color: #333;">Datum</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CSLocus</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cloc</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">ostream</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">&</span></span><span class="n" style="color: #333;"><span class="idiff right addition" style="background-color: #c7f0d2;">log_fh</span></span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="259" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
259
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<td class="new_line diff-line-num" data-linenumber="260" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
260
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC260" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">keep_single_snp</span><span class="p">(</span><span class="n" style="color: #333;">CSLocus</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cloc</span><span class="p">,</span> <span class="n" style="color: #333;">Datum</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n_samples</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">LocTally</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">t</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="260" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
260
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<td class="new_line diff-line-num" data-linenumber="261" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
261
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC261" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">keep_random_snp</span><span class="p">(</span><span class="n" style="color: #333;">CSLocus</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cloc</span><span class="p">,</span> <span class="n" style="color: #333;">Datum</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n_samples</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">LocTally</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">t</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="261" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
261
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<td class="new_line diff-line-num" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
262
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC262" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="266" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="267" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -266,6 +267,7 @@ public:</td>
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<td class="old_line diff-line-num" data-linenumber="266" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
266
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<td class="new_line diff-line-num" data-linenumber="267" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
267
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC267" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">batch_seen</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_batch_seen_loci</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="267" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
267
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<td class="new_line diff-line-num" data-linenumber="268" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
268
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC268" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">batch_total</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_batch_total_loci</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="268" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
268
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<td class="new_line diff-line-num" data-linenumber="269" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
269
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC269" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">filtered_sites</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_filtered_sites</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="269" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="270" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
270
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC270" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">filtered_genotypes</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_filtered_genotypes</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="269" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
269
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<td class="new_line diff-line-num" data-linenumber="271" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
271
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC271" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">total_sites</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_total_sites</span><span class="p">;</span> <span class="p">}</span></span>
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270
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<td class="new_line diff-line-num" data-linenumber="272" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
272
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC272" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">variant_sites</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_variant_sites</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="271" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
271
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<td class="new_line diff-line-num" data-linenumber="273" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
273
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC273" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">locus_seen</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="291" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="293" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -291,6 +293,7 @@ private:</td>
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<td class="old_line diff-line-num" data-linenumber="291" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
291
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<td class="new_line diff-line-num" data-linenumber="293" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
293
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC293" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">_batch_total_loci</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="292" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
292
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<td class="new_line diff-line-num" data-linenumber="294" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
294
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC294" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">_batch_seen_loci</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="293" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
293
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<td class="new_line diff-line-num" data-linenumber="295" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
295
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC295" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">_filtered_sites</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="294" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="296" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
296
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC296" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">_filtered_genotypes</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="294" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
294
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<td class="new_line diff-line-num" data-linenumber="297" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
297
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC297" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">_total_sites</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="295" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
295
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<td class="new_line diff-line-num" data-linenumber="298" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
298
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC298" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">_variant_sites</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="296" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
296
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<td class="new_line diff-line-num" data-linenumber="299" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
299
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC299" class="line" lang="cpp"></span>
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<li id="6b229f74a1c1dafec515b59e2082ef52596e4d1a">
<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#6b229f74a1c1dafec515b59e2082ef52596e4d1a"><strong style="font-weight: 600;">src/process_radtags.cc</strong></a>
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1
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<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-</span></span>
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<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2
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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3
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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2011-202<span class="idiff left right deletion" style="background-color: #fac5cd;">3</span>, Julian Catchen <jcatchen@illinois.edu></span></span>
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<td class="old_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2011-202<span class="idiff left right addition" style="background-color: #c7f0d2;">4</span>, Julian Catchen <jcatchen@illinois.edu></span></span>
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<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// This file is part of Stacks.</span></span>
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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6
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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="37" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -37,12 +37,14 @@ using namespace std;</td>
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<td class="old_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC37" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
38
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<td class="new_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
38
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC38" class="line" lang="cpp"><span class="n" style="color: #333;">FileT</span> <span class="n" style="color: #333;">in_file_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FileT</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unknown</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
39
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<td class="new_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
39
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC39" class="line" lang="cpp"><span class="n" style="color: #333;">FileT</span> <span class="n" style="color: #333;">out_file_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FileT</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unknown</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
40
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC40" class="line" lang="cpp"><span class="n" style="color: #333;">InputT</span> <span class="n" style="color: #333;">in_path_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">InputT</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">files</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
40
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<td class="new_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
41
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC41" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">in_file</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
41
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<td class="new_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
42
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC42" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">in_file_p1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
42
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<td class="new_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
43
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC43" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">in_file_p2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
43
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<td class="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
44
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC44" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">in_path_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
44
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<td class="new_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
45
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC45" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">in_path_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
45
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<td class="new_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
46
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC46" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">out_path</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
47
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC47" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">out_basename</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
46
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<td class="new_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
48
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC48" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">barcode_file</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
47
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<td class="new_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
49
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC49" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">renz_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
48
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<td class="new_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
50
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC50" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">renz_2</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="63" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="65" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -63,6 +65,8 @@ bool discards = false;</td>
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<td class="old_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
63
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<td class="new_line diff-line-num" data-linenumber="65" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
65
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC65" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">overhang</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="64" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
64
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<td class="new_line diff-line-num" data-linenumber="66" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
66
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC66" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">filter_illumina</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="65" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
65
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<td class="new_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
67
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC67" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">check_radtag</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
68
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC68" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">check_poly_g</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
69
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC69" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">force_poly_g</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="66" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
66
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<td class="new_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
70
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC70" class="line" lang="cpp"><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">truncate_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
67
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<td class="new_line diff-line-num" data-linenumber="71" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
71
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC71" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">barcode_dist_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="68" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
68
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<td class="new_line diff-line-num" data-linenumber="72" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
72
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC72" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">barcode_dist_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="147" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -147,6 +151,10 @@ int main (int argc, char* argv[]) {</td>
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<td class="old_line diff-line-num" data-linenumber="147" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
147
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<td class="new_line diff-line-num" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
151
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="old_line diff-line-num" data-linenumber="148" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
148
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<td class="new_line diff-line-num" data-linenumber="152" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
152
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Processing single-end data.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="149" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
149
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<td class="new_line diff-line-num" data-linenumber="153" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
153
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC153" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Using Phred+"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">qual_offset</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" encoding for quality scores.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
154
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC154" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">force_poly_g</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
155
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC155" class="line" lang="cpp"> <span class="n" style="color: #333;">check_poly_g</span> <span class="o" style="font-weight: 600;">?</span></span>
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<td class="old_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
156
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Checks for poly-G runs have been forced.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
157
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC157" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Checks for poly-G runs have been disabled.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
150
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<td class="new_line diff-line-num" data-linenumber="158" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
158
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC158" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">truncate_seq</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
151
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<td class="new_line diff-line-num" data-linenumber="159" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
159
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC159" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Reads will be truncated to "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">truncate_seq</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"bp</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="152" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
152
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<td class="new_line diff-line-num" data-linenumber="160" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
160
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC160" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filter_illumina</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="206" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="214" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -206,7 +214,11 @@ int main (int argc, char* argv[]) {</td>
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<td class="old_line diff-line-num" data-linenumber="206" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
206
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<td class="new_line diff-line-num" data-linenumber="214" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
214
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC214" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="207" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
207
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<td class="new_line diff-line-num" data-linenumber="215" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
215
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC215" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="208" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
208
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<td class="new_line diff-line-num" data-linenumber="216" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
216
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC216" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="209" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
209
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<td class="new_line diff-line-num old" data-linenumber="217" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC209" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Processing file "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" of "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" ["</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="217" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
217
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC217" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
218
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC218" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">paired</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="219" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
219
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC219" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Processing file-pair "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" of "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="220" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
220
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC220" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="old_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="221" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
221
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Processing file "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" of "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="210" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
210
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<td class="new_line diff-line-num" data-linenumber="222" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
222
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC222" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="211" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
211
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<td class="new_line diff-line-num" data-linenumber="223" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
223
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;">initialize_counters</span><span class="p">(</span><span class="n" style="color: #333;">counters</span><span class="p">[</span><span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">]);</span></span>
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<td class="old_line diff-line-num" data-linenumber="212" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
212
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<td class="new_line diff-line-num" data-linenumber="224" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
224
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC224" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="268" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="280" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -268,8 +280,10 @@ int main (int argc, char* argv[]) {</td>
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<td class="old_line diff-line-num" data-linenumber="268" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
268
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<td class="new_line diff-line-num" data-linenumber="280" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
280
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC280" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">counters</span><span class="p">[</span><span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">][</span><span class="s" style="color: #d14;">"ambiguous"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" ambiguous barcodes; "</span></span>
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<td class="old_line diff-line-num" data-linenumber="269" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
269
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<td class="new_line diff-line-num" data-linenumber="281" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
281
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC281" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">counters</span><span class="p">[</span><span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">][</span><span class="s" style="color: #d14;">"noradtag"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" ambiguous RAD-Tags; "</span></span>
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<td class="old_line diff-line-num" data-linenumber="270" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
270
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<td class="new_line diff-line-num" data-linenumber="282" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
282
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC282" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"+"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">counters</span><span class="p">[</span><span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">][</span><span class="s" style="color: #d14;">"recovered"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" recovered; "</span></span>
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271
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<td class="new_line diff-line-num old" data-linenumber="283" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC271" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">counters</span><span class="p">[</span><span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">][</span><span class="s" style="color: #d14;">"low_quality"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" low quality reads; "</span></span>
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<td class="old_line diff-line-num old" data-linenumber="272" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
272
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<td class="new_line diff-line-num old" data-linenumber="283" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC272" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">counters</span><span class="p">[</span><span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">][</span><span class="s" style="color: #d14;">"retained"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" retained reads.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="273" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="283" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
283
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC283" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">counters</span><span class="p">[</span><span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">][</span><span class="s" style="color: #d14;">"low_quality"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" low quality reads; "</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="273" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="284" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
284
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC284" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">check_poly_g</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="273" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="285" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
285
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC285" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">counters</span><span class="p">[</span><span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">][</span><span class="s" style="color: #d14;">"poly_g"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" reads with poly-G runs; "</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="273" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="286" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
286
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC286" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">counters</span><span class="p">[</span><span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">][</span><span class="s" style="color: #d14;">"retained"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" retained reads.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="273" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
273
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<td class="new_line diff-line-num" data-linenumber="287" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
287
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC287" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filter_adapter</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="274" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
274
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<td class="new_line diff-line-num" data-linenumber="288" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
288
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC288" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span></span>
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<td class="old_line diff-line-num" data-linenumber="275" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
275
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<td class="new_line diff-line-num" data-linenumber="289" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
289
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC289" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">counters</span><span class="p">[</span><span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">][</span><span class="s" style="color: #d14;">"adapter"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" reads with adapter sequence.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="298" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="312" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -298,7 +312,7 @@ int main (int argc, char* argv[]) {</td>
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<td class="old_line diff-line-num" data-linenumber="298" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
298
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<td class="new_line diff-line-num" data-linenumber="312" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
312
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC312" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="299" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
299
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<td class="new_line diff-line-num" data-linenumber="313" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
313
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC313" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"done.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="300" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
300
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<td class="new_line diff-line-num" data-linenumber="314" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
314
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC314" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num old" data-linenumber="301" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
301
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<td class="new_line diff-line-num old" data-linenumber="315" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC301" class="line" lang="cpp"> <span class="n" style="color: #333;">print_results</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="n" style="color: #333;">barcodes</span><span class="p">,</span> <span class="n" style="color: #333;">counters</span><span class="p">,</span> <span class="n" style="color: #333;">barcode_log</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="302" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="315" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
315
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC315" class="line" lang="cpp"> <span class="n" style="color: #333;">print_results</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left addition" style="background-color: #c7f0d2;">out_basename</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">barcodes</span><span class="p">,</span> <span class="n" style="color: #333;">counters</span><span class="p">,</span> <span class="n" style="color: #333;">barcode_log</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="302" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
302
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<td class="new_line diff-line-num" data-linenumber="316" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
316
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC316" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="303" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
303
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<td class="new_line diff-line-num" data-linenumber="317" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
317
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC317" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"process_radtags is done.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="304" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
304
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<td class="new_line diff-line-num" data-linenumber="318" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
318
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC318" class="line" lang="cpp"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="337" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="351" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -337,6 +351,7 @@ initialize_counters(map<string, long> &counter)</td>
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<td class="old_line diff-line-num" data-linenumber="337" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
337
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<td class="new_line diff-line-num" data-linenumber="351" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
351
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC351" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span><span class="p">[</span><span class="s" style="color: #d14;">"ill_filtered"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="338" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
338
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<td class="new_line diff-line-num" data-linenumber="352" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
352
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC352" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span><span class="p">[</span><span class="s" style="color: #d14;">"adapter"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
339
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<td class="new_line diff-line-num" data-linenumber="353" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
353
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC353" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span><span class="p">[</span><span class="s" style="color: #d14;">"low_quality"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="340" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="354" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
354
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC354" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span><span class="p">[</span><span class="s" style="color: #d14;">"poly_g"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="340" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
340
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<td class="new_line diff-line-num" data-linenumber="355" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
355
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC355" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span><span class="p">[</span><span class="s" style="color: #d14;">"noradtag"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="341" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
341
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<td class="new_line diff-line-num" data-linenumber="356" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
356
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC356" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span><span class="p">[</span><span class="s" style="color: #d14;">"ambiguous"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="342" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
342
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<td class="new_line diff-line-num" data-linenumber="357" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
357
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC357" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span><span class="p">[</span><span class="s" style="color: #d14;">"retained"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="357" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="372" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -357,6 +372,7 @@ consolidate_counters(map<string, long> &counter,</td>
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<td class="old_line diff-line-num" data-linenumber="357" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
357
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<td class="new_line diff-line-num" data-linenumber="372" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
372
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC372" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span><span class="p">[</span><span class="s" style="color: #d14;">"ill_filtered"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cntr</span><span class="p">[</span><span class="s" style="color: #d14;">"ill_filtered"</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="358" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
358
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<td class="new_line diff-line-num" data-linenumber="373" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
373
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC373" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span><span class="p">[</span><span class="s" style="color: #d14;">"adapter"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cntr</span><span class="p">[</span><span class="s" style="color: #d14;">"adapter"</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
359
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<td class="new_line diff-line-num" data-linenumber="374" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
374
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC374" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span><span class="p">[</span><span class="s" style="color: #d14;">"low_quality"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cntr</span><span class="p">[</span><span class="s" style="color: #d14;">"low_quality"</span><span class="p">];</span></span>
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<td class="old_line diff-line-num new" data-linenumber="360" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="375" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
375
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC375" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span><span class="p">[</span><span class="s" style="color: #d14;">"poly_g"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cntr</span><span class="p">[</span><span class="s" style="color: #d14;">"poly_g"</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="360" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
360
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<td class="new_line diff-line-num" data-linenumber="376" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
376
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC376" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span><span class="p">[</span><span class="s" style="color: #d14;">"noradtag"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cntr</span><span class="p">[</span><span class="s" style="color: #d14;">"noradtag"</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="361" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
361
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<td class="new_line diff-line-num" data-linenumber="377" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
377
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC377" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span><span class="p">[</span><span class="s" style="color: #d14;">"ambiguous"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cntr</span><span class="p">[</span><span class="s" style="color: #d14;">"ambiguous"</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="362" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
362
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<td class="new_line diff-line-num" data-linenumber="378" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
378
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC378" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span><span class="p">[</span><span class="s" style="color: #d14;">"retained"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cntr</span><span class="p">[</span><span class="s" style="color: #d14;">"retained"</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="381" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="397" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -381,12 +397,14 @@ consolidate_barcode_logs(map<BarcodePair, map<string, long>> &barcode_log,</td>
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<td class="old_line diff-line-num" data-linenumber="381" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
381
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<td class="new_line diff-line-num" data-linenumber="397" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
397
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC397" class="line" lang="cpp"> <span class="n" style="color: #333;">barcode_log</span><span class="p">[</span><span class="n" style="color: #333;">bc</span><span class="p">][</span><span class="s" style="color: #d14;">"noradtag"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="382" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
382
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<td class="new_line diff-line-num" data-linenumber="398" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
398
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC398" class="line" lang="cpp"> <span class="n" style="color: #333;">barcode_log</span><span class="p">[</span><span class="n" style="color: #333;">bc</span><span class="p">][</span><span class="s" style="color: #d14;">"total"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="383" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
383
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<td class="new_line diff-line-num" data-linenumber="399" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
399
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC399" class="line" lang="cpp"> <span class="n" style="color: #333;">barcode_log</span><span class="p">[</span><span class="n" style="color: #333;">bc</span><span class="p">][</span><span class="s" style="color: #d14;">"low_qual"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="384" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
400
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC400" class="line" lang="cpp"> <span class="n" style="color: #333;">barcode_log</span><span class="p">[</span><span class="n" style="color: #333;">bc</span><span class="p">][</span><span class="s" style="color: #d14;">"poly_g"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="384" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
384
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<td class="new_line diff-line-num" data-linenumber="401" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
401
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC401" class="line" lang="cpp"> <span class="n" style="color: #333;">barcode_log</span><span class="p">[</span><span class="n" style="color: #333;">bc</span><span class="p">][</span><span class="s" style="color: #d14;">"retained"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="385" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
385
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<td class="new_line diff-line-num" data-linenumber="402" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
402
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC402" class="line" lang="cpp"> <span class="n" style="color: #333;">barcode_log</span><span class="p">[</span><span class="n" style="color: #333;">bc</span><span class="p">][</span><span class="s" style="color: #d14;">"proppair"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="386" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
386
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<td class="new_line diff-line-num" data-linenumber="403" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
403
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC403" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="387" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
387
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<td class="new_line diff-line-num" data-linenumber="404" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
404
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC404" class="line" lang="cpp"> <span class="n" style="color: #333;">barcode_log</span><span class="p">[</span><span class="n" style="color: #333;">bc</span><span class="p">][</span><span class="s" style="color: #d14;">"noradtag"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"noradtag"</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="388" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
388
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<td class="new_line diff-line-num" data-linenumber="405" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
405
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC405" class="line" lang="cpp"> <span class="n" style="color: #333;">barcode_log</span><span class="p">[</span><span class="n" style="color: #333;">bc</span><span class="p">][</span><span class="s" style="color: #d14;">"total"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"total"</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="389" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
389
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<td class="new_line diff-line-num" data-linenumber="406" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
406
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC406" class="line" lang="cpp"> <span class="n" style="color: #333;">barcode_log</span><span class="p">[</span><span class="n" style="color: #333;">bc</span><span class="p">][</span><span class="s" style="color: #d14;">"low_qual"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"low_qual"</span><span class="p">];</span></span>
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<td class="old_line diff-line-num new" data-linenumber="390" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="407" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
407
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC407" class="line" lang="cpp"> <span class="n" style="color: #333;">barcode_log</span><span class="p">[</span><span class="n" style="color: #333;">bc</span><span class="p">][</span><span class="s" style="color: #d14;">"poly_g"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"poly_g"</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="390" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
390
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<td class="new_line diff-line-num" data-linenumber="408" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
408
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC408" class="line" lang="cpp"> <span class="n" style="color: #333;">barcode_log</span><span class="p">[</span><span class="n" style="color: #333;">bc</span><span class="p">][</span><span class="s" style="color: #d14;">"retained"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"retained"</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="391" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
391
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<td class="new_line diff-line-num" data-linenumber="409" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
409
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC409" class="line" lang="cpp"> <span class="n" style="color: #333;">barcode_log</span><span class="p">[</span><span class="n" style="color: #333;">bc</span><span class="p">][</span><span class="s" style="color: #d14;">"proppair"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"proppair"</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="392" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
392
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<td class="new_line diff-line-num" data-linenumber="410" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
410
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC410" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="473" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="491" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -473,7 +491,7 @@ process_paired_reads(string prefix_1,</td>
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473
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<td class="new_line diff-line-num" data-linenumber="491" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
491
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC491" class="line" lang="cpp"></span>
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474
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<td class="new_line diff-line-num" data-linenumber="492" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
492
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC492" class="line" lang="cpp"> <span class="n" style="color: #333;">r_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">RawRead</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">s_1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">min_bc_size_1</span><span class="p">,</span> <span class="n" style="color: #333;">win_size</span><span class="p">);</span></span>
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475
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<td class="new_line diff-line-num" data-linenumber="493" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
493
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC493" class="line" lang="cpp"> <span class="n" style="color: #333;">r_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">RawRead</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">s_2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">),</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">min_bc_size_2</span><span class="p">,</span> <span class="n" style="color: #333;">win_size</span><span class="p">);</span></span>
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476
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC476" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" data-linenumber="494" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
494
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC494" class="line" lang="cpp"> </span>
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477
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<td class="new_line diff-line-num" data-linenumber="495" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
495
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC495" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="478" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
478
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<td class="new_line diff-line-num" data-linenumber="496" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
496
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC496" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Set len_limit so that if we encounter reads already shorter than truncate_seq limit</span></span>
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<td class="old_line diff-line-num" data-linenumber="479" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
479
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<td class="new_line diff-line-num" data-linenumber="497" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
497
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC497" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// they will be discarded.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="508" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="526" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -508,6 +526,8 @@ process_paired_reads(string prefix_1,</td>
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508
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<td class="new_line diff-line-num" data-linenumber="526" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
526
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC526" class="line" lang="cpp"> <span class="n" style="color: #333;">parse_input_record</span><span class="p">(</span><span class="n" style="color: #333;">s_2</span><span class="p">,</span> <span class="n" style="color: #333;">r_2</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="509" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
509
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<td class="new_line diff-line-num" data-linenumber="527" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
527
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC527" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span><span class="p">[</span><span class="s" style="color: #d14;">"total"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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510
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<td class="new_line diff-line-num" data-linenumber="528" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
528
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC528" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="511" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="529" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
529
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC529" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">force_poly_g</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">r_1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">check_poly_g</span><span class="p">())</span> <span class="n" style="color: #333;">check_poly_g</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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530
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC530" class="line" lang="cpp"> </span>
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511
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<td class="new_line diff-line-num" data-linenumber="531" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
531
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC531" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="512" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
512
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<td class="new_line diff-line-num" data-linenumber="532" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
532
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC532" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If a BestRAD protocol was used, check which read the barcode/restriction cutsite is on</span></span>
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<td class="old_line diff-line-num" data-linenumber="513" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
513
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<td class="new_line diff-line-num" data-linenumber="533" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
533
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC533" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// and transpose the reads if necessary.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="748" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="768" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -748,9 +768,18 @@ process_paired_reads_parallel(string prefix_1,</td>
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748
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768
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC768" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="749" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
749
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769
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC769" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="750" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
750
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<td class="new_line diff-line-num" data-linenumber="770" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
770
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC770" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BarcodePair</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">output_thread_map</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="751" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
751
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<td class="new_line diff-line-num old" data-linenumber="771" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC751" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="752" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="771" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
771
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC771" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num new" data-linenumber="752" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="772" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
772
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC772" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// We must take care because multiple barcodes can point to the same output file,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="752" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="773" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
773
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC773" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// so we must assign all barcodes for a single output file to the same thread for writing.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="774" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
774
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC774" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num new" data-linenumber="752" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="775" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
775
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC775" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">fhType</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BarcodePair</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">rev_fh_map</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="752" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
752
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<td class="new_line diff-line-num" data-linenumber="776" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
776
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC776" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pair_1_fhs</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">pair_1_fhs</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="753" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
753
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<td class="new_line diff-line-num old" data-linenumber="777" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC753" class="line" lang="cpp"> <span class="n" style="color: #333;">output_thread_map</span><span class="p">[</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">num_output_threads</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">num_input_threads</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="777" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
777
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC777" class="line" lang="cpp"> <span class="n" style="color: #333;">rev_fh_map</span><span class="p">[</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="778" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
778
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC778" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="754" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="779" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
779
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC779" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="754" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="780" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
780
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC780" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rev_fh_map</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">rev_fh_map</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="754" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="781" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
781
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC781" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="782" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
782
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC782" class="line" lang="cpp"> <span class="n" style="color: #333;">output_thread_map</span><span class="p">[</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">num_output_threads</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">num_input_threads</span><span class="p">;</span></span>
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754
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<td class="new_line diff-line-num" data-linenumber="783" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
783
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC783" class="line" lang="cpp"> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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755
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784
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC784" class="line" lang="cpp"> <span class="p">}</span></span>
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756
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785
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC785" class="line" lang="cpp"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="998" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1027" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -998,11 +1027,13 @@ process_paired_reads_parallel(string prefix_1,</td>
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998
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<td class="new_line diff-line-num" data-linenumber="1027" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1027
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1027" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num" data-linenumber="999" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
999
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<td class="new_line diff-line-num" data-linenumber="1028" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1028
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1028" class="line" lang="cpp"> <span class="n" style="color: #333;">r_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">RawRead</span><span class="p">(</span><span class="n" style="color: #333;">seq_init_len_1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">min_bc_size_1</span><span class="p">,</span> <span class="n" style="color: #333;">win_size</span><span class="p">);</span></span>
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1000
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<td class="new_line diff-line-num" data-linenumber="1029" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1029
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1029" class="line" lang="cpp"> <span class="n" style="color: #333;">r_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">RawRead</span><span class="p">(</span><span class="n" style="color: #333;">seq_init_len_2</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">min_bc_size_2</span><span class="p">,</span> <span class="n" style="color: #333;">win_size</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1001" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1001
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<td class="new_line diff-line-num old" data-linenumber="1030" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1001" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="1002" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1030" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1030
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1030" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num" data-linenumber="1002" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1002
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<td class="new_line diff-line-num" data-linenumber="1031" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1031
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1031" class="line" lang="cpp"> <span class="n" style="color: #333;">parse_input_record</span><span class="p">(</span><span class="n" style="color: #333;">s_1</span><span class="p">,</span> <span class="n" style="color: #333;">r_1</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1003" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1003
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<td class="new_line diff-line-num" data-linenumber="1032" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1032
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1032" class="line" lang="cpp"> <span class="n" style="color: #333;">parse_input_record</span><span class="p">(</span><span class="n" style="color: #333;">s_2</span><span class="p">,</span> <span class="n" style="color: #333;">r_2</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1004" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1004
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<td class="new_line diff-line-num" data-linenumber="1033" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1033
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1033" class="line" lang="cpp"> <span class="n" style="color: #333;">cntr</span><span class="p">[</span><span class="s" style="color: #d14;">"total"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1005" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1005
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<td class="new_line diff-line-num" data-linenumber="1034" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1034
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1034" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="1006" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1035" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1035
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1035" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">force_poly_g</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">r_1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">check_poly_g</span><span class="p">())</span> <span class="n" style="color: #333;">check_poly_g</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1036" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1036
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1036" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num" data-linenumber="1006" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1006
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<td class="new_line diff-line-num" data-linenumber="1037" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1037
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1037" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="1007" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1007
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<td class="new_line diff-line-num" data-linenumber="1038" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1038
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1038" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If a BestRAD protocol was used, check which read the barcode/restriction cutsite is on</span></span>
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1008
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<td class="new_line diff-line-num" data-linenumber="1039" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1039
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1039" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// and transpose the reads if necessary.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1201" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1170,7 +1201,7 @@ process_reads(string prefix,</td>
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1170
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1201
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1201" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1171" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1171
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<td class="new_line diff-line-num" data-linenumber="1202" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1202
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1202" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="1172" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1172
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<td class="new_line diff-line-num" data-linenumber="1203" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1203
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1203" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">RawRead</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">min_bc_size_1</span><span class="p">,</span> <span class="n" style="color: #333;">win_size</span><span class="p">);</span></span>
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1173
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1173" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="1174" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1204" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1204
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1204" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num" data-linenumber="1174" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1174
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<td class="new_line diff-line-num" data-linenumber="1205" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1205
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1205" class="line" lang="cpp"> <span class="n" style="color: #333;">BarcodePair</span> <span class="n" style="color: #333;">bc</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1175" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1175
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<td class="new_line diff-line-num" data-linenumber="1206" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1206
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1206" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="1176" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1176
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<td class="new_line diff-line-num" data-linenumber="1207" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1207
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1207" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If no barcodes were specified, set the barcode object to be the input file name so</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1201" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1232" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1201,6 +1232,8 @@ process_reads(string prefix,</td>
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1201
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<td class="new_line diff-line-num" data-linenumber="1232" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1232
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1232" class="line" lang="cpp"></span>
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1202
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<td class="new_line diff-line-num" data-linenumber="1233" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1233
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1233" class="line" lang="cpp"> <span class="n" style="color: #333;">parse_input_record</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">);</span></span>
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1203
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<td class="new_line diff-line-num" data-linenumber="1234" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1234
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1234" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="1204" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1235" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1235
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1235" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">force_poly_g</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">check_poly_g</span><span class="p">())</span> <span class="n" style="color: #333;">check_poly_g</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1236" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1236
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1236" class="line" lang="cpp"> </span>
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1204
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<td class="new_line diff-line-num" data-linenumber="1237" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1237
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1237" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">barcode_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">inline_null</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="old_line diff-line-num" data-linenumber="1205" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1205
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<td class="new_line diff-line-num" data-linenumber="1238" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1238
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1238" class="line" lang="cpp"> <span class="n" style="color: #333;">barcode_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">index_null</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="1206" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1206
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<td class="new_line diff-line-num" data-linenumber="1239" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1239
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1239" class="line" lang="cpp"> <span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">set</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">se_bc</span><span class="p">);</span></span>
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<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1345,9 +1378,18 @@ process_reads_parallel(string prefix,</td>
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1345
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1378
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1378" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1346" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1346
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1379
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1379" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="1347" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1347
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<td class="new_line diff-line-num" data-linenumber="1380" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1380
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1380" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BarcodePair</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">output_thread_map</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1348" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1348
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<td class="new_line diff-line-num old" data-linenumber="1381" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1348" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1349" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1381" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1381
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1381" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1349" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1382" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1382
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1382" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// We must take care because multiple barcodes can point to the same output file,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1349" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1383" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1383
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1383" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// so we must assign all barcodes for a single output file to the same thread for writing.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1384" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1384
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1384" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1385" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1385
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1385" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">fhType</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BarcodePair</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">rev_fh_map</span><span class="p">;</span></span>
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1349
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<td class="new_line diff-line-num" data-linenumber="1386" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1386
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1386" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pair_1_fhs</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">pair_1_fhs</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1350" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1350
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<td class="new_line diff-line-num old" data-linenumber="1387" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1350" class="line" lang="cpp"> <span class="n" style="color: #333;">output_thread_map</span><span class="p">[</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">num_output_threads</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">num_input_threads</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1387" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1387
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1387" class="line" lang="cpp"> <span class="n" style="color: #333;">rev_fh_map</span><span class="p">[</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1388" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1388
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1388" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1351" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1389" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1389
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1389" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1351" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1390" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1390
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1390" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rev_fh_map</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">rev_fh_map</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1391
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1391" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1392" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1392
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1392" class="line" lang="cpp"> <span class="n" style="color: #333;">output_thread_map</span><span class="p">[</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">num_output_threads</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">num_input_threads</span><span class="p">;</span></span>
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1351
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<td class="new_line diff-line-num" data-linenumber="1393" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1393
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1393" class="line" lang="cpp"> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1352
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1394
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1394" class="line" lang="cpp"> <span class="p">}</span></span>
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1353
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1395
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1395" class="line" lang="cpp"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1557" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1599" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1557,6 +1599,8 @@ process_reads_parallel(string prefix,</td>
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1557
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<td class="new_line diff-line-num" data-linenumber="1599" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1599
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1599" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num" data-linenumber="1558" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1558
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<td class="new_line diff-line-num" data-linenumber="1600" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1600
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1600" class="line" lang="cpp"> <span class="n" style="color: #333;">parse_input_record</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1559" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1559
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<td class="new_line diff-line-num" data-linenumber="1601" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1601
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1601" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="1560" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1602" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1602
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1602" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">force_poly_g</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">check_poly_g</span><span class="p">())</span> <span class="n" style="color: #333;">check_poly_g</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1603" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1603
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1603" class="line" lang="cpp"> </span>
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1560
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<td class="new_line diff-line-num" data-linenumber="1604" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1604
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1604" class="line" lang="cpp"> <span class="n" style="color: #333;">bc</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">BarcodePair</span><span class="p">();</span></span>
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<td class="old_line diff-line-num" data-linenumber="1561" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1561
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<td class="new_line diff-line-num" data-linenumber="1605" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1605
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1605" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="1562" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1562
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<td class="new_line diff-line-num" data-linenumber="1606" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1606
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1606" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If no barcodes were specified, set the barcode object to be the input file name so</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1708" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1752" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1708,6 +1752,20 @@ process_singlet(RawRead *href,</td>
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1708
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<td class="new_line diff-line-num" data-linenumber="1752" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1752
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1752" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1709" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1709
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1753
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1753" class="line" lang="cpp"> <span class="p">}</span></span>
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1710
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1754
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1754" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="1711" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1755" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1755
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1755" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1756" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1756
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1756" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Drop this sequence if it has a run of poly-Gs at the 3' end.</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1711" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1757" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1757
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1757" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Either the user has forced the check on, and check_poly_g is true, or we turned it on</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1711" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1758" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1758
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1758" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// internally via href->check_poly_g because of the machine type that generated the data.</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1711" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1759" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1759
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1759" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1711" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1760" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1760
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1760" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">check_poly_g</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">check_poly_g</span><span class="p">())</span> <span class="o" style="font-weight: 600;">&&</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1711" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1761" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1761
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1761" class="line" lang="cpp"> <span class="n" style="color: #333;">check_poly_g_run</span><span class="p">(</span><span class="n" style="color: #333;">href</span><span class="p">,</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">inline_bc_len</span><span class="p">,</span> <span class="n" style="color: #333;">len_limit</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1711" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1762" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1762
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1762" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span><span class="p">[</span><span class="s" style="color: #d14;">"poly_g"</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1711" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1763" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1763
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1763" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">barcode_type</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">null_null</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1711" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1764" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1764
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1764" class="line" lang="cpp"> <span class="n" style="color: #333;">bc_log</span><span class="p">[</span><span class="s" style="color: #d14;">"poly_g"</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1711" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1765" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1765
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1765" class="line" lang="cpp"> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">retain</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1711" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1766" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1766
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1766" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1767" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1767
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1767" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1768" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1768
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1768" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="1711" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1711
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<td class="new_line diff-line-num" data-linenumber="1769" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1769
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1769" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="1712" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1712
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<td class="new_line diff-line-num" data-linenumber="1770" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1770
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1770" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Drop this sequence if it contains adapter sequence.</span></span>
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<td class="old_line diff-line-num" data-linenumber="1713" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1713
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<td class="new_line diff-line-num" data-linenumber="1771" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1771
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1771" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1896" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1954" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1896,6 +1954,7 @@ int dist(const char *res_enz, char *seq) {</td>
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<td class="old_line diff-line-num" data-linenumber="1896" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1896
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<td class="new_line diff-line-num" data-linenumber="1954" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1954
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1954" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="1897" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1897
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<td class="new_line diff-line-num" data-linenumber="1955" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1955
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1955" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span></span>
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<td class="old_line diff-line-num" data-linenumber="1898" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1898
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<td class="new_line diff-line-num" data-linenumber="1956" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1956
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1956" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">print_results</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">argv</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1899" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1957" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1957
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1957" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">out_basename</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="1899" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1899
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<td class="new_line diff-line-num" data-linenumber="1958" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1958
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1958" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BarcodePair</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">barcodes</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="1900" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1900
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<td class="new_line diff-line-num" data-linenumber="1959" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1959
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1959" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">counters</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="1901" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1901
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<td class="new_line diff-line-num" data-linenumber="1960" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1960
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1960" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BarcodePair</span><span class="p">,</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">barcode_log</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1903" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1962" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1903,9 +1962,12 @@ print_results(int argc, char **argv,</td>
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<td class="old_line diff-line-num" data-linenumber="1903" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1903
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<td class="new_line diff-line-num" data-linenumber="1962" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1962
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1962" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1904" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1904
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<td class="new_line diff-line-num" data-linenumber="1963" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1963
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1963" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="1905" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1905
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<td class="new_line diff-line-num" data-linenumber="1964" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1964
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1964" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">log_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"process_radtags.log"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1906" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1906
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<td class="new_line diff-line-num old" data-linenumber="1965" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1906" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">in_path_1</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1907" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1965" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1965
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1965" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="1907" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1966" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1966
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1966" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">in_path_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">InputT</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">directory</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1907" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1967" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1967
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1967" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="1907" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1907
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<td class="new_line diff-line-num" data-linenumber="1968" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1968
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1968" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// In directory mode, use `$out_path/process_radtags.$(basename $in_path).log`.</span></span>
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<td class="old_line diff-line-num" data-linenumber="1908" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1908
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<td class="new_line diff-line-num" data-linenumber="1969" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1969
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1969" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// For consistency we always use realpath().</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1909" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1970" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1970
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1970" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="1909" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1909
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<td class="new_line diff-line-num" data-linenumber="1971" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1971
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1971" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">abspath</span> <span class="p">[</span><span class="n" style="color: #333;">PATH_MAX</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="1910" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1910
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<td class="new_line diff-line-num" data-linenumber="1972" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1972
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1972" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">realpath</span><span class="p">(</span><span class="n" style="color: #333;">in_path_1</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">abspath</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1911" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1911
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<td class="new_line diff-line-num" data-linenumber="1973" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1973
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1973" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rv</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1917" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1979" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1917,6 +1979,13 @@ print_results(int argc, char **argv,</td>
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<td class="old_line diff-line-num" data-linenumber="1917" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1917
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<td class="new_line diff-line-num" data-linenumber="1979" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1979
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1979" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abspath_s</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="sc" style="color: #d14;">'/'</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1918" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1918
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<td class="new_line diff-line-num" data-linenumber="1980" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1980
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1980" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">in_dir_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abspath_s</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1919" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1919
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<td class="new_line diff-line-num" data-linenumber="1981" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1981
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1981" class="line" lang="cpp"> <span class="n" style="color: #333;">log_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"process_radtags."</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">in_dir_name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".log"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1920" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1982" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1982
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1982" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num new" data-linenumber="1920" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1983" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1983
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1983" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">in_path_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">InputT</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">files</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">out_basename</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1920" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1984" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1984
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1984" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1920" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1985" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1985
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1985" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// We are executing on a single (-f) or pair of files (-1/-2), and user has</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1920" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1986" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1986
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1986" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// supplied an output basename.</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1920" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1987" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1987
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1987" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1920" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1988" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1988
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1988" class="line" lang="cpp"> <span class="n" style="color: #333;">log_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">out_basename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".log"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1920" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1920
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<td class="new_line diff-line-num" data-linenumber="1989" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1989
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1989" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1921" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1921
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<td class="new_line diff-line-num" data-linenumber="1990" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1990
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1990" class="line" lang="cpp"> <span class="n" style="color: #333;">ofstream</span> <span class="nf" style="color: #900; font-weight: 600;">log</span><span class="p">(</span><span class="n" style="color: #333;">log_path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<td class="old_line diff-line-num" data-linenumber="1922" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1922
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<td class="new_line diff-line-num" data-linenumber="1991" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1991
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1991" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1943" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2012" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1943,8 +2012,10 @@ print_results(int argc, char **argv,</td>
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<td class="old_line diff-line-num" data-linenumber="1943" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1943
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<td class="new_line diff-line-num" data-linenumber="2012" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2012
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2012" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Adapter Seq"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1944" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1944
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<td class="new_line diff-line-num" data-linenumber="2013" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2013
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2013" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bestrad</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="1945" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1945
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<td class="new_line diff-line-num" data-linenumber="2014" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2014
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2014" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Transposed Reads"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1946" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1946
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<td class="new_line diff-line-num old" data-linenumber="2015" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1946" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Low Quality</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1947" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1947
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<td class="new_line diff-line-num old" data-linenumber="2015" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1947" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Barcode Not Found</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1948" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2015" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2015
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2015" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Low Quality</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1948" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2016" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2016
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2016" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">check_poly_g</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1948" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2017" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2017
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2017" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Poly-G</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1948" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2018" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2018
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2018" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Barcode Not Found</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="1948" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1948
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<td class="new_line diff-line-num" data-linenumber="2019" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2019
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2019" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"RAD cutsite Not Found</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="1949" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1949
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<td class="new_line diff-line-num" data-linenumber="2020" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2020
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2020" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Total</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1950" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1950
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<td class="new_line diff-line-num" data-linenumber="2021" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2021
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2021" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1957" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2028" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1957,8 +2028,10 @@ print_results(int argc, char **argv,</td>
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<td class="old_line diff-line-num" data-linenumber="1957" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1957
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<td class="new_line diff-line-num" data-linenumber="2028" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2028
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2028" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"adapter"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1958" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1958
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<td class="new_line diff-line-num" data-linenumber="2029" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2029
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2029" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bestrad</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="1959" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1959
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<td class="new_line diff-line-num" data-linenumber="2030" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2030
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2030" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"transposed"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1960" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1960
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<td class="new_line diff-line-num old" data-linenumber="2031" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1960" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"low_quality"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1961" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1961
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<td class="new_line diff-line-num old" data-linenumber="2031" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1961" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"ambiguous"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1962" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2031" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2031
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2031" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"low_quality"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1962" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2032" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2032
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2032" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">check_poly_g</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1962" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2033" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2033
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2033" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"poly_g"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1962" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="2034" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2034
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2034" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"ambiguous"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="1962" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1962
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<td class="new_line diff-line-num" data-linenumber="2035" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2035
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2035" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"noradtag"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="1963" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1963
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<td class="new_line diff-line-num" data-linenumber="2036" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2036
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2036" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"total"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1964" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1964
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<td class="new_line diff-line-num" data-linenumber="2037" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2037
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2037" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1967" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2040" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1967,6 +2040,7 @@ print_results(int argc, char **argv,</td>
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<td class="old_line diff-line-num" data-linenumber="1967" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1967
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<td class="new_line diff-line-num" data-linenumber="2040" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2040
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2040" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1968" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1968
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<td class="new_line diff-line-num" data-linenumber="2041" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2041
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2041" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"total"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1969" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1969
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<td class="new_line diff-line-num" data-linenumber="2042" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2042
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2042" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"low_quality"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1970" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="2043" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2043
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2043" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"poly_g"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1970" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1970
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<td class="new_line diff-line-num" data-linenumber="2044" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2044
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2044" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"adapter"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1971" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1971
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<td class="new_line diff-line-num" data-linenumber="2045" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2045
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2045" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"ill_filtered"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1972" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1972
</td>
<td class="new_line diff-line-num" data-linenumber="2046" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2046
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2046" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"ambiguous"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1981" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2055" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1981,6 +2055,7 @@ print_results(int argc, char **argv,</td>
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<td class="old_line diff-line-num" data-linenumber="1981" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1981
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<td class="new_line diff-line-num" data-linenumber="2055" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2055
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2055" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"total"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"total"</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="1982" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1982
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<td class="new_line diff-line-num" data-linenumber="2056" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2056
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2056" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"ill_filtered"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"ill_filtered"</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="1983" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1983
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<td class="new_line diff-line-num" data-linenumber="2057" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2057
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2057" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"low_quality"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"low_quality"</span><span class="p">];</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1984" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="2058" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2058
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2058" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"poly_g"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"poly_g"</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="1984" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1984
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<td class="new_line diff-line-num" data-linenumber="2059" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2059
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2059" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"adapter"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"adapter"</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="1985" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1985
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<td class="new_line diff-line-num" data-linenumber="2060" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2060
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2060" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"ambiguous"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"ambiguous"</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="1986" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1986
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<td class="new_line diff-line-num" data-linenumber="2061" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2061
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2061" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"noradtag"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">[</span><span class="s" style="color: #d14;">"noradtag"</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2005" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2080" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2005,6 +2080,7 @@ print_results(int argc, char **argv,</td>
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<td class="old_line diff-line-num" data-linenumber="2005" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2005
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<td class="new_line diff-line-num" data-linenumber="2080" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2080
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2080" class="line" lang="cpp"> <span class="n" style="color: #333;">print_nreads</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"adapter"</span><span class="p">],</span> <span class="s" style="color: #d14;">"reads contained adapter sequence"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="2006" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2006
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<td class="new_line diff-line-num" data-linenumber="2081" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2081
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2081" class="line" lang="cpp"> <span class="n" style="color: #333;">print_nreads</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"ambiguous"</span><span class="p">],</span> <span class="s" style="color: #d14;">"barcode not found drops"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="2007" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2007
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<td class="new_line diff-line-num" data-linenumber="2082" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2082
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2082" class="line" lang="cpp"> <span class="n" style="color: #333;">print_nreads</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"low_quality"</span><span class="p">],</span> <span class="s" style="color: #d14;">"low quality read drops"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2008" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="2083" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2083
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2083" class="line" lang="cpp"> <span class="n" style="color: #333;">print_nreads</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"poly_g"</span><span class="p">],</span> <span class="s" style="color: #d14;">"poly-G run drops"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="2008" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2008
</td>
<td class="new_line diff-line-num" data-linenumber="2084" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2084
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2084" class="line" lang="cpp"> <span class="n" style="color: #333;">print_nreads</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"noradtag"</span><span class="p">],</span> <span class="s" style="color: #d14;">"RAD cutsite not found drops"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="2009" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2009
</td>
<td class="new_line diff-line-num" data-linenumber="2085" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2085
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2085" class="line" lang="cpp"> <span class="n" style="color: #333;">print_nreads</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"retained"</span><span class="p">],</span> <span class="s" style="color: #d14;">"retained reads"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="2010" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2010
</td>
<td class="new_line diff-line-num" data-linenumber="2086" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2086
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2086" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2031" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2107" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2031,8 +2107,10 @@ print_results(int argc, char **argv,</td>
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<td class="old_line diff-line-num" data-linenumber="2031" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2031
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<td class="new_line diff-line-num" data-linenumber="2107" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2107
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2107" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filter_adapter</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="2032" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2032
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<td class="new_line diff-line-num" data-linenumber="2108" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2108
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2108" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Reads containing adapter sequence</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"adapter"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">as_percentage</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"adapter"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"total"</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2033" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2033
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<td class="new_line diff-line-num" data-linenumber="2109" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2109
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2109" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Barcode Not Found</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"ambiguous"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">as_percentage</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"ambiguous"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"total"</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2034" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2034
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<td class="new_line diff-line-num old" data-linenumber="2110" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2034" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Low Quality</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"low_quality"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">as_percentage</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"low_quality"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"total"</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2035" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2035
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<td class="new_line diff-line-num old" data-linenumber="2110" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2035" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"RAD Cutsite Not Found</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"noradtag"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">as_percentage</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"noradtag"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"total"</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2036" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2110" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2110
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2110" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Low Quality</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"low_quality"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">as_percentage</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"low_quality"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"total"</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2036" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2111" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2111
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2111" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">check_poly_g</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2036" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2112" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2112
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2112" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Poly-G Runs</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"poly_g"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">as_percentage</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"poly_g"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"total"</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2036" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2113" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2113
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2113" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"RAD Cutsite Not Found</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"noradtag"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">as_percentage</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"noradtag"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"total"</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2036" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2036
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<td class="new_line diff-line-num" data-linenumber="2114" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2114
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2114" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Retained Reads</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"retained"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">as_percentage</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"retained"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"total"</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2037" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2037
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<td class="new_line diff-line-num" data-linenumber="2115" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2115
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2115" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">paired</span><span class="p">)</span> </span>
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<td class="old_line diff-line-num" data-linenumber="2038" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2038
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<td class="new_line diff-line-num" data-linenumber="2116" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2116
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2116" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Properly Paired</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"proppair"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">as_percentage</span><span class="p">(((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"proppair"</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">2.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"total"</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2060" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2138" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2060,8 +2138,10 @@ print_results(int argc, char **argv,</td>
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<td class="old_line diff-line-num" data-linenumber="2060" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2060
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<td class="new_line diff-line-num" data-linenumber="2138" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2138
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2138" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Filename</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2061" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2061
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<td class="new_line diff-line-num" data-linenumber="2139" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2139
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2139" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Total</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2062" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2062
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<td class="new_line diff-line-num" data-linenumber="2140" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2140
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2140" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"RAD Cutsite Not Found</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2063" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2063
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<td class="new_line diff-line-num old" data-linenumber="2141" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2063" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Low Quality</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2064" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2064
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<td class="new_line diff-line-num old" data-linenumber="2141" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2064" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Retained Reads</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2065" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2141" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2141
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2141" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Low Quality</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2065" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2142" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2142
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2142" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">check_poly_g</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2065" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2143" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2143
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2143" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Poly-G Runs</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2065" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2144" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2144
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2144" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Retained Reads</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2065" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2065
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<td class="new_line diff-line-num" data-linenumber="2145" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2145
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2145" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Pct Retained</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2066" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2066
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<td class="new_line diff-line-num" data-linenumber="2146" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2146
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2146" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">paired</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="2067" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2067
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<td class="new_line diff-line-num" data-linenumber="2147" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2147
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2147" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Properly Paired</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2078" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2158" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2078,11 +2158,13 @@ print_results(int argc, char **argv,</td>
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2078
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<td class="new_line diff-line-num" data-linenumber="2158" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2158
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2158" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">barcodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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2079
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<td class="new_line diff-line-num" data-linenumber="2159" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2159
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2159" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="2080" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2080
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<td class="new_line diff-line-num" data-linenumber="2160" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2160
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2160" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">barcode_log</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">barcodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2081" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2081
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<td class="new_line diff-line-num old" data-linenumber="2161" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2081" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"0</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2082" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2161" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2161
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2161" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;"><span class="idiff left addition" style="background-color: #c7f0d2;">"0</span></span><span class="se" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">\t</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;"><<</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="s" style="color: #d14;">"0</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2082" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2082
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<td class="new_line diff-line-num" data-linenumber="2162" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2162
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2162" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="2083" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2083
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<td class="new_line diff-line-num" data-linenumber="2163" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2163
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2163" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">barcode_log</span><span class="p">[</span><span class="n" style="color: #333;">barcodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]][</span><span class="s" style="color: #d14;">"total"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2084" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2084
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<td class="new_line diff-line-num old" data-linenumber="2164" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2084" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">barcode_log</span><span class="p">[</span><span class="n" style="color: #333;">barcodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]][</span><span class="s" style="color: #d14;">"noradtag"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2085" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2085
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<td class="new_line diff-line-num old" data-linenumber="2164" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2085" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">barcode_log</span><span class="p">[</span><span class="n" style="color: #333;">barcodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]][</span><span class="s" style="color: #d14;">"low_qual"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2086" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2164" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2164
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2164" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">barcode_log</span><span class="p">[</span><span class="n" style="color: #333;">barcodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]][</span><span class="s" style="color: #d14;">"noradtag"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2086" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2165" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2165
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2165" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">check_poly_g</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2086" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2166" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2166
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2166" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">barcode_log</span><span class="p">[</span><span class="n" style="color: #333;">barcodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]][</span><span class="s" style="color: #d14;">"poly_g"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2086" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2167" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2167
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2167" class="line" lang="cpp"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">barcode_log</span><span class="p">[</span><span class="n" style="color: #333;">barcodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]][</span><span class="s" style="color: #d14;">"low_qual"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2086" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2086
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<td class="new_line diff-line-num" data-linenumber="2168" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2168
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2168" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">barcode_log</span><span class="p">[</span><span class="n" style="color: #333;">barcodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]][</span><span class="s" style="color: #d14;">"retained"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2087" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2087
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<td class="new_line diff-line-num" data-linenumber="2169" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2169
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2169" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">as_percentage</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">barcode_log</span><span class="p">[</span><span class="n" style="color: #333;">barcodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]][</span><span class="s" style="color: #d14;">"retained"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">barcode_log</span><span class="p">[</span><span class="n" style="color: #333;">barcodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]][</span><span class="s" style="color: #d14;">"total"</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2088" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2088
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<td class="new_line diff-line-num" data-linenumber="2170" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2170
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2170" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">paired</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2142" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2224" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2142,6 +2224,8 @@ int parse_command_line(int argc, char* argv[]) {</td>
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<td class="old_line diff-line-num" data-linenumber="2142" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2142
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<td class="new_line diff-line-num" data-linenumber="2224" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2224
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2224" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"interleaved"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'I'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="2143" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2143
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<td class="new_line diff-line-num" data-linenumber="2225" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2225
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2225" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"merge"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'m'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="2144" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2144
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<td class="new_line diff-line-num" data-linenumber="2226" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2226
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2226" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"disable-rad-check"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'R'</span><span class="p">},</span> <span class="p">{</span><span class="s" style="color: #d14;">"disable_rad_check"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'R'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2145" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2227" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2227
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2227" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"disable-poly-g-check"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">1004</span><span class="p">},</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2145" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2228" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2228
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2228" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"force-poly-g-check"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">1005</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="2145" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2145
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<td class="new_line diff-line-num" data-linenumber="2229" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2229
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2229" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"filter-illumina"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'F'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="2146" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2146
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<td class="new_line diff-line-num" data-linenumber="2230" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2230
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2230" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"retain-header"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'H'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="2147" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2147
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<td class="new_line diff-line-num" data-linenumber="2231" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2231
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2231" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"bestrad"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">1000</span><span class="p">},</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2160" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2244" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2160,6 +2244,7 @@ int parse_command_line(int argc, char* argv[]) {</td>
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<td class="old_line diff-line-num" data-linenumber="2160" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2160
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<td class="new_line diff-line-num" data-linenumber="2244" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2244
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2244" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"file"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'f'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="2161" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2161
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<td class="new_line diff-line-num" data-linenumber="2245" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2245
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2245" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"file-p1"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'1'</span><span class="p">},</span> <span class="p">{</span><span class="s" style="color: #d14;">"file_p1"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'1'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="2162" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2162
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<td class="new_line diff-line-num" data-linenumber="2246" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2246
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2246" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"file-p2"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'2'</span><span class="p">},</span> <span class="p">{</span><span class="s" style="color: #d14;">"file_p2"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'2'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2163" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2247" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2247
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2247" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"basename"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">1003</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="2163" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2163
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<td class="new_line diff-line-num" data-linenumber="2248" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2248
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2248" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"in-path"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'p'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="2164" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2164
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<td class="new_line diff-line-num" data-linenumber="2249" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2249
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2249" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"out-path"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="2165" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2165
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<td class="new_line diff-line-num" data-linenumber="2250" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2250
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2250" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"truncate"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'t'</span><span class="p">},</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2224" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2309" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2224,8 +2309,9 @@ int parse_command_line(int argc, char* argv[]) {</td>
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<td class="old_line diff-line-num" data-linenumber="2224" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2224
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<td class="new_line diff-line-num" data-linenumber="2309" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2309
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2309" class="line" lang="cpp"> <span class="n" style="color: #333;">in_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2225" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2225
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<td class="new_line diff-line-num" data-linenumber="2310" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2310
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2310" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2226" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2226
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<td class="new_line diff-line-num" data-linenumber="2311" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2311
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2311" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'p'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2227" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2227
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<td class="new_line diff-line-num old" data-linenumber="2312" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2227" class="line" lang="cpp"> <span class="n" style="color: #333;">in_path_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2228" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2228
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<td class="new_line diff-line-num old" data-linenumber="2312" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2228" class="line" lang="cpp"> <span class="n" style="color: #333;">in_path_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">in_path_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2229" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2312" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2312
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2312" class="line" lang="cpp"> <span class="n" style="color: #333;">in_path_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2229" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2313" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2313
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2313" class="line" lang="cpp"> <span class="n" style="color: #333;">in_path_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">in_path_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2229" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2314" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2314
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2314" class="line" lang="cpp"> <span class="n" style="color: #333;">in_path_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">InputT</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">directory</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2229" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2229
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<td class="new_line diff-line-num" data-linenumber="2315" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2315
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2315" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2230" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2230
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<td class="new_line diff-line-num" data-linenumber="2316" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2316
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2316" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'1'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="2231" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2231
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<td class="new_line diff-line-num" data-linenumber="2317" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2317
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2317" class="line" lang="cpp"> <span class="n" style="color: #333;">paired</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2235" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2321" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2235,6 +2321,9 @@ int parse_command_line(int argc, char* argv[]) {</td>
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<td class="old_line diff-line-num" data-linenumber="2235" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2235
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<td class="new_line diff-line-num" data-linenumber="2321" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2321
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2321" class="line" lang="cpp"> <span class="n" style="color: #333;">paired</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2236" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2236
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<td class="new_line diff-line-num" data-linenumber="2322" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2322
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2322" class="line" lang="cpp"> <span class="n" style="color: #333;">in_file_p2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2237" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2237
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<td class="new_line diff-line-num" data-linenumber="2323" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2323
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2323" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2238" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2324" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2324
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2324" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">1003</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2238" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2325" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2325
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2325" class="line" lang="cpp"> <span class="n" style="color: #333;">out_basename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2238" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2326" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2326
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2326" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2238" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2238
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<td class="new_line diff-line-num" data-linenumber="2327" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2327
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2327" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'P'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="2239" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2239
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<td class="new_line diff-line-num" data-linenumber="2328" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2328
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2328" class="line" lang="cpp"> <span class="n" style="color: #333;">paired</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2240" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2240
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<td class="new_line diff-line-num" data-linenumber="2329" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2329
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2329" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2293" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2382" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2293,6 +2382,14 @@ int parse_command_line(int argc, char* argv[]) {</td>
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<td class="old_line diff-line-num" data-linenumber="2293" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2293
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<td class="new_line diff-line-num" data-linenumber="2382" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2382
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2382" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'R'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="2294" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2294
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<td class="new_line diff-line-num" data-linenumber="2383" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2383
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2383" class="line" lang="cpp"> <span class="n" style="color: #333;">check_radtag</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2295" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2295
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<td class="new_line diff-line-num" data-linenumber="2384" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2384
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2384" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2296" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2385" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2385
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2385" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">1004</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2296" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2386" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2386
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2386" class="line" lang="cpp"> <span class="n" style="color: #333;">force_poly_g</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2296" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2387" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2387
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2387" class="line" lang="cpp"> <span class="n" style="color: #333;">check_poly_g</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2296" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2388" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2388
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2388" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2296" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2389" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2389
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2389" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">1005</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2296" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2390" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2390
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2390" class="line" lang="cpp"> <span class="n" style="color: #333;">force_poly_g</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2296" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2391" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2391
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2391" class="line" lang="cpp"> <span class="n" style="color: #333;">check_poly_g</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2296" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2392" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2392
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2392" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2296" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2296
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<td class="new_line diff-line-num" data-linenumber="2393" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2393
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2393" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'F'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="2297" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2297
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<td class="new_line diff-line-num" data-linenumber="2394" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2394
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2394" class="line" lang="cpp"> <span class="n" style="color: #333;">filter_illumina</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2298" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2298
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<td class="new_line diff-line-num" data-linenumber="2395" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2395
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2395" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2388" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2485" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2388,6 +2485,11 @@ int parse_command_line(int argc, char* argv[]) {</td>
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<td class="old_line diff-line-num" data-linenumber="2388" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2388
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<td class="new_line diff-line-num" data-linenumber="2485" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2485
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2485" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">in_path_2</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">in_path_2</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">in_path_2</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'/'</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="2389" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2389
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<td class="new_line diff-line-num" data-linenumber="2486" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2486
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2486" class="line" lang="cpp"> <span class="n" style="color: #333;">in_path_2</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"/"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2390" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2390
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<td class="new_line diff-line-num" data-linenumber="2487" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2487
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2487" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="2391" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2488" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2488
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2488" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">in_path_1</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">out_basename</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2489" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2489
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2489" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"You can only specify --basename with the -f or -1/-2 options.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2490" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2490
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2490" class="line" lang="cpp"> <span class="n" style="color: #333;">help</span><span class="p">();</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2391" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2491" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2491
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2491" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2492" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2492
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2492" class="line" lang="cpp"> </span>
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<td class="old_line diff-line-num" data-linenumber="2391" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2391
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<td class="new_line diff-line-num" data-linenumber="2493" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2493
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2493" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_path</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="2392" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2392
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<td class="new_line diff-line-num" data-linenumber="2494" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2494
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2494" class="line" lang="cpp"> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"."</span><span class="p">;</span></span>
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2393
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2495
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2495" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2477" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2579" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2477,19 +2579,18 @@ void help() {</td>
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<td class="old_line diff-line-num" data-linenumber="2477" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2477
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<td class="new_line diff-line-num" data-linenumber="2579" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2579
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2579" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -p,--in-path: path to a directory of files.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2478" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2478
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<td class="new_line diff-line-num" data-linenumber="2580" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2580
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2580" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -P,--paired: files contained within the directory are paired.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2479" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2479
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<td class="new_line diff-line-num" data-linenumber="2581" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2581
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2581" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -I,--interleaved: specify that the paired-end reads are interleaved in single files.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2480" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2480
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<td class="new_line diff-line-num old" data-linenumber="2582" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2480" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -i,--in-type: input file type, either 'fastq', 'gzfastq' (gzipped fastq), 'bam', or 'bustard' (default: guess, or gzfastq if unable to).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2481" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2481
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<td class="new_line diff-line-num" data-linenumber="2582" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2582
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2582" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -b,--barcodes: path to a file containing barcodes for this run, omit to ignore any barcoding or for already demultiplexed data.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2482" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2482
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<td class="new_line diff-line-num old" data-linenumber="2583" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2482" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -o,--out-path: path to output the processed files.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2483" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2483
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<td class="new_line diff-line-num" data-linenumber="2583" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2583
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2583" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -f: path to the input file if processing single-end sequences.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2484" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2484
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<td class="new_line diff-line-num" data-linenumber="2584" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2584
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2584" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -1: first input file in a set of paired-end sequences.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2485" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2485
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<td class="new_line diff-line-num" data-linenumber="2585" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2585
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2585" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -2: second input file in a set of paired-end sequences.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2486" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2586" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2586
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2586" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -o,--out-path: path to output the processed files.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2486" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2587" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2587
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2587" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --basename: specify the prefix of the output files when using -f or -1/-2.</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2486" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2486
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<td class="new_line diff-line-num" data-linenumber="2588" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2588
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2588" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --threads: number of threads to run.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2487" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2487
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<td class="new_line diff-line-num" data-linenumber="2589" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2589
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2589" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -c,--clean: clean data, remove any read with an uncalled base ('N').</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2488
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<td class="new_line diff-line-num" data-linenumber="2590" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2590
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2590" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -q,--quality: discard reads with low quality (phred) scores.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2489" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2489
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<td class="new_line diff-line-num" data-linenumber="2591" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2591
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2591" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -r,--rescue: rescue barcodes and RAD-Tag cut sites.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2490
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<td class="new_line diff-line-num" data-linenumber="2592" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2592
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2592" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -t,--truncate: truncate final read length to this value.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2491" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2491
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<td class="new_line diff-line-num" data-linenumber="2593" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2593
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2593" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -D,--discards: capture discarded reads to a file.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2492" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2492
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<td class="new_line diff-line-num old" data-linenumber="2594" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2492" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -y,--out-type: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default: match input type).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2493
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<td class="new_line diff-line-num" data-linenumber="2594" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2594
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2594" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2494" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2494
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<td class="new_line diff-line-num" data-linenumber="2595" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2595
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2595" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Barcode options:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2495" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2495
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<td class="new_line diff-line-num" data-linenumber="2596" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2596
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2596" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --inline-null: barcode is inline with sequence, occurs only on single-end read (default).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2531" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2632" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2531,12 +2632,16 @@ void help() {</td>
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<td class="old_line diff-line-num" data-linenumber="2531" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2531
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<td class="new_line diff-line-num" data-linenumber="2632" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2632
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2632" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --adapter-1 <sequence>: provide adaptor sequence that may occur on the single-end read for filtering.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2532" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2532
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<td class="new_line diff-line-num" data-linenumber="2633" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2633
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2633" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --adapter-2 <sequence>: provide adaptor sequence that may occur on the paired-read for filtering.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2533" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2533
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<td class="new_line diff-line-num" data-linenumber="2634" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2634
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2634" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --adapter-mm <mismatches>: number of mismatches allowed in the adapter sequence.</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2534" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2534
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<td class="new_line diff-line-num old" data-linenumber="2635" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2534" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Output options:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2535" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2635" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2635
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2635" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Input/Output options:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2535" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2636" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2636
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2636" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --in-type: input file type, either 'fastq', 'gzfastq' (gzipped fastq), 'bam', or 'bustard' (default: guess, or gzfastq if unable to).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2535" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2637" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2637
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2637" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --out-type: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default: match input type).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2535" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2535
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<td class="new_line diff-line-num" data-linenumber="2638" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2638
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2638" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --retain-header: retain unmodified FASTQ headers in the output.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2536" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2536
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<td class="new_line diff-line-num" data-linenumber="2639" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2639
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2639" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --merge: if no barcodes are specified, merge all input files into a single output file.</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2537" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2537
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<td class="new_line diff-line-num" data-linenumber="2640" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2640
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2640" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Advanced options:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2538" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2538
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<td class="new_line diff-line-num" data-linenumber="2641" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2641
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2641" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2539" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2539
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<td class="new_line diff-line-num" data-linenumber="2642" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2642
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2642" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --disable-rad-check: disable checking if the RAD cut site is intact.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2540" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2643" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2643
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2643" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --force-poly-g-check: force a check for runs of poly-Gs (default: autodetect based on machine type in FASTQ header).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2540" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2644" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2644
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2644" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --disable-poly-g-check: disable checking for runs of poly-Gs (default: autodetect based on machine type in FASTQ header).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2540
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2645
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2645" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --encoding: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2541" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2541
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<td class="new_line diff-line-num" data-linenumber="2646" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2646
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2646" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --window-size: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2542" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2542
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<td class="new_line diff-line-num" data-linenumber="2647" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2647
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2647" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --score-limit: set the phred score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#dc87fdb3f7c40b9a1ff34020178c9c55c2c063f7"><strong style="font-weight: 600;">src/process_radtags.h</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="92" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="92" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -92,7 +92,7 @@ int check_for_transposed_reads(RawRead *, RawRead *, string);</td>
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<td class="old_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
92
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<td class="new_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
92
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC92" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">correct_radtag</span><span class="p">(</span><span class="n" style="color: #333;">RawRead</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
93
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<td class="new_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
93
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC93" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">check_quality_scores</span><span class="p">(</span><span class="n" style="color: #333;">RawRead</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
94
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<td class="new_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
94
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC94" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">dist</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
95
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<td class="new_line diff-line-num old" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC95" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">print_results</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BarcodePair</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BarcodePair</span><span class="p">,</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
95
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC95" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">print_results</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left addition" style="background-color: #c7f0d2;">string</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BarcodePair</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BarcodePair</span><span class="p">,</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
96
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<td class="new_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
96
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC96" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
97
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<td class="new_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
97
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC97" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">compare_barcodes</span><span class="p">(</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BarcodePair</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">,</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BarcodePair</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC98" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#fd57d93bef1cff07dc69b266458b5e78af39be25"><strong style="font-weight: 600;">src/process_shortreads.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -31,12 +31,14 @@</td>
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<td class="old_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC31" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
32
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<td class="new_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
32
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC32" class="line" lang="cpp"><span class="n" style="color: #333;">FileT</span> <span class="n" style="color: #333;">in_file_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FileT</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unknown</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
33
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<td class="new_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
33
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC33" class="line" lang="cpp"><span class="n" style="color: #333;">FileT</span> <span class="n" style="color: #333;">out_file_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FileT</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unknown</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
34
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC34" class="line" lang="cpp"><span class="n" style="color: #333;">InputT</span> <span class="n" style="color: #333;">in_path_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">InputT</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">files</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
34
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<td class="new_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
35
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC35" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">in_file</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
35
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<td class="new_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
36
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC36" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">in_file_p1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
36
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<td class="new_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
37
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC37" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">in_file_p2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
37
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<td class="new_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
38
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC38" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">in_path_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
38
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<td class="new_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
39
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC39" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">in_path_2</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
39
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<td class="new_line diff-line-num" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
40
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC40" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">out_path</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
41
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC41" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">out_basename</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
40
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<td class="new_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
42
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC42" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">barcode_file</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
41
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<td class="new_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
43
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC43" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">adapter_1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
42
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<td class="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
44
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC44" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">adapter_2</span><span class="p">;</span></span>
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<li id="a229ae1cb4c1ccb3f041e58c9ac02711c0114043">
<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#a229ae1cb4c1ccb3f041e58c9ac02711c0114043"><strong style="font-weight: 600;">src/sstacks.cc</strong></a>
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1
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<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-</span></span>
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<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2
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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3
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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2010-202<span class="idiff left right deletion" style="background-color: #fac5cd;">3</span>, Julian Catchen <jcatchen@illinois.edu></span></span>
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<td class="old_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2010-202<span class="idiff left right addition" style="background-color: #c7f0d2;">4</span>, Julian Catchen <jcatchen@illinois.edu></span></span>
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4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// This file is part of Stacks.</span></span>
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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6
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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1298" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1298" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1298,21 +1298,21 @@ int parse_command_line(int argc, char* argv[]) {</td>
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<td class="old_line diff-line-num" data-linenumber="1298" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1298
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<td class="new_line diff-line-num" data-linenumber="1298" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1298
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1298" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"help"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'h'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="1299" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1299
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<td class="new_line diff-line-num" data-linenumber="1299" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1299
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1299" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"version"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'v'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="1300" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1300
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<td class="new_line diff-line-num" data-linenumber="1300" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1300
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1300" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"aligned"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'g'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1301" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1301
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<td class="new_line diff-line-num old" data-linenumber="1301" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1301" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"verify-hap"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'x'</span><span class="p">},</span><span class="idiff left deletion" style="background-color: #fac5cd;"> </span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"verify_hap"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">no_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'x'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">},</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="1302" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1302
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<td class="new_line diff-line-num old" data-linenumber="1301" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1302" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"uniq-haplotypes"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'u'</span><span class="p">},</span><span class="idiff left deletion" style="background-color: #fac5cd;"> </span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"uniq_haplotypes"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">no_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'u'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">},</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="1303" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1303
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<td class="new_line diff-line-num old" data-linenumber="1301" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1303" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"disable-gapped"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'G'</span><span class="p">},</span><span class="idiff left deletion" style="background-color: #fac5cd;"> </span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"disable_gapped"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">no_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'G'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">},</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="1304" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1304
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<td class="new_line diff-line-num old" data-linenumber="1301" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1304" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"threads"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'<span class="idiff left right deletion" style="background-color: #fac5cd;">p</span>'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1305" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1301" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1301
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1301" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"verify-hap"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'x'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1305" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1302" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1302
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1302" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"uniq-haplotypes"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'u'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1305" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1303" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1303
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1303" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"disable-gapped"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'G'</span><span class="p">},</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1304" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1304
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1304" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"threads"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'<span class="idiff left right addition" style="background-color: #c7f0d2;">t</span>'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="1305" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1305
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<td class="new_line diff-line-num" data-linenumber="1305" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1305
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1305" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"catalog"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'c'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="1306" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1306
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<td class="new_line diff-line-num" data-linenumber="1306" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1306
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1306" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sample"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'s'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1307" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1307
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<td class="new_line diff-line-num old" data-linenumber="1307" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1307" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"out-path"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">},</span><span class="idiff left deletion" style="background-color: #fac5cd;"> </span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"out_path"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">required_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'o'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">},</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="1308" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1308
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<td class="new_line diff-line-num old" data-linenumber="1307" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1308" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"in-path"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'P'</span><span class="p">},</span><span class="idiff left deletion" style="background-color: #fac5cd;"> </span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"in_path"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">required_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'P'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">},</span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="1309" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1307" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1307
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1307" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"out-path"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1309" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1308" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1308
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1308" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"in-path"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'P'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="1309" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1309
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<td class="new_line diff-line-num" data-linenumber="1309" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1309
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1309" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"popmap"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'M'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="1310" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1310
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<td class="new_line diff-line-num" data-linenumber="1310" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1310
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1310" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"write-all-matches"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">2001</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="1311" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1311
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<td class="new_line diff-line-num" data-linenumber="1311" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1311
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1311" class="line" lang="cpp"> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1312" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1312
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<td class="new_line diff-line-num" data-linenumber="1312" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1312
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1312" class="line" lang="cpp"> <span class="p">};</span></span>
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<td class="old_line diff-line-num" data-linenumber="1313" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1313
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<td class="new_line diff-line-num" data-linenumber="1313" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1313
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1313" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="1314" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1314
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<td class="new_line diff-line-num" data-linenumber="1314" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1314
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1314" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">option_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1315" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1315
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<td class="new_line diff-line-num old" data-linenumber="1315" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1315" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt_long</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"hgGxuvs:c:o:p:P:M:"</span><span class="p">,</span> <span class="n" style="color: #333;">long_options</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">option_index</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1315" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1315
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1315" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt_long</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"hgGxuvs:c:o:p:<span class="idiff left right addition" style="background-color: #c7f0d2;">t:</span>P:M:"</span><span class="p">,</span> <span class="n" style="color: #333;">long_options</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">option_index</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1316" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1316
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<td class="new_line diff-line-num" data-linenumber="1316" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1316
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1316" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="1317" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1317
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<td class="new_line diff-line-num" data-linenumber="1317" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1317
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1317" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Detect the end of the options.</span></span>
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<td class="old_line diff-line-num" data-linenumber="1318" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1318
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<td class="new_line diff-line-num" data-linenumber="1318" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1318
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1318" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1323" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1323" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1323,6 +1323,7 @@ int parse_command_line(int argc, char* argv[]) {</td>
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<td class="old_line diff-line-num" data-linenumber="1323" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1323
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<td class="new_line diff-line-num" data-linenumber="1323" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1323
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1323" class="line" lang="cpp"> <span class="n" style="color: #333;">help</span><span class="p">();</span></span>
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<td class="old_line diff-line-num" data-linenumber="1324" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1324
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<td class="new_line diff-line-num" data-linenumber="1324" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1324
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1324" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1325" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1325
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<td class="new_line diff-line-num" data-linenumber="1325" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1325
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1325" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'p'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1326" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1326" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1326
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1326" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'t'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="1326" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1326
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<td class="new_line diff-line-num" data-linenumber="1327" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1327
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1327" class="line" lang="cpp"> <span class="n" style="color: #333;">num_threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atoi</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1327" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1327
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<td class="new_line diff-line-num" data-linenumber="1328" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1328
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1328" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1328" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1328
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<td class="new_line diff-line-num" data-linenumber="1329" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1329
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1329" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'s'</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1435" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1436" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1435,13 +1436,13 @@ void version() {</td>
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<td class="old_line diff-line-num" data-linenumber="1435" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1435
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<td class="new_line diff-line-num" data-linenumber="1436" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1436
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1436" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="1436" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1436
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<td class="new_line diff-line-num" data-linenumber="1437" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1437
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1437" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">help</span><span class="p">()</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1437" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1437
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<td class="new_line diff-line-num" data-linenumber="1438" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1438
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1438" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"sstacks "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1438" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1438
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<td class="new_line diff-line-num old" data-linenumber="1439" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1438" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"sstacks -P dir -M popmap [-<span class="idiff left right deletion" style="background-color: #fac5cd;">p</span> n_threads]"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1439" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1439
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<td class="new_line diff-line-num old" data-linenumber="1439" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1439" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-<span class="idiff left right deletion" style="background-color: #fac5cd;">p</span> n_threads]"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1440" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1439" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1439
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1439" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"sstacks -P dir -M popmap [-<span class="idiff left right addition" style="background-color: #c7f0d2;">t</span> n_threads]"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1440
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1440" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-<span class="idiff left right addition" style="background-color: #c7f0d2;">t</span> n_threads]"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1440
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<td class="new_line diff-line-num" data-linenumber="1441" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1441
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1441" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -P,--in-path: path to the directory containing Stacks files.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1441
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<td class="new_line diff-line-num" data-linenumber="1442" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1442
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1442" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -M,--popmap: path to a population map file from which to take sample names.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1442
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<td class="new_line diff-line-num" data-linenumber="1443" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1443
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1443" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -s,--sample: filename prefix from which to load sample loci."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1443
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<td class="new_line diff-line-num" data-linenumber="1444" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1444
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1444" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -c,--catalog: path to the catalog."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num old" data-linenumber="1445" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1444" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -<span class="idiff left right deletion" style="background-color: #fac5cd;">p</span>,--threads: enable parallel execution with n_threads threads.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1445" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1445
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1445" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -<span class="idiff left right addition" style="background-color: #c7f0d2;">t</span>,--threads: enable parallel execution with n_threads threads.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num" data-linenumber="1446" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1446" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -o,--out-path: output path to write results."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1447
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1447" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -x: don't verify haplotype of matching locus."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1448" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#115f7027957c0ea3ba55c87ad3b1eaea3b5ebe8d"><strong style="font-weight: 600;">src/ustacks.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2293" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2293" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2293,7 +2293,7 @@ calc_coverage_distribution(map<int, MergedStack *> &merged,</td>
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2293
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<td class="new_line diff-line-num" data-linenumber="2293" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2293
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2293" class="line" lang="cpp"> <span class="n" style="color: #333;">tot_depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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2294
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2294
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2294" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="2295" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2295
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<td class="new_line diff-line-num" data-linenumber="2295" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2295
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2295" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">not_blacklisted</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2296" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2296
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<td class="new_line diff-line-num old" data-linenumber="2296" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2296" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">MergedStack</span><span class="o" style="font-weight: 600;">*>&</span> <span class="n" style="color: #333;">mtag</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">merged</span><span class="p">)</span> <span class="p">{</span></span>
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2296
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2296" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">const</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">MergedStack</span><span class="o" style="font-weight: 600;">*>&</span> <span class="n" style="color: #333;">mtag</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">merged</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="2297" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2297
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<td class="new_line diff-line-num" data-linenumber="2297" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2297
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2297" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mtag</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blacklisted</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="2298" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2298
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<td class="new_line diff-line-num" data-linenumber="2298" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2298
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2298" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2299" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2299
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<td class="new_line diff-line-num" data-linenumber="2299" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2299
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2299" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">not_blacklisted</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2305" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2305" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2305,7 +2305,7 @@ calc_coverage_distribution(map<int, MergedStack *> &merged,</td>
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<td class="old_line diff-line-num" data-linenumber="2305" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2305
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<td class="new_line diff-line-num" data-linenumber="2305" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2305
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2305" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="2306" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2306
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<td class="new_line diff-line-num" data-linenumber="2306" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2306
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2306" class="line" lang="cpp"> <span class="n" style="color: #333;">mean</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tot_depth</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">not_blacklisted</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2307" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2307
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<td class="new_line diff-line-num" data-linenumber="2307" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2307
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2307" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="2308" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2308
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<td class="new_line diff-line-num old" data-linenumber="2308" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2308" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">MergedStack</span><span class="o" style="font-weight: 600;">*>&</span> <span class="n" style="color: #333;">mtag</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">merged</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2309" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2308" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2308
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2308" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">const</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">MergedStack</span><span class="o" style="font-weight: 600;">*>&</span> <span class="n" style="color: #333;">mtag</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">merged</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="2309" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2309
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<td class="new_line diff-line-num" data-linenumber="2309" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2309
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2309" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">mtag</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blacklisted</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="2310" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2310
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<td class="new_line diff-line-num" data-linenumber="2310" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2310
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2310" class="line" lang="cpp"> <span class="n" style="color: #333;">stdev</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">mtag</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">mean</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="2311" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2311
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<td class="new_line diff-line-num" data-linenumber="2311" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2311
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2311" class="line" lang="cpp"> <span class="n" style="color: #333;">stdev</span> <span class="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">not_blacklisted</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2785" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2785" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2785,30 +2785,30 @@ int parse_command_line(int argc, char* argv[]) {</td>
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<td class="old_line diff-line-num" data-linenumber="2785" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2785
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<td class="new_line diff-line-num" data-linenumber="2785" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2785
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2785" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">option</span> <span class="n" style="color: #333;">long_options</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="2786" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2786
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<td class="new_line diff-line-num" data-linenumber="2786" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2786
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2786" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"help"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'h'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="2787" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2787
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<td class="new_line diff-line-num" data-linenumber="2787" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2787
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2787" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"version"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'v'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2788" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2788
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<td class="new_line diff-line-num old" data-linenumber="2788" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2788" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"in<span class="idiff left deletion" style="background-color: #fac5cd;">file</span>-type"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'t'</span><span class="p">},</span> <span class="p">{</span><span class="s" style="color: #d14;">"infile<span class="idiff right deletion" style="background-color: #fac5cd;">_</span>type"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'t'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2789" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2788" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2788
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2788" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"in-type"</span><span class="p">,</span> <span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'t'</span><span class="p">},</span> <span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="p">{</span><span class="s" style="color: #d14;">"infile<span class="idiff right addition" style="background-color: #c7f0d2;">-</span>type"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'t'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="2789" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2789
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<td class="new_line diff-line-num" data-linenumber="2789" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2789
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2789" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"file"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'f'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2790" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2790
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<td class="new_line diff-line-num old" data-linenumber="2790" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2790" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"outpath"</span><span class="p">,</span> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2791" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2791
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<td class="new_line diff-line-num old" data-linenumber="2790" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2791" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right deletion" style="background-color: #fac5cd;">1002</span></span><span class="p">},</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2792" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2790" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2790
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2790" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"out<span class="idiff left right addition" style="background-color: #c7f0d2;">-</span>path"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2792" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2791" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2791
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2791" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;"><span class="idiff left right addition" style="background-color: #c7f0d2;">'n'</span></span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="2792" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2792
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<td class="new_line diff-line-num" data-linenumber="2792" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2792
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2792" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"id"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'i'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2793" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2793
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<td class="new_line diff-line-num old" data-linenumber="2793" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2793" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"min-cov"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'m'</span><span class="p">},</span> <span class="p">{</span><span class="s" style="color: #d14;">"min_cov"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'m'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2794" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2794
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<td class="new_line diff-line-num old" data-linenumber="2793" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2794" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"max-dist"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'M'</span><span class="p">},</span> <span class="p">{</span><span class="s" style="color: #d14;">"max_dist"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'M'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2795" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2795
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<td class="new_line diff-line-num old" data-linenumber="2793" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2795" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"max-sec-dist"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">},</span> <span class="p">{</span><span class="s" style="color: #d14;">"max_sec_dist"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2796" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2796
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<td class="new_line diff-line-num old" data-linenumber="2793" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2796" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"max-locus-stacks"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'K'</span><span class="p">},</span> <span class="p">{</span><span class="s" style="color: #d14;">"max_locus_stacks"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'K'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2797" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2797
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<td class="new_line diff-line-num old" data-linenumber="2793" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2797" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"k-len"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'k'</span><span class="p">},</span> <span class="p">{</span><span class="s" style="color: #d14;">"k_len"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'k'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2798" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2798
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<td class="new_line diff-line-num old" data-linenumber="2793" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2798" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"<span class="idiff left deletion" style="background-color: #fac5cd;">num-</span>threads"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">required_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'p'</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">},</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"num_threads"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff right deletion" style="background-color: #fac5cd;"> </span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'p'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2799" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2793" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2793
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2793" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"min-cov"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'m'</span><span class="p">},</span> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span><span class="p">{</span><span class="s" style="color: #d14;">"min_cov"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'m'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2799" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2794" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2794
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2794" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"max-dist"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'M'</span><span class="p">},</span> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span><span class="p">{</span><span class="s" style="color: #d14;">"max_dist"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'M'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2799" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2795" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2795
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2795" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"max-sec-dist"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">},</span> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span><span class="p">{</span><span class="s" style="color: #d14;">"max_sec_dist"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2799" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2796" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2796
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2796" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"max-locus-stacks"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'K'</span><span class="p">},</span> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span><span class="p">{</span><span class="s" style="color: #d14;">"max_locus_stacks"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'K'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2799" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2797" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2797
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2797" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"k-len"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'k'</span><span class="p">},</span> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span><span class="p">{</span><span class="s" style="color: #d14;">"k_len"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'k'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2799" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2798" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2798
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2798" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"threads"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'p'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="2799" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2799
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<td class="new_line diff-line-num" data-linenumber="2799" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2799
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2799" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"deleverage"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'d'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="2800" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2800
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<td class="new_line diff-line-num" data-linenumber="2800" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2800
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2800" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"keep-high-cov"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">1000</span><span class="p">},</span> <span class="p">{</span><span class="s" style="color: #d14;">"keep_high_cov"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">1000</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="2801" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2801
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<td class="new_line diff-line-num" data-linenumber="2801" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2801
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2801" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"high-cov-thres"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">1001</span><span class="p">},</span> <span class="p">{</span><span class="s" style="color: #d14;">"high_cov_thres"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">1001</span><span class="p">},</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2802" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2802
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<td class="new_line diff-line-num old" data-linenumber="2802" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2802" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"retain-rem"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'R'</span><span class="p">},</span> <span class="p">{</span><span class="s" style="color: #d14;">"retain_rem"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'R'</span><span class="p">},</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2802" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2802
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2802" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"retain-rem"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'R'</span><span class="p">},</span> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span><span class="p">{</span><span class="s" style="color: #d14;">"retain_rem"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'R'</span><span class="p">},</span></span>
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2803
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<td class="new_line diff-line-num" data-linenumber="2803" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2803
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2803" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"graph"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'g'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2804" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2804
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<td class="new_line diff-line-num old" data-linenumber="2804" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2804" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sec-hapl"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'H'</span><span class="p">},</span> <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"sec_hapl"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">no_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'H'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">},</span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="2805" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2804" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2804
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2804" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sec-hapl"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'H'</span><span class="p">},</span> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span></span>
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<td class="old_line diff-line-num" data-linenumber="2805" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2805
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<td class="new_line diff-line-num" data-linenumber="2805" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2805
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2805" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"disable-gapped"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'G'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2806" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2806
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<td class="new_line diff-line-num old" data-linenumber="2806" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2806" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"max-gaps"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'X'</span><span class="p">},</span> <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"max_gaps"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">required_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'X'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">},</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="2807" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2807
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<td class="new_line diff-line-num old" data-linenumber="2806" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2807" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"min-aln-len"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'x'</span><span class="p">},</span> <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"min_aln_len"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">required_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'x'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">},</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="2808" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2808
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<td class="new_line diff-line-num old" data-linenumber="2806" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2808" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"model-type"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'T'</span><span class="p">},</span> <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"model_type"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">required_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'T'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">},</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="2809" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2809
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<td class="new_line diff-line-num old" data-linenumber="2806" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2809" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"bc-err-freq"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'e'</span><span class="p">},</span> <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"bc_err_freq"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">required_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'e'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">},</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="2810" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2810
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<td class="new_line diff-line-num old" data-linenumber="2806" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2810" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"bound-low"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'L'</span><span class="p">},</span> <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"bound_low"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">required_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'L'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">},</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="2811" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2811
</td>
<td class="new_line diff-line-num old" data-linenumber="2806" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2811" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"bound-high"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'U'</span><span class="p">},</span> <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">{</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"bound_high"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">required_argument</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion" style="background-color: #fac5cd;">NULL</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="sc" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">'U'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">},</span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="2812" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2806" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2806
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2806" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"max-gaps"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'X'</span><span class="p">},</span> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="2812" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2807" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2807
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2807" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"min-aln-len"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'x'</span><span class="p">},</span> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="2812" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2808" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2808
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2808" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"model-type"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'T'</span><span class="p">},</span> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="2812" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2809" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2809
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2809" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"bc-err-freq"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'e'</span><span class="p">},</span> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="2812" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2810" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2810
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2810" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"bound-low"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'L'</span><span class="p">},</span> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="2812" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2811" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2811
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2811" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"bound-high"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'U'</span><span class="p">},</span> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span></span>
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<td class="old_line diff-line-num" data-linenumber="2812" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2812
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<td class="new_line diff-line-num" data-linenumber="2812" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2812
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2812" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"alpha"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'A'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="2813" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2813
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<td class="new_line diff-line-num" data-linenumber="2813" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2813
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2813" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"r-deprecated"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'r'</span><span class="p">},</span></span>
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<td class="old_line diff-line-num" data-linenumber="2814" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2814
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<td class="new_line diff-line-num" data-linenumber="2814" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2814
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2814" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"force-diff-len"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">1003</span><span class="p">},</span> <span class="p">{</span><span class="s" style="color: #d14;">"force_diff_len"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">1003</span><span class="p">},</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2818" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2818" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2818,7 +2818,7 @@ int parse_command_line(int argc, char* argv[]) {</td>
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<td class="old_line diff-line-num" data-linenumber="2818" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2818
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<td class="new_line diff-line-num" data-linenumber="2818" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2818
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2818" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// getopt_long stores the option index here.</span></span>
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<td class="old_line diff-line-num" data-linenumber="2819" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2819
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<td class="new_line diff-line-num" data-linenumber="2819" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2819
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2819" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">option_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2820" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2820
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<td class="new_line diff-line-num" data-linenumber="2820" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2820
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2820" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="2821" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2821
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<td class="new_line diff-line-num old" data-linenumber="2821" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2821" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt_long</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"GhHvdrgRA:L:U:f:o:s:i:m:e:p:t:M:N:K:k:T:X:x:"</span><span class="p">,</span> <span class="n" style="color: #333;">long_options</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">option_index</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2822" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2821" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2821
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2821" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt_long</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"GhHvdrgRA:L:U:f:o:s:i:m:<span class="idiff left right addition" style="background-color: #c7f0d2;">n:</span>e:p:t:M:N:K:k:T:X:x:"</span><span class="p">,</span> <span class="n" style="color: #333;">long_options</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">option_index</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="2822" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2822
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<td class="new_line diff-line-num" data-linenumber="2822" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2822
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2822" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="2823" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2823
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<td class="new_line diff-line-num" data-linenumber="2823" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2823
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2823" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Detect the end of the options.</span></span>
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<td class="old_line diff-line-num" data-linenumber="2824" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2824
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<td class="new_line diff-line-num" data-linenumber="2824" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2824
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2824" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2828" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2828" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2828,7 +2828,7 @@ int parse_command_line(int argc, char* argv[]) {</td>
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<td class="old_line diff-line-num" data-linenumber="2828" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2828
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<td class="new_line diff-line-num" data-linenumber="2828" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2828
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2828" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'h'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="2829" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2829
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<td class="new_line diff-line-num" data-linenumber="2829" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2829
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2829" class="line" lang="cpp"> <span class="n" style="color: #333;">help</span><span class="p">();</span></span>
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<td class="old_line diff-line-num" data-linenumber="2830" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2830
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<td class="new_line diff-line-num" data-linenumber="2830" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2830
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2830" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2831" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2831
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<td class="new_line diff-line-num old" data-linenumber="2831" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2831" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'<span class="idiff left right deletion" style="background-color: #fac5cd;">t</span>'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2832" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2831" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2831
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2831" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'<span class="idiff left right addition" style="background-color: #c7f0d2;">i</span>'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="2832" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2832
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<td class="new_line diff-line-num" data-linenumber="2832" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2832
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2832" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="s" style="color: #d14;">"tsv"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="2833" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2833
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<td class="new_line diff-line-num" data-linenumber="2833" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2833
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2833" class="line" lang="cpp"> <span class="n" style="color: #333;">in_file_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FileT</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tsv</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2834" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2834
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<td class="new_line diff-line-num" data-linenumber="2834" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2834
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2834" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2848" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2848" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2848,11 +2848,9 @@ int parse_command_line(int argc, char* argv[]) {</td>
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<td class="old_line diff-line-num" data-linenumber="2848" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2848
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<td class="new_line diff-line-num" data-linenumber="2848" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2848
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2848" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="2849" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2849
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<td class="new_line diff-line-num" data-linenumber="2849" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2849
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2849" class="line" lang="cpp"> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2850" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2850
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<td class="new_line diff-line-num" data-linenumber="2850" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2850
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2850" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2851" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2851
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<td class="new_line diff-line-num old" data-linenumber="2851" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2851" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;"><span class="idiff left right deletion" style="background-color: #fac5cd;">1002</span></span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2852" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2851" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2851
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2851" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;"><span class="idiff left right addition" style="background-color: #c7f0d2;">'n'</span></span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="2852" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2852
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<td class="new_line diff-line-num" data-linenumber="2852" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2852
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2852" class="line" lang="cpp"> <span class="n" style="color: #333;">sample_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2853" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2853
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<td class="new_line diff-line-num" data-linenumber="2853" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2853
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2853" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2854" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2854
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<td class="new_line diff-line-num old" data-linenumber="2854" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2854" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'i'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2855" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2855
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<td class="new_line diff-line-num old" data-linenumber="2854" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2855" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2856" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2856
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<td class="new_line diff-line-num" data-linenumber="2854" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2854
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2854" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'m'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="2857" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2857
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<td class="new_line diff-line-num" data-linenumber="2855" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2855
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2855" class="line" lang="cpp"> <span class="n" style="color: #333;">min_merge_cov</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">is_integer</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="2858" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2858
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<td class="new_line diff-line-num" data-linenumber="2856" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2856
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2856" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2925" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2923" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2925,6 +2923,7 @@ int parse_command_line(int argc, char* argv[]) {</td>
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<td class="old_line diff-line-num" data-linenumber="2925" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2925
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<td class="new_line diff-line-num" data-linenumber="2923" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2923
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2923" class="line" lang="cpp"> <span class="n" style="color: #333;">call_sec_hapl</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2926" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2926
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<td class="new_line diff-line-num" data-linenumber="2924" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2924
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2924" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2927" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2927
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<td class="new_line diff-line-num" data-linenumber="2925" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2925
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2925" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'p'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2928" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2926" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2926
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2926" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'t'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="2928" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2928
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<td class="new_line diff-line-num" data-linenumber="2927" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2927
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2927" class="line" lang="cpp"> <span class="n" style="color: #333;">num_threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">is_integer</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="2929" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2929
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<td class="new_line diff-line-num" data-linenumber="2928" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2928
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2928" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2930" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2930
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<td class="new_line diff-line-num" data-linenumber="2929" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2929
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2929" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'v'</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2933" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2932" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2933,9 +2932,6 @@ int parse_command_line(int argc, char* argv[]) {</td>
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<td class="old_line diff-line-num" data-linenumber="2933" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2933
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<td class="new_line diff-line-num" data-linenumber="2932" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2932
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2932" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">1003</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="2934" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2934
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<td class="new_line diff-line-num" data-linenumber="2933" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2933
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2933" class="line" lang="cpp"> <span class="n" style="color: #333;">force_diff_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2935" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2935
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<td class="new_line diff-line-num" data-linenumber="2934" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2934
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2934" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2936" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2936
</td>
<td class="new_line diff-line-num old" data-linenumber="2935" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2936" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'r'</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;">// deprecated Dec 2016, v1.45</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2937" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2937
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<td class="new_line diff-line-num old" data-linenumber="2935" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2937" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: Ignoring deprecated option -r (this has become the default).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2938" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2938
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<td class="new_line diff-line-num old" data-linenumber="2935" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2938" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2939" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2939
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<td class="new_line diff-line-num" data-linenumber="2935" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2935
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2935" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'?'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="2940" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2940
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<td class="new_line diff-line-num" data-linenumber="2936" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2936
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2936" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// getopt_long already printed an error message.</span></span>
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<td class="old_line diff-line-num" data-linenumber="2941" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2941
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<td class="new_line diff-line-num" data-linenumber="2937" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2937
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2937" class="line" lang="cpp"> <span class="n" style="color: #333;">help</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3024" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3020" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -3024,29 +3020,29 @@ void version() {</td>
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<td class="old_line diff-line-num" data-linenumber="3024" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3024
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<td class="new_line diff-line-num" data-linenumber="3020" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3020
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3020" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="3025" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3025
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<td class="new_line diff-line-num" data-linenumber="3021" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3021
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3021" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">help</span><span class="p">()</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="3026" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3026
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<td class="new_line diff-line-num" data-linenumber="3022" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3022
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3022" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"ustacks "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3027" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3027
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<td class="new_line diff-line-num old" data-linenumber="3023" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3027" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"ustacks -f <span class="idiff left deletion" style="background-color: #fac5cd;">file</span>_path -o path [-M max_dist] [-m min_<span class="idiff deletion" style="background-color: #fac5cd;">cov</span>] [-<span class="idiff right deletion" style="background-color: #fac5cd;">p</span> num_threads]"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3028" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3028
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<td class="new_line diff-line-num old" data-linenumber="3023" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3028" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <span class="idiff left right deletion" style="background-color: #fac5cd;">f</span>: input file path.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3029" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3029
</td>
<td class="new_line diff-line-num old" data-linenumber="3023" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3029" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <span class="idiff left right deletion" style="background-color: #fac5cd;">o</span>: output path to write results.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3030" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3030
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<td class="new_line diff-line-num old" data-linenumber="3023" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3030" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" M: Maximum distance (in nucleotides) allowed between stacks (default 2).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3031" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3031
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<td class="new_line diff-line-num old" data-linenumber="3023" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3031" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" m: Minimum <span class="idiff left right deletion" style="background-color: #fac5cd;">depth of coverage required to create a</span> stack (default 3).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3032" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3032
</td>
<td class="new_line diff-line-num old" data-linenumber="3023" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3032" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" N: Maximum distance allowed to align secondary reads to primary stacks (default: M + 2).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3033" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3033
</td>
<td class="new_line diff-line-num old" data-linenumber="3023" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3033" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <span class="idiff left right deletion" style="background-color: #fac5cd;">p</span>: enable parallel execution with num_threads threads.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3034" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3034
</td>
<td class="new_line diff-line-num old" data-linenumber="3023" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3034" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <span class="idiff left right deletion" style="background-color: #fac5cd;">t</span>: input file type. Supported types: fasta, fastq, gzfasta, or gzfastq (default: guess).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3035" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3035
</td>
<td class="new_line diff-line-num old" data-linenumber="3023" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3035" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --name: a name for the sample (default: input file name minus the suffix).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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3036
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<td class="new_line diff-line-num old" data-linenumber="3023" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3036" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" R: retain unused reads.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3037" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3037
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<td class="new_line diff-line-num old" data-linenumber="3023" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3037" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" H: disable calling haplotypes from secondary reads.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3038" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3023" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3023
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3023" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"ustacks -f <span class="idiff left addition" style="background-color: #c7f0d2;">in</span>_path -o <span class="idiff addition" style="background-color: #c7f0d2;">out_</span>path [-M max_dist] [-m min_<span class="idiff addition" style="background-color: #c7f0d2;">reads</span>] [-<span class="idiff right addition" style="background-color: #c7f0d2;">t</span> num_threads]"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3038" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3024" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3024
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3024" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <span class="idiff left right addition" style="background-color: #c7f0d2;">-f,--file</span>: input file path.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3038" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3025" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3025
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3025" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <span class="idiff left right addition" style="background-color: #c7f0d2;">-o,--out-path</span>: output path to write results.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3038" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3026" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3026
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3026" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <span class="idiff left right addition" style="background-color: #c7f0d2;">-</span>M: Maximum distance (in nucleotides) allowed between stacks (default 2).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3038" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3027" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3027
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3027" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <span class="idiff left addition" style="background-color: #c7f0d2;">-</span>m: Minimum <span class="idiff right addition" style="background-color: #c7f0d2;">number of reads to seed a new</span> stack (default 3).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3038" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3028" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3028
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3028" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <span class="idiff left right addition" style="background-color: #c7f0d2;">-</span>N: Maximum distance allowed to align secondary reads to primary stacks (default: M + 2).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3038" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3029" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3029
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3029" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <span class="idiff left right addition" style="background-color: #c7f0d2;">-t,--threads</span>: enable parallel execution with num_threads threads.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3038" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3030" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3030
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3030" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <span class="idiff left right addition" style="background-color: #c7f0d2;">-i,--in-type</span>: input file type. Supported types: fasta, fastq, gzfasta, or gzfastq (default: guess).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3038" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3031" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3031
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3031" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <span class="idiff left right addition" style="background-color: #c7f0d2;">-n,</span>--name: a name for the sample (default: input file name minus the suffix).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3038" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3032" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3032
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3032" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <span class="idiff left right addition" style="background-color: #c7f0d2;">-</span>R: retain unused reads.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3038" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3033" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3033
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3033" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <span class="idiff left right addition" style="background-color: #c7f0d2;">-</span>H: disable calling haplotypes from secondary reads.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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3038
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<td class="new_line diff-line-num" data-linenumber="3034" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3034
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3034" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="3039" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3039
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<td class="new_line diff-line-num" data-linenumber="3035" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3035
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3035" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Stack assembly options:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="3040" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3040
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<td class="new_line diff-line-num" data-linenumber="3036" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3036
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3036" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --force-diff-len: allow raw input reads of different lengths, e.g. after trimming (default: ustacks perfers raw input reads of uniform length).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="3041" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3041
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<td class="new_line diff-line-num" data-linenumber="3037" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3037
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3037" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --keep-high-cov: disable the algorithm that removes highly-repetitive stacks and nearby errors.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="3042" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3042
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<td class="new_line diff-line-num" data-linenumber="3038" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3038
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3038" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --high-cov-thres: highly-repetitive stacks threshold, in standard deviation units (default: 3.0).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="3043" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3043
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<td class="new_line diff-line-num" data-linenumber="3039" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3039
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3039" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --max-locus-stacks <num>: maximum number of stacks at a single de novo locus (default 3).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3044" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3044
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<td class="new_line diff-line-num old" data-linenumber="3040" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3044" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span>--k-len <len>: specify k-mer size for matching between alleles and loci (automatically calculated by default).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3045" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3040" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3040
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3040" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --k-len <len>: specify k-mer size for matching between alleles and loci (automatically calculated by default).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="3045" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3045
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<td class="new_line diff-line-num" data-linenumber="3041" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3041
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3041" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --deleverage: enable the Deleveraging algorithm, used for resolving over merged tags.</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="3046" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3046
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<td class="new_line diff-line-num" data-linenumber="3042" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3042
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3042" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Gapped assembly options:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="3047" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3047
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<td class="new_line diff-line-num" data-linenumber="3043" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3043
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3043" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --max-gaps: number of gaps allowed between stacks before merging (default: 2).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3048" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3048
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<td class="new_line diff-line-num old" data-linenumber="3044" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3048" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80).</span><span class="se" style="color: #d14;">\n<span class="idiff left right deletion" style="background-color: #fac5cd;">\n</span></span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3049" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3049
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<td class="new_line diff-line-num old" data-linenumber="3044" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3049" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --disable-gapped: do not preform gapped alignments between stacks (default: gapped alignements enabled).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3050" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3044" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3044
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3044" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3050" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3045" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3045
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3045" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --disable-gapped: do not preform gapped alignments between stacks (default: gapped alignements enabled).</span><span class="se" style="color: #d14;">\n<span class="idiff left right addition" style="background-color: #c7f0d2;">\n</span></span><span class="s" style="color: #d14;">"</span></span>
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3050
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<td class="new_line diff-line-num" data-linenumber="3046" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3046
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3046" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Model options:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="3051" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3051
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<td class="new_line diff-line-num" data-linenumber="3047" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3047
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3047" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --model-type: either 'snp' (default), 'bounded', or 'fixed'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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3052
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<td class="new_line diff-line-num" data-linenumber="3048" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3048
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3048" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" For the SNP or Bounded SNP model:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/fded9fa152f34c36d424a8f8a7afe941a3c31bf1#b44ce7d7ddbd794f98496d8179231949622e498e"><strong style="font-weight: 600;">src/write.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -47,7 +47,7 @@ write_fasta(ofstream *fh, RawRead *href, bool overhang) {</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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48
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48
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC48" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="old_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
49
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<td class="new_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
49
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC49" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;"><<</span></span>
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50
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<td class="new_line diff-line-num old" data-linenumber="50" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC50" class="line" lang="cpp"> <span class="s" style="color: #d14;">">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine</span> <span class="o" style="font-weight: 600;"><<</span></span>
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50
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC50" class="line" lang="cpp"> <span class="s" style="color: #d14;">">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine</span><span class="p"><span class="idiff left right addition" style="background-color: #c7f0d2;">()</span></span> <span class="o" style="font-weight: 600;"><<</span></span>
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51
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC51" class="line" lang="cpp"> <span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC52" class="line" lang="cpp"> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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53
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC53" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -76,7 +76,7 @@ write_fasta(gzFile *fh, RawRead *href, bool overhang) {</td>
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<td class="old_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
76
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<td class="new_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
76
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC76" class="line" lang="cpp"> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
77
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<td class="new_line diff-line-num" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
77
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC77" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="old_line diff-line-num" data-linenumber="78" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
78
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<td class="new_line diff-line-num" data-linenumber="78" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
78
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC78" class="line" lang="cpp"> <span class="n" style="color: #333;">sstr</span> <span class="o" style="font-weight: 600;"><<</span></span>
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<td class="old_line diff-line-num old" data-linenumber="79" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
79
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<td class="new_line diff-line-num old" data-linenumber="79" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC79" class="line" lang="cpp"> <span class="s" style="color: #d14;">">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine</span> <span class="o" style="font-weight: 600;"><<</span></span>
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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
79
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC79" class="line" lang="cpp"> <span class="s" style="color: #d14;">">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine</span><span class="p"><span class="idiff left right addition" style="background-color: #c7f0d2;">()</span></span> <span class="o" style="font-weight: 600;"><<</span></span>
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80
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC80" class="line" lang="cpp"> <span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span></span>
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<td class="old_line diff-line-num" data-linenumber="81" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
81
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81
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="82" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
82
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82
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC82" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="135" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="135" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -135,7 +135,7 @@ write_fastq(ofstream *fh, RawRead *href, bool overhang) {</td>
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135
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135
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">phred</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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136
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<td class="new_line diff-line-num" data-linenumber="136" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
136
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC136" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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137
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<td class="new_line diff-line-num" data-linenumber="137" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
137
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC137" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;"><<</span></span>
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138
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<td class="new_line diff-line-num old" data-linenumber="138" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC138" class="line" lang="cpp"> <span class="s" style="color: #d14;">"@"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine</span> <span class="o" style="font-weight: 600;"><<</span></span>
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138
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC138" class="line" lang="cpp"> <span class="s" style="color: #d14;">"@"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine</span><span class="p"><span class="idiff left right addition" style="background-color: #c7f0d2;">()</span></span> <span class="o" style="font-weight: 600;"><<</span></span>
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139
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139
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC139" class="line" lang="cpp"> <span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span></span>
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140
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140
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span></span>
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141
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141
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC141" class="line" lang="cpp"> <span class="s" style="color: #d14;">"+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="171" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="171" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,.24); padding: inherit;" bgcolor="#fbfafd">@@ -171,7 +171,7 @@ write_fastq(gzFile *fh, RawRead *href, bool overhang) {</td>
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171
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171
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC171" class="line" lang="cpp"> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">phred</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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172
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<td class="new_line diff-line-num" data-linenumber="172" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
172
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC172" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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173
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<td class="new_line diff-line-num" data-linenumber="173" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
173
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC173" class="line" lang="cpp"> <span class="n" style="color: #333;">sstr</span> <span class="o" style="font-weight: 600;"><<</span></span>
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174
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<td class="new_line diff-line-num old" data-linenumber="174" style="width: 35px; color: rgba(31,30,36,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC174" class="line" lang="cpp"> <span class="s" style="color: #d14;">"@"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine</span> <span class="o" style="font-weight: 600;"><<</span></span>
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174
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC174" class="line" lang="cpp"> <span class="s" style="color: #d14;">"@"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">machine</span><span class="p"><span class="idiff left right addition" style="background-color: #c7f0d2;">()</span></span> <span class="o" style="font-weight: 600;"><<</span></span>
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175
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175
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC175" class="line" lang="cpp"> <span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span></span>
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176
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176
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC176" class="line" lang="cpp"> <span class="n" style="color: #333;">href</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span></span>
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177
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