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<h3>
Alexandre Mestiashvili pushed to branch master
at <a href="https://salsa.debian.org/med-team/bowtie2">Debian Med / bowtie2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/be7df110efc3562e1282c236658e1caefa7c134b">be7df110</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-25T07:56:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.3.4.3</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/e2e138ec64df9e34ffbf742d9653743a5ca36200">e2e138ec</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-25T07:56:50Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.3.4.3'
Update to upstream version '2.3.4.3'
with Debian dir fbf1b4a0156d70c1a3d4a1ef9a7b294e9aca34a0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/c4b56855866b1a6eb87f84c96af852b11034409e">c4b56855</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-25T07:58:18Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump Policy to 4.2.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/7596be203863526cfedcc8e03063d5632c9ea907">7596be20</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-25T08:43:39Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
Gbp-Dch: Ignore
</pre>
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</ul>
<h4>17 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8">
NEWS
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<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
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<li class="file-stats">
<a href="#464ce98392db4e108605b7a12696e7c3434eaf56">
bowtie2-build
</a>
</li>
<li class="file-stats">
<a href="#622d3bcfba0df0e4ae8a0849416ed2d2cf987528">
bowtie2-inspect
</a>
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<li class="file-stats">
<a href="#999fd61d6ccb4c3bc242370d11e9095438b9e1d1">
bt2_build.cpp
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<li class="file-stats">
<a href="#8900eca5df34d74c6e0548d5c00714f6e70c5a77">
bt2_inspect.cpp
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<li class="file-stats">
<a href="#6026283a643bf7fb08c2ef0b797486df93cf0698">
bt2_search.cpp
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#a1ba375e8deab5b12b1347797835e927dca95425">
doc/website/manual.ssi
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<li class="file-stats">
<a href="#9485aa1b2c39982f48264019fde0712132ed80f5">
doc/website/recent_news.ssi
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<li class="file-stats">
<a href="#59bf596910fb7006481a4d8a45de81ff2bd75a4d">
doc/website/rhsidebar.ssi
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<li class="file-stats">
<a href="#e09def9b31d68cc22ed618a45007cec090ea243c">
<span class="new-file">
+
example/reads/conversion_utilities.sh
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<li class="file-stats">
<a href="#ca0679d32b003b8024f4d51789e4d6e5b06db9c9">
formats.h
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<li class="file-stats">
<a href="#7c4ae52e4a13c990d16c9530fb874ed79064a5cd">
pat.cpp
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<li class="file-stats">
<a href="#6c8922e214bc665a49b5acea11b505cbd36446c5">
pat.h
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</ul>
<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/bowtie2/compare/b5fd5c31d9d324d1c724e965365932c64231f2db...7596be203863526cfedcc8e03063d5632c9ea907#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@ cmake_minimum_required(VERSION 2.8)</td>
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">cmake_policy</span><span class="p">(</span>SET CMP0048 NEW<span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">cmake_policy</span><span class="p">(</span>SET CMP0005 NEW<span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="cmake"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC6" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span>bowtie2 LANGUAGES CXX VERSION <span class="s2" style="color: #d14;">"2.3.4.<span class="idiff left right">2</span>"</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span>bowtie2 LANGUAGES CXX VERSION <span class="s2" style="color: #d14;">"2.3.4.<span class="idiff left right">3</span>"</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="cmake"></span>
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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">enable_testing</span><span class="p">()</span></span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="cmake"></span>
</pre>
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<br>
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<li id="9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8">
<a href="https://salsa.debian.org/med-team/bowtie2/compare/b5fd5c31d9d324d1c724e965365932c64231f2db...7596be203863526cfedcc8e03063d5632c9ea907#9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8"><strong>NEWS</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,6 +19,14 @@ Please report any issues to the Bowtie 2 Github page or using the Sourceforge bu</td>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Version Release History</span>
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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">=======================</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Version 2.3.4.3 - Sep 17, 2018</span>
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> * Fixed an issue causing `bowtie2-build` and `bowtie2-inspect`</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> to output incomplete help text.</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> * Fixed an issue causing `bowtie2-inspect` to crash.</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> * Fixed an issue preventing `bowtie2` from processing paired and/or</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> unpaired FASTQ reads together with interleaved FASTQ reads.</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">Version 2.3.4.2 - Aug 7, 2018</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> * Fixed issue causing `bowtie2` to fail in `--fast-local` mode.</span>
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<a href="https://salsa.debian.org/med-team/bowtie2/compare/b5fd5c31d9d324d1c724e965365932c64231f2db...7596be203863526cfedcc8e03063d5632c9ea907#b33892fbddeffc3368077b4904ad0b3d562a7312"><strong>VERSION</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">2.3.4.<span class="idiff left right">2</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2.3.4.<span class="idiff left right">3</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie2/compare/b5fd5c31d9d324d1c724e965365932c64231f2db...7596be203863526cfedcc8e03063d5632c9ea907#464ce98392db4e108605b7a12696e7c3434eaf56"><strong>bowtie2-build</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,15 +29,15 @@ import subprocess</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">deque</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC31" 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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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">add_help</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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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--large-index'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--verbose'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_mutually_exclusive_group</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--debug'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--sanitized'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--verbose'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--large-index'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basicConfig</span><span class="p">(</span><span class="n" style="color: #333;">level</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ERROR</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">format</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%(levelname)</span><span class="s" style="color: #d14;">s: </span><span class="si" style="color: #d14;">%(message)</span><span class="s" style="color: #d14;">s'</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -51,8 +51,12 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">build_bin_spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">ex_path</span><span class="p">,</span><span class="n" style="color: #333;">build_bin_s</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">script_options</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_known_args</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">print_help</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">argv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">deque</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'-h'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">argv</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">'--help'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">argv</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">print_help</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">script_options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">verbose</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">INFO</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,6 +22,7 @@</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">imp</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">inspect</span></span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,7 +30,7 @@ import subprocess</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">deque</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC32" 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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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">add_help</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_mutually_exclusive_group</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--debug'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/compare/b5fd5c31d9d324d1c724e965365932c64231f2db...7596be203863526cfedcc8e03063d5632c9ea907#999fd61d6ccb4c3bc242370d11e9095438b9e1d1"><strong>bt2_build.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -142,7 +142,10 @@ static void printUsage(ostream& out) {</td>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <reference_in>)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">wrapper</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"basic-0"</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --large-index force generated index to be 'large', even if ref"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" has fewer than 4 billion nucleotides"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" has fewer than 4 billion nucleotides"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --debug use the debug binary; slower, assertions enabled"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --sanitized use sanitized binary; slower, uses ASan and/or UBSan"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --verbose log the issued command"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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146
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"> <span class="p">}</span></span>
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147
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -a/--noauto disable automatic -p/--bmax/--dcv memory-fitting"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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148
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -p/--packed use packed strings internally; slower, less memory"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/compare/b5fd5c31d9d324d1c724e965365932c64231f2db...7596be203863526cfedcc8e03063d5632c9ea907#8900eca5df34d74c6e0548d5c00714f6e70c5a77"><strong>bt2_inspect.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -76,14 +76,16 @@ static void printUsage(ostream& out) {</td>
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76
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Options:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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77
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">wrapper</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"basic-0"</span><span class="p">)</span> <span class="p">{</span></span>
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78
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --large-index force inspection of the 'large' index, even if a"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" 'small' one is present."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" 'small' one is present."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --debug use the debug binary; slower, assertions enabled"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --sanitized use sanitized binary; slower, uses ASan and/or UBSan"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --verbose log the issued command"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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80
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"> <span class="p">}</span></span>
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81
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -a/--across <int> Number of characters across in FASTA output (default: 60)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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82
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<td class="diff-line-num new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -n/--names Print reference sequence names only"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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83
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<td class="diff-line-num new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -s/--summary Print summary incl. ref names, lengths, index properties"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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84
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -v/--verbose Verbose output (for debugging)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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85
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -h/--help print detailed description of tool and its options"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --help print this usage message"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="p">;</span></span>
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<pre style="margin: 0;"> <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;">wrapper</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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91
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<pre style="margin: 0;"> <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="n" style="color: #333;">endl</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/compare/b5fd5c31d9d324d1c724e965365932c64231f2db...7596be203863526cfedcc8e03063d5632c9ea907#6026283a643bf7fb08c2ef0b797486df93cf0698"><strong>bt2_search.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -84,6 +84,7 @@ static bool startVerbose; // be talkative at startup</td>
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84
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gQuiet</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// print nothing but the alignments</span></span>
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85
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sanityCheck</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// enable expensive sanity checks</span></span>
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86
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">format</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// default read format is FASTQ</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</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 class="c1" style="color: #998; font-style: italic;">// reads are interleaved</span></span>
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87
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">origString</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// reference text, or filename(s)</span></span>
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88
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seed</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// srandom() seed</span></span>
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89
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">timing</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// whether to report basic timing data</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -278,6 +279,7 @@ static void resetOptions() {</td>
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278
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="cpp"> <span class="n" style="color: #333;">gQuiet</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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279
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="cpp"> <span class="n" style="color: #333;">sanityCheck</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// enable expensive sanity checks</span></span>
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280
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="cpp"> <span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FASTQ</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// default read format is FASTQ</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <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 class="c1" style="color: #998; font-style: italic;">// reads are not interleaved by default</span></span>
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281
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp"> <span class="n" style="color: #333;">origString</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// reference text, or filename(s)</span></span>
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282
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="cpp"> <span class="n" style="color: #333;">seed</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// srandom() seed</span></span>
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283
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285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="cpp"> <span class="n" style="color: #333;">timing</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// whether to report basic timing data</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -999,7 +1001,12 @@ static void parseOption(int next_option, const char *arg) {</td>
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999
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1001
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<pre style="margin: 0;"> <span id="LC1001" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ARG_ONETWO</span><span class="p">:</span> <span class="n" style="color: #333;">tokenize</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">,</span> <span class="s" style="color: #d14;">","</span><span class="p">,</span> <span class="n" style="color: #333;">mates12</span><span class="p">);</span> <span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TAB_MATE5</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1002
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<pre style="margin: 0;"> <span id="LC1002" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ARG_TAB5</span><span class="p">:</span> <span class="n" style="color: #333;">tokenize</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">,</span> <span class="s" style="color: #d14;">","</span><span class="p">,</span> <span class="n" style="color: #333;">mates12</span><span class="p">);</span> <span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TAB_MATE5</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1001
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1003
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<pre style="margin: 0;"> <span id="LC1003" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ARG_TAB6</span><span class="p">:</span> <span class="n" style="color: #333;">tokenize</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">,</span> <span class="s" style="color: #d14;">","</span><span class="p">,</span> <span class="n" style="color: #333;">mates12</span><span class="p">);</span> <span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TAB_MATE6</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1002
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<pre style="margin: 0;">-<span id="LC1002" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ARG_INTERLEAVED_FASTQ</span><span class="p">:</span> <span class="n" style="color: #333;">tokenize</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">,</span> <span class="s" style="color: #d14;">","</span><span class="p">,</span> <span class="n" style="color: #333;">mates12</span><span class="p">);</span> <span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INTERLEAVED</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ARG_INTERLEAVED_FASTQ</span><span class="p">:</span> <span class="p">{</span></span>
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1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="cpp"> <span class="n" style="color: #333;">tokenize</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">,</span> <span class="s" style="color: #d14;">","</span><span class="p">,</span> <span class="n" style="color: #333;">mates12</span><span class="p">);</span></span>
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1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="cpp"> <span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FASTQ</span><span class="p">;</span></span>
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1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="cpp"> <span class="n" style="color: #333;">interleaved</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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1008
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<pre style="margin: 0;">+<span id="LC1008" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1009
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<pre style="margin: 0;">+<span id="LC1009" class="line" lang="cpp"> <span class="p">}</span></span>
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1003
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1010
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<pre style="margin: 0;"> <span id="LC1010" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'b'</span><span class="p">:</span> <span class="p">{</span></span>
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1004
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1011
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<pre style="margin: 0;"> <span id="LC1011" class="line" lang="cpp"> <span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BAM</span><span class="p">;</span></span>
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1005
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1012
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<pre style="margin: 0;"> <span id="LC1012" class="line" lang="cpp"> <span class="n" style="color: #333;">saw_bam</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="1735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1735,7 +1742,7 @@ createPatsrcFactory(</td>
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1735
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1742
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<pre style="margin: 0;"> <span id="LC1742" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tid</span><span class="p">)</span></span>
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1736
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1743
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<pre style="margin: 0;"> <span id="LC1743" class="line" lang="cpp"><span class="p">{</span></span>
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1737
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1744
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<pre style="margin: 0;"> <span id="LC1744" class="line" lang="cpp"> <span class="n" style="color: #333;">PatternSourcePerThreadFactory</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">patsrcFact</span><span class="p">;</span></span>
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1738
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<pre style="margin: 0;">-<span id="LC1738" class="line" lang="cpp"> <span class="n" style="color: #333;">patsrcFact</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">PatternSourcePerThreadFactory</span><span class="p">(</span><span class="n" style="color: #333;">patcomp</span><span class="p">,</span> <span class="n" style="color: #333;">pp</span><span class="p">);</span></span>
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1745
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<pre style="margin: 0;">+<span id="LC1745" class="line" lang="cpp"> <span class="n" style="color: #333;">patsrcFact</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">PatternSourcePerThreadFactory</span><span class="p">(</span><span class="n" style="color: #333;">patcomp</span><span class="p">,</span> <span class="n" style="color: #333;">pp</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tid</span></span><span class="p">);</span></span>
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1739
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1746
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<pre style="margin: 0;"> <span id="LC1746" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">patsrcFact</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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1740
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1747
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<pre style="margin: 0;"> <span id="LC1747" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">patsrcFact</span><span class="p">;</span></span>
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1741
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1748
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<pre style="margin: 0;"> <span id="LC1748" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4782,6 +4789,7 @@ static void driver(</td>
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4782
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4789
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<pre style="margin: 0;"> <span id="LC4789" class="line" lang="cpp"> <span class="p">}</span></span>
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4783
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4790
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<pre style="margin: 0;"> <span id="LC4790" class="line" lang="cpp"> <span class="n" style="color: #333;">PatternParams</span> <span class="n" style="color: #333;">pp</span><span class="p">(</span></span>
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4784
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4791
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<pre style="margin: 0;"> <span id="LC4791" class="line" lang="cpp"> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// file format</span></span>
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4792
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<pre style="margin: 0;">+<span id="LC4792" class="line" lang="cpp"> <span class="n" style="color: #333;">interleaved</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// some or all of the reads are interleaved</span></span>
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4785
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4793
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<pre style="margin: 0;"> <span id="LC4793" class="line" lang="cpp"> <span class="n" style="color: #333;">fileParallel</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// true -> wrap files with separate PairedPatternSources</span></span>
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4786
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4794
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<pre style="margin: 0;"> <span id="LC4794" class="line" lang="cpp"> <span class="n" style="color: #333;">seed</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// pseudo-random seed</span></span>
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4787
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4795
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<pre style="margin: 0;"> <span id="LC4795" class="line" lang="cpp"> <span class="n" style="color: #333;">readsPerBatch</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// # reads in a light parsing batch</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/compare/b5fd5c31d9d324d1c724e965365932c64231f2db...7596be203863526cfedcc8e03063d5632c9ea907#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bowtie2 (2.3.4.3-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Steffen Möller ]</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Updated OMICtools ref in d/u/metadata</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> [ Alexandre Mestiashvili ]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * New upstream version 2.3.4.3:</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> - Fixed an issue causing `bowtie2-build` and `bowtie2-inspect`</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> to output incomplete help text.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> - Fixed an issue causing `bowtie2-inspect` to crash.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> - Fixed an issue preventing `bowtie2` from processing paired and/or</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> unpaired FASTQ reads together with interleaved FASTQ reads.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Bump Policy to 4.2.1</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> -- Alexandre Mestiashvili <mestia@debian.org> Tue, 25 Sep 2018 07:58:26 +0000</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">bowtie2 (2.3.4.2-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> * New upstream version 2.3.4.2</span>
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<a href="https://salsa.debian.org/med-team/bowtie2/compare/b5fd5c31d9d324d1c724e965365932c64231f2db...7596be203863526cfedcc8e03063d5632c9ea907#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +12,7 @@ Build-Depends: debhelper (>= 11),</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libtest-deep-perl,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libclone-perl,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> zlib1g-dev</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">Standards-Version: 4.2.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Standards-Version: 4.2.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/bowtie2</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/bowtie2.git</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Homepage: http://bowtie-bio.sourceforge.net/bowtie2</span>
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<a href="https://salsa.debian.org/med-team/bowtie2/compare/b5fd5c31d9d324d1c724e965365932c64231f2db...7596be203863526cfedcc8e03063d5632c9ea907#a1ba375e8deab5b12b1347797835e927dca95425"><strong>doc/website/manual.ssi</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -152,7 +152,7 @@ Fedora, CentOS</td>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="plaintext"><pre><code>yum check-update</code></pre></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="plaintext"></td></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="plaintext"><td></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="plaintext"><p<span class="idiff left right">>yum search tbb</p</span>></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"><p<span class="idiff left right">re><code>yum search tbb</code></pre</span>></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="plaintext"></td></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="plaintext"><td></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="plaintext"><pre><code>yum install tbb-devel.x86_64</code></pre></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/compare/b5fd5c31d9d324d1c724e965365932c64231f2db...7596be203863526cfedcc8e03063d5632c9ea907#9485aa1b2c39982f48264019fde0712132ed80f5"><strong>doc/website/recent_news.ssi</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><h2>Version 2.3.4.<span class="idiff left right">2 - August 07, 1987</span></h2></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><h2>Version 2.3.4.<span class="idiff left right">3 - September 17, 2018</span></h2></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"><ul></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> <li>Fixed issue causing <code>bowtie2</code> to fail in <code><a href="bowtie2-options-fast-local">--fast-local</a></code> mode.</li></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> <li>Fixed issue causing <code><a href="bowtie2-options-soft-clipped-unmapped-tlen>--soft-clipped-unmapped-tlen</a></code> to be a positional argument.</li></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> <li>New option <code><a href="bowtie2-options-trim-to">--trim-to</a> N</code> causes <code>bowtie2</code> to trim reads longer than <code>N</code> bases to exactly <code>N</code> bases. Can trim from either 3' or 5' end, e.g. <code><a href="bowtie2-options-trim-to">--trim-to</a> 5:30</code> trims reads to 30 bases, truncating at the 5' end.</li></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> <li>Updated <a href="#building-from-source">"Building from source"</a> manual section with additional instructions on installing TBB.</li></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> <li>Fixed an issue causing <code>bowtie2-build</code> and <code>bowtie2-inspect</code> to output incomplete help text.</li></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> <li>Fixed an issue causing <code>bowtie2-align</code> to crash.</li></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> <li>Fixed an issue preventing <code>bowtie2</code> from processing paired and/or unpaired FASTQ reads together with interleaved FASTQ reads.</li></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></ul></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"><h2>Version 2.3.4.2 - August 07, 2018</h2></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"><ul></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> <li>Fixed issue causing <code>bowtie2</code> to fail in <code><a href="manual.shtml#bowtie2-options-fast-local">--fast-local</a></code> mode.</li></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> <li>Fixed issue causing <code><a href="manual.shtml#bowtie2-options-soft-clipped-unmapped-tlen">--soft-clipped-unmapped-tlen</a></code> to be a positional argument.</li></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> <li>New option <code><a href="manual.shtml#bowtie2-options-trim-to">--trim-to</a> N</code> causes <code>bowtie2</code> to trim reads longer than <code>N</code> bases to exactly <code>N</code> bases. Can trim from either 3' or 5' end, e.g. <code><a href="manual.shtml#bowtie2-options-trim-to">--trim-to</a> 5:30</code> trims reads to 30 bases, truncating at the 5' end.</li></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> <li>Updated <a href="manual.shtml#building-from-source">"Building from source"</a> manual section with additional instructions on installing TBB.</li></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> <li>Several other updates to manual, including new mentions of <a href="http://bioconda.github.io">Bioconda</a> and <a href="https://biocontainers.pro">Biocontainers</a>.</li></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> <li>Fixed an issue preventing <code>bowtie2</code> from processing more than one pattern source when running single threaded.</li></span>
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9
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> <li>Fixed an issue causing <code>bowtie2</code> and <code>bowtie2-inspect</code> to crash if the index contains a gap-only segment.</li></span>
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10
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> <li>Added <i>experimental</i> BAM input mode <code>-b</code>. Works only with unpaired input reads and BAM files that are sorted by read name (<code>samtools sort -n</code>). BAM input mode also supports the following options:<li></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> <ul></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> <li><code>--preserve-sam-tags</code>: Preserve any optional fields present in BAM record</li></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> <li><code>--align-paired-reads</code>: Paired-end mode for BAM files</li></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> </ul></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">     <code>--preserve-sam-tags</code>: Preserve any optional fields present in BAM record</li></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">     <code>--align-paired-reads</code>: Paired-end mode for BAM files</li></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> <li>Add <i>experimental</i> CMake support</li></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.<span class="idiff left right">2">Bowtie2 2.3.4.2</span></a></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.<span class="idiff left right">3">Bowtie2 2.3.4.3</span></a></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> 0<span class="idiff left right">8/0</span>7/18 </span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="plaintext"> <h2>Related publications</h2></span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="plaintext"> <ul></span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext"> <li style="font-size: x-small; line-height: 130%">Langmead B, Wilks C., Antonescu V., Charles R. <a href="https://doi.org/10.1093/bioinformatics/bty648"><b>Scaling read aligners to hundreds of threads on general-purpose processors</b></a>. <i><a href="https://academic.oup.com/bioinformatics">Bioinformatics</a></i>. bty648.<br/><br/></li></span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="plaintext"> <li style="font-size: x-small; line-height: 130%">Langmead B, Salzberg S. <a href="http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1923.html"><b>Fast gapped-read alignment with Bowtie 2</b></a>. <i><a href="http://www.nature.com/nmeth">Nature Methods</a></i>. 2012, 9:357-359.<br/><br/></li></span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="plaintext"> <li style="font-size: x-small; line-height: 130%">Langmead B, Trapnell C, Pop M, Salzberg SL. <a href="http://genomebiology.com/2009/10/3/R25"><b>Ultrafast and memory-efficient alignment of short DNA sequences to the human genome</b></a>. <i><a href="http://genomebiology.com">Genome Biology</a></i> <b>10</b>:R25.<br/><br/></li></span>
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="plaintext"> </ul></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/compare/b5fd5c31d9d324d1c724e965365932c64231f2db...7596be203863526cfedcc8e03063d5632c9ea907#e09def9b31d68cc22ed618a45007cec090ea243c"><strong>example/reads/conversion_utilities.sh</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># aliases for converting sample read files</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># `source conversion_utilities.sh` to add them to your environment</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nb" style="color: #0086b3;">alias </span><span class="nv" style="color: teal;">fastq_to_fasta</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"sed 'N;x;N;N;x;s/@/>/"</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nb" style="color: #0086b3;">alias </span><span class="nv" style="color: teal;">paired_to_tab5</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"paste <(sed 'N;x;N;g;N;s/</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">/ /g' reads_1.fq) <(sed -n 'n;h;n;g;N;s/</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">/ /g;p' reads_2.fq) > reads_12.tab5"</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">alias </span><span class="nv" style="color: teal;">paired_to_tab6</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"paste <(sed 'N;x;N;g;N;s/</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">/ /g' reads_1.fq) <(sed 'N;x;N;g;N;s/</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">/ /g' reads_2.fq) > reads_12.tab6"</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">alias </span><span class="nv" style="color: teal;">paired_to_interleaved</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"paste -d'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">' <(sed 'N;N;N;s/</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">/ /g' reads_1.fq) <(sed 'N;N;N;s/</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">/ /g' reads_2.fq) | tr '</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">' '</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">' > reads_12.fq"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie2/compare/b5fd5c31d9d324d1c724e965365932c64231f2db...7596be203863526cfedcc8e03063d5632c9ea907#ca0679d32b003b8024f4d51789e4d6e5b06db9c9"><strong>formats.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,7 +30,6 @@ enum file_format {</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"> <span class="n" style="color: #333;">FASTA</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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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"> <span class="n" style="color: #333;">FASTA_CONT</span><span class="p">,</span></span>
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"> <span class="n" style="color: #333;">FASTQ</span><span class="p">,</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="c"> <span class="n" style="color: #333;">INTERLEAVED</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"> <span class="n" style="color: #333;">BAM</span><span class="p">,</span></span>
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35
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"> <span class="n" style="color: #333;">TAB_MATE5</span><span class="p">,</span></span>
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36
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"> <span class="n" style="color: #333;">TAB_MATE6</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,7 +43,6 @@ static const std::string file_format_names[] = {</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"> <span class="s" style="color: #d14;">"FASTA"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"> <span class="s" style="color: #d14;">"FASTA sampling"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"> <span class="s" style="color: #d14;">"FASTQ"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="c"> <span class="s" style="color: #d14;">"Interleaved FASTQ"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"> <span class="s" style="color: #d14;">"BAM"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"> <span class="s" style="color: #d14;">"Tabbed mated"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"> <span class="s" style="color: #d14;">"Raw"</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -100,9 +100,8 @@ PatternSource* PatternSource::patsrcFromStrings(</td>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">FASTA</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FastaPatternSource</span><span class="p">(</span><span class="n" style="color: #333;">qs</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">FASTA_CONT</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FastaContinuousPatternSource</span><span class="p">(</span><span class="n" style="color: #333;">qs</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">RAW</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">RawPatternSource</span><span class="p">(</span><span class="n" style="color: #333;">qs</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">FASTQ</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FastqPatternSource</span><span class="p">(</span><span class="n" style="color: #333;">qs</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">FASTQ</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FastqPatternSource</span><span class="p">(</span><span class="n" style="color: #333;">qs</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">interleaved</span></span><span class="p">);</span></span>
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BAM</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BAMPatternSource</span><span class="p">(</span><span class="n" style="color: #333;">qs</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">INTERLEAVED</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FastqPatternSource</span><span class="p">(</span><span class="n" style="color: #333;">qs</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span> <span class="cm" style="color: #998; font-style: italic;">/* interleaved */</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">TAB_MATE5</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">TabbedPatternSource</span><span class="p">(</span><span class="n" style="color: #333;">qs</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">TAB_MATE6</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">TabbedPatternSource</span><span class="p">(</span><span class="n" style="color: #333;">qs</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">CMDLINE</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">VectorPatternSource</span><span class="p">(</span><span class="n" style="color: #333;">qs</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -232,14 +231,13 @@ pair<bool, int> DualPatternComposer::nextBatch(PerThreadReadBuf& pt) {</td>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp"> <span class="n" style="color: #333;">pt</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp"> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// batch A (or pairs)</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp"> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// grab lock below</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">done</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">res</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC236" 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;">done</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">res</span><span class="p">.</span><span class="n" style="color: #333;">second</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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<pre style="margin: 0;">+<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;">res</span><span class="p">.</span><span class="n" style="color: #333;">second</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;">cur</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">srca_</span><span class="o" style="font-weight: 600;">-></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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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237
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp"> <span class="n" style="color: #333;">ThreadSafe</span> <span class="n" style="color: #333;">ts</span><span class="p">(</span><span class="n" style="color: #333;">mutex_m</span><span class="p">);</span></span>
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236
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cur</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;">cur_</span><span class="p">)</span> <span class="n" style="color: #333;">cur_</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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239
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"> <span class="n" style="color: #333;">cur</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Move on to next PatternSource</span></span>
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240
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// on to next pair of PatternSources</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">done</span></span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">res</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">first</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cur</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">srca_</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC241" 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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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"> <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;">bool</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;">resa</span><span class="p">,</span> <span class="n" style="color: #333;">resb</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Lock to ensure that this thread gets parallel reads</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -295,12 +293,11 @@ PatternComposer* PatternComposer::setupPatternComposer(</td>
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295
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EList</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;">q</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// qualities associated with singles</span></span>
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296
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EList</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;">q1</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// qualities associated with m1</span></span>
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297
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EList</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;">q2</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// qualities associated with m2</span></span>
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298
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">PatternParams</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// read-in parameters</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"> <span class="n" style="color: #333;">PatternParams</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// read-in parameters</span></span>
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<pre style="margin: 0;"> <span id="LC297" 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="p">)</span> <span class="c1" style="color: #998; font-style: italic;">// be talkative?</span></span>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cpp"> <span class="n" style="color: #333;">EList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">PatternSource</span><span class="o" style="font-weight: 600;">*>*</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">EList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">PatternSource</span><span class="o" style="font-weight: 600;">*></span><span class="p">();</span></span>
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302
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="cpp"> <span class="n" style="color: #333;">EList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">PatternSource</span><span class="o" style="font-weight: 600;">*>*</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">EList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">PatternSource</span><span class="o" style="font-weight: 600;">*></span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="cpp"> <span class="n" style="color: #333;">EList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">PatternSource</span><span class="o" style="font-weight: 600;">*>*</span> <span class="n" style="color: #333;">ab</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">EList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">PatternSource</span><span class="o" style="font-weight: 600;">*></span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Create list of pattern sources for paired reads appearing</span></span>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// interleaved in a single file</span></span>
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306
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<pre style="margin: 0;"> <span id="LC303" 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="n" style="color: #333;">m12</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="diff-line-num unfold js-unfold old_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -312,7 +309,9 @@ PatternComposer* PatternComposer::setupPatternComposer(</td>
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312
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">m12</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="cpp"> <span class="n" style="color: #333;">ab</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">PatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">patsrcFromStrings</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;">qs</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp"> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">PatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">patsrcFromStrings</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;">qs</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</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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<pre style="margin: 0;"> <span id="LC315" 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;">p</span><span class="p">.</span><span class="n" style="color: #333;">fileParallel</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -376,16 +375,7 @@ PatternComposer* PatternComposer::setupPatternComposer(</td>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="cpp"> <span class="n" style="color: #333;">PatternComposer</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">patsrc</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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<pre style="margin: 0;">-<span id="LC379" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m12</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="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="cpp"> <span class="n" style="color: #333;">patsrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">SoloPatternComposer</span><span class="p">(</span><span class="n" style="color: #333;">ab</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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381
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<pre style="margin: 0;">-<span id="LC381" 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="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></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="k" style="font-weight: 600;">delete</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="p">)[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC382" 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="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></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="k" style="font-weight: 600;">delete</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">b</span><span class="p">)[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">a</span><span class="p">;</span> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC384" 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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<pre style="margin: 0;">-<span id="LC385" class="line" lang="cpp"> <span class="n" style="color: #333;">patsrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">DualPatternComposer</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC386" 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="n" style="color: #333;">ab</span><span class="o" style="font-weight: 600;">-></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="k" style="font-weight: 600;">delete</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ab</span><span class="p">)[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">ab</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"> <span class="n" style="color: #333;">patsrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">DualPatternComposer</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">patsrc</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -471,9 +461,15 @@ void CFilePatternSource::open() {</td>
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471
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461
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="cpp"> <span class="p">}</span></span>
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472
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462
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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473
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463
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<pre style="margin: 0;"> <span id="LC463" 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;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">infiles_</span><span class="p">[</span><span class="n" style="color: #333;">filecur_</span><span class="p">].</span><span class="n" style="color: #333;">c_str</span><span class="p">();</span></span>
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474
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="cpp"> <span class="n" style="color: #333;">compressed_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">is_gzipped_file</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">compressed_</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC464" 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;">ext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">infiles_</span><span class="p">[</span><span class="n" style="color: #333;">filecur_</span><span class="p">].</span><span class="n" style="color: #333;">length</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Only temporary until we have a separate BGZFPatternSource</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">*--</span><span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'.'</span><span class="p">)</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">bam_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">ext</span><span class="p">,</span> <span class="s" style="color: #d14;">".bam"</span><span class="p">,</span> <span class="mi" style="color: #099;">4</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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<pre style="margin: 0;">+<span id="LC469" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC470" 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;">bam_file</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_gzipped_file</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="cpp"> <span class="n" style="color: #333;">zfp_</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;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="cpp"> <span class="n" style="color: #333;">compressed_</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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<pre style="margin: 0;"> <span id="LC473" 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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<pre style="margin: 0;"> <span id="LC474" class="line" lang="cpp"> <span class="n" style="color: #333;">fp_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC475" 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="1146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1146,6 +1142,12 @@ const int BAMPatternSource::offset[] = {</td>
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<pre style="margin: 0;"> <span id="LC1142" class="line" lang="cpp"> <span class="mi" style="color: #099;">32</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//read_name</span></span>
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<pre style="margin: 0;"> <span id="LC1143" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC1144" class="line" lang="cpp"></span>
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1145
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<pre style="margin: 0;">+<span id="LC1145" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">BAMPatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EOF_MARKER</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1146" class="line" lang="cpp"> <span class="mh" style="color: #099;">0x1f</span><span class="p">,</span> <span class="mh" style="color: #099;">0x8b</span><span class="p">,</span> <span class="mh" style="color: #099;">0x08</span><span class="p">,</span> <span class="mh" style="color: #099;">0x04</span><span class="p">,</span> <span class="mh" style="color: #099;">0x00</span><span class="p">,</span> <span class="mh" style="color: #099;">0x00</span><span class="p">,</span> <span class="mh" style="color: #099;">0x00</span><span class="p">,</span> <span class="mh" style="color: #099;">0x00</span><span class="p">,</span> <span class="mh" style="color: #099;">0x00</span><span class="p">,</span> <span class="mh" style="color: #099;">0xff</span><span class="p">,</span></span>
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1147
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<pre style="margin: 0;">+<span id="LC1147" class="line" lang="cpp"> <span class="mh" style="color: #099;">0x06</span><span class="p">,</span> <span class="mh" style="color: #099;">0x00</span><span class="p">,</span> <span class="mh" style="color: #099;">0x42</span><span class="p">,</span> <span class="mh" style="color: #099;">0x43</span><span class="p">,</span> <span class="mh" style="color: #099;">0x02</span><span class="p">,</span> <span class="mh" style="color: #099;">0x00</span><span class="p">,</span> <span class="mh" style="color: #099;">0x1b</span><span class="p">,</span> <span class="mh" style="color: #099;">0x00</span><span class="p">,</span> <span class="mh" style="color: #099;">0x03</span><span class="p">,</span> <span class="mh" style="color: #099;">0x00</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1148" class="line" lang="cpp"> <span class="mh" style="color: #099;">0x00</span><span class="p">,</span> <span class="mh" style="color: #099;">0x00</span><span class="p">,</span> <span class="mh" style="color: #099;">0x00</span><span class="p">,</span> <span class="mh" style="color: #099;">0x00</span><span class="p">,</span> <span class="mh" style="color: #099;">0x00</span><span class="p">,</span> <span class="mh" style="color: #099;">0x00</span><span class="p">,</span> <span class="mh" style="color: #099;">0x00</span><span class="p">,</span> <span class="mh" style="color: #099;">0x00</span></span>
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<pre style="margin: 0;">+<span id="LC1149" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC1150" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1151" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">BAMPatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parse_bam_header</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1152" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">magic</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC1153" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1203,58 +1205,281 @@ bool BAMPatternSource::parse_bam_header() {</td>
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<pre style="margin: 0;"> <span id="LC1205" 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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<pre style="margin: 0;"> <span id="LC1206" class="line" lang="cpp"><span class="p">}</span></span>
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1207
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<pre style="margin: 0;"> <span id="LC1207" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1206" class="line" lang="cpp"><span class="n" style="color: #333;">std</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;">bool</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;">BAMPatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">nextBatchFromFile</span><span class="p">(</span><span class="n" style="color: #333;">PerThreadReadBuf</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pt</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1207" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">batch_a</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">readi</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1208" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">first_</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1209" class="line" lang="cpp"> <span class="n" style="color: #333;">first_</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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<pre style="margin: 0;">-<span id="LC1210" 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;">parse_bam_header</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1211" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Unable to parse BAM file"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1212" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1208" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">BAMPatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">nextBGZFBlockFromFile</span><span class="p">(</span><span class="n" style="color: #333;">BGZF</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">b</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1209" class="line" lang="cpp"> <span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">fp_</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1210" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">feof_unlocked</span><span class="p">(</span><span class="n" style="color: #333;">fp_</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ferror_unlocked</span><span class="p">(</span><span class="n" style="color: #333;">fp_</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1211" 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 new new_line" data-linenumber="1212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1212
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<pre style="margin: 0;">+<span id="LC1212" class="line" lang="cpp"> <span class="p">}</span></span>
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1213
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<pre style="margin: 0;">+<span id="LC1213" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1214
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<pre style="margin: 0;">+<span id="LC1214" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">extra</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;">uint8_t</span><span class="p">[</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">.</span><span class="n" style="color: #333;">xlen</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1215
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<pre style="margin: 0;">+<span id="LC1215" class="line" lang="cpp"> <span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="n" style="color: #333;">extra</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">.</span><span class="n" style="color: #333;">xlen</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">fp_</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1216
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<pre style="margin: 0;">+<span id="LC1216" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ferror_unlocked</span><span class="p">(</span><span class="n" style="color: #333;">fp_</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1217
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<pre style="margin: 0;">+<span id="LC1217" 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 new new_line" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1218
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<pre style="margin: 0;">+<span id="LC1218" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1219
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<pre style="margin: 0;">+<span id="LC1219" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1220
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<pre style="margin: 0;">+<span id="LC1220" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memcmp</span><span class="p">(</span><span class="n" style="color: #333;">EOF_MARKER</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">hdr</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="diff-line-num new new_line" data-linenumber="1221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1221
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<pre style="margin: 0;">+<span id="LC1221" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">memcmp</span><span class="p">(</span><span class="n" style="color: #333;">EOF_MARKER</span> <span class="o" style="font-weight: 600;">+</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">),</span> <span class="n" style="color: #333;">extra</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span> <span class="cm" style="color: #998; font-style: italic;">/* sizeof BAM subfield */</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 new new_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1222
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<pre style="margin: 0;">+<span id="LC1222" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1223
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<pre style="margin: 0;">+<span id="LC1223" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">extra</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1224
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<pre style="margin: 0;">+<span id="LC1224" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">fp_</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1225
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<pre style="margin: 0;">+<span id="LC1225" 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 new new_line" data-linenumber="1226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1226
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<pre style="margin: 0;">+<span id="LC1226" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1227
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<pre style="margin: 0;">+<span id="LC1227" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1228
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<pre style="margin: 0;">+<span id="LC1228" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">bsize</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 new new_line" data-linenumber="1229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1229
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<pre style="margin: 0;">+<span id="LC1229" 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;">uint16_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="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">.</span><span class="n" style="color: #333;">xlen</span><span class="p">;)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1230
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<pre style="margin: 0;">+<span id="LC1230" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">extra</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="mi" style="color: #099;">66</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">extra</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="mi" style="color: #099;">67</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1231
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<pre style="margin: 0;">+<span id="LC1231" class="line" lang="cpp"> <span class="n" style="color: #333;">bsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="n" style="color: #333;">extra</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">4</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1232
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<pre style="margin: 0;">+<span id="LC1232" class="line" lang="cpp"> <span class="n" style="color: #333;">bsize</span> <span class="o" style="font-weight: 600;">-=</span> <span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">.</span><span class="n" style="color: #333;">xlen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">19</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1233
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<pre style="margin: 0;">+<span id="LC1233" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1213
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<td class="diff-line-num new_line" data-linenumber="1234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1234
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<pre style="margin: 0;"> <span id="LC1234" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1235
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<pre style="margin: 0;">+<span id="LC1235" class="line" lang="cpp"> <span class="n" style="color: #333;">i</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;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1236
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<pre style="margin: 0;">+<span id="LC1236" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">sub_field_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="n" style="color: #333;">extra</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="diff-line-num new new_line" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1237
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<pre style="margin: 0;">+<span id="LC1237" class="line" lang="cpp"> <span class="n" style="color: #333;">i</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;">2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sub_field_len</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1238
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<pre style="margin: 0;">+<span id="LC1238" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1239
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<pre style="margin: 0;">+<span id="LC1239" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1240
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<pre style="margin: 0;">+<span id="LC1240" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">extra</span><span class="p">;</span></span>
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1241
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<pre style="margin: 0;">+<span id="LC1241" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1242
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<pre style="margin: 0;">+<span id="LC1242" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bsize</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="diff-line-num new new_line" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1243
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<pre style="margin: 0;">+<span id="LC1243" 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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1244
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<pre style="margin: 0;">+<span id="LC1244" class="line" lang="cpp"> <span class="p">}</span></span>
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1245
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<pre style="margin: 0;">+<span id="LC1245" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1246
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<pre style="margin: 0;">+<span id="LC1246" class="line" lang="cpp"> <span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">cdata</span><span class="p">,</span> <span class="n" style="color: #333;">bsize</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">fp_</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1247
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<pre style="margin: 0;">+<span id="LC1247" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ferror_unlocked</span><span class="p">(</span><span class="n" style="color: #333;">fp_</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1248
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<pre style="margin: 0;">+<span id="LC1248" 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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1214
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<td class="diff-line-num new_line" data-linenumber="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1249
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<pre style="margin: 0;"> <span id="LC1249" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1215
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<td class="diff-line-num new_line" data-linenumber="1250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1250
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<pre style="margin: 0;"> <span id="LC1250" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1251
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<pre style="margin: 0;">+<span id="LC1251" class="line" lang="cpp"> <span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">ftr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">ftr</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">fp_</span><span class="p">);</span></span>
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1252
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<pre style="margin: 0;">+<span id="LC1252" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ferror_unlocked</span><span class="p">(</span><span class="n" style="color: #333;">fp_</span><span class="p">))</span> <span class="p">{</span></span>
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1253
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<pre style="margin: 0;">+<span id="LC1253" 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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1254
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<pre style="margin: 0;">+<span id="LC1254" class="line" lang="cpp"> <span class="p">}</span></span>
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1255
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<pre style="margin: 0;">+<span id="LC1255" class="line" lang="cpp"></span>
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1256
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<pre style="margin: 0;">+<span id="LC1256" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bsize</span><span class="p">;</span></span>
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1257
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<pre style="margin: 0;">+<span id="LC1257" class="line" lang="cpp"><span class="p">}</span></span>
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1258
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<pre style="margin: 0;">+<span id="LC1258" class="line" lang="cpp"></span>
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1259
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<pre style="margin: 0;">+<span id="LC1259" class="line" lang="cpp"><span class="n" style="color: #333;">std</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;">bool</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;">BAMPatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">nextBatch</span><span class="p">(</span><span class="n" style="color: #333;">PerThreadReadBuf</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">batch_a</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">lock</span><span class="p">)</span> <span class="p">{</span></span>
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1260
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<pre style="margin: 0;">+<span id="LC1260" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">cdata_len</span><span class="p">;</span></span>
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1261
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<pre style="margin: 0;">+<span id="LC1261" class="line" lang="cpp"></span>
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1262
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<pre style="margin: 0;">+<span id="LC1262" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">nread</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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1263
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<pre style="margin: 0;">+<span id="LC1263" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">done</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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1264
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<pre style="margin: 0;">+<span id="LC1264" class="line" lang="cpp"></span>
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1265
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<pre style="margin: 0;">+<span id="LC1265" class="line" lang="cpp"> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">setReadId</span><span class="p">(</span><span class="n" style="color: #333;">readCnt_</span><span class="p">);</span></span>
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1266
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<pre style="margin: 0;">+<span id="LC1266" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1267
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<pre style="margin: 0;">+<span id="LC1267" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">do</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1268
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<pre style="margin: 0;">+<span id="LC1268" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bam_batch_indexes_</span><span class="p">[</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">tid_</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">bam_batches_</span><span class="p">[</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">tid_</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1269
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<pre style="margin: 0;">+<span id="LC1269" class="line" lang="cpp"> <span class="n" style="color: #333;">BGZF</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">block</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">blocks_</span><span class="p">[</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">tid_</span><span class="p">];</span></span>
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1270
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<pre style="margin: 0;">+<span id="LC1270" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</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;">uint8_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">batch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_batches_</span><span class="p">[</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">tid_</span><span class="p">];</span></span>
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1271
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<pre style="margin: 0;">+<span id="LC1271" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">lock</span><span class="p">)</span> <span class="p">{</span></span>
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1272
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<pre style="margin: 0;">+<span id="LC1272" class="line" lang="cpp"> <span class="n" style="color: #333;">ThreadSafe</span> <span class="n" style="color: #333;">ts</span><span class="p">(</span><span class="n" style="color: #333;">mutex</span><span class="p">);</span></span>
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1273
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<pre style="margin: 0;">+<span id="LC1273" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">first_</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1274
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<pre style="margin: 0;">+<span id="LC1274" class="line" lang="cpp"> <span class="n" style="color: #333;">nextBGZFBlockFromFile</span><span class="p">(</span><span class="n" style="color: #333;">block</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1275
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<pre style="margin: 0;">+<span id="LC1275" class="line" lang="cpp"> <span class="n" style="color: #333;">first_</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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1276
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<pre style="margin: 0;">+<span id="LC1276" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1277
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<pre style="margin: 0;">+<span id="LC1277" class="line" lang="cpp"> <span class="n" style="color: #333;">cdata_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextBGZFBlockFromFile</span><span class="p">(</span><span class="n" style="color: #333;">block</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1278
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<pre style="margin: 0;">+<span id="LC1278" 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="diff-line-num new new_line" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1279
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<pre style="margin: 0;">+<span id="LC1279" class="line" lang="cpp"> <span class="n" style="color: #333;">cdata_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextBGZFBlockFromFile</span><span class="p">(</span><span class="n" style="color: #333;">block</span><span class="p">);</span></span>
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1280
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<pre style="margin: 0;">+<span id="LC1280" class="line" lang="cpp"> <span class="p">}</span></span>
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1281
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<pre style="margin: 0;">+<span id="LC1281" class="line" lang="cpp"></span>
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1282
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<pre style="margin: 0;">+<span id="LC1282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cdata_len</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="diff-line-num new new_line" data-linenumber="1283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1283
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<pre style="margin: 0;">+<span id="LC1283" class="line" lang="cpp"> <span class="n" style="color: #333;">ThreadSafe</span> <span class="n" style="color: #333;">ts</span><span class="p">(</span><span class="n" style="color: #333;">orphan_mates_mutex_</span><span class="p">);</span></span>
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1284
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<pre style="margin: 0;">+<span id="LC1284" class="line" lang="cpp"> <span class="n" style="color: #333;">get_orphaned_pairs</span><span class="p">(</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">bufa_</span><span class="p">,</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">bufb_</span><span class="p">,</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">max_buf_</span><span class="p">,</span> <span class="n" style="color: #333;">nread</span><span class="p">);</span></span>
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1285
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<pre style="margin: 0;">+<span id="LC1285" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">nread</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;">nread</span><span class="p">);</span></span>
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1286
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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="cpp"> <span class="p">}</span></span>
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1287
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<pre style="margin: 0;">+<span id="LC1287" class="line" lang="cpp"></span>
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1288
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<pre style="margin: 0;">+<span id="LC1288" class="line" lang="cpp"> <span class="n" style="color: #333;">bam_batch_indexes_</span><span class="p">[</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">tid_</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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1289
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<pre style="margin: 0;">+<span id="LC1289" class="line" lang="cpp"></span>
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1290
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<pre style="margin: 0;">+<span id="LC1290" class="line" lang="cpp"> <span class="n" style="color: #333;">batch</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">block</span><span class="p">.</span><span class="n" style="color: #333;">ftr</span><span class="p">.</span><span class="n" style="color: #333;">isize</span><span class="p">);</span></span>
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1291
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<pre style="margin: 0;">+<span id="LC1291" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1292
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<pre style="margin: 0;">+<span id="LC1292" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret_code</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decompress_bgzf_block</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">batch</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">block</span><span class="p">.</span><span class="n" style="color: #333;">ftr</span><span class="p">.</span><span class="n" style="color: #333;">isize</span><span class="p">,</span> <span class="n" style="color: #333;">block</span><span class="p">.</span><span class="n" style="color: #333;">cdata</span><span class="p">,</span> <span class="n" style="color: #333;">cdata_len</span><span class="p">);</span></span>
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1293
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<pre style="margin: 0;">+<span id="LC1293" class="line" lang="cpp"></span>
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1294
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<pre style="margin: 0;">+<span id="LC1294" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ret_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">Z_OK</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1295
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<pre style="margin: 0;">+<span id="LC1295" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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1296
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<pre style="margin: 0;">+<span id="LC1296" class="line" lang="cpp"> <span class="p">}</span></span>
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1297
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<pre style="margin: 0;">+<span id="LC1297" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1298
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<pre style="margin: 0;">+<span id="LC1298" class="line" lang="cpp"> <span class="n" style="color: #333;">uLong</span> <span class="n" style="color: #333;">crc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">crc32</span><span class="p">(</span><span class="mi" style="color: #099;">0L</span><span class="p">,</span> <span class="n" style="color: #333;">Z_NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1299
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<pre style="margin: 0;">+<span id="LC1299" class="line" lang="cpp"> <span class="n" style="color: #333;">crc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">crc32</span><span class="p">(</span><span class="n" style="color: #333;">crc</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">batch</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">batch</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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1300
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<pre style="margin: 0;">+<span id="LC1300" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">crc</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">block</span><span class="p">.</span><span class="n" style="color: #333;">ftr</span><span class="p">.</span><span class="n" style="color: #333;">crc32</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1301
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<pre style="margin: 0;">+<span id="LC1301" class="line" lang="cpp"> <span class="p">}</span></span>
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1302
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<pre style="margin: 0;">+<span id="LC1302" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1303
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<pre style="margin: 0;">+<span id="LC1303" class="line" lang="cpp"> <span class="n" style="color: #333;">std</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;">bool</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;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_alignments</span><span class="p">(</span><span class="n" style="color: #333;">pt</span><span class="p">,</span> <span class="n" style="color: #333;">batch_a</span><span class="p">,</span> <span class="n" style="color: #333;">nread</span><span class="p">);</span></span>
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1304
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<pre style="margin: 0;">+<span id="LC1304" class="line" lang="cpp"></span>
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1305
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<pre style="margin: 0;">+<span id="LC1305" class="line" lang="cpp"> <span class="n" style="color: #333;">done</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ret</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1306
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<pre style="margin: 0;">+<span id="LC1306" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">done</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nread</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">max_buf_</span><span class="p">);</span></span>
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1307
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<pre style="margin: 0;">+<span id="LC1307" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1308
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<pre style="margin: 0;">+<span id="LC1308" class="line" lang="cpp"> <span class="n" style="color: #333;">readCnt_</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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1309
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<pre style="margin: 0;">+<span id="LC1309" class="line" lang="cpp"></span>
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1310
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<pre style="margin: 0;">+<span id="LC1310" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">done</span><span class="p">,</span> <span class="n" style="color: #333;">nread</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1311
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<pre style="margin: 0;">+<span id="LC1311" class="line" lang="cpp"><span class="p">}</span></span>
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1312
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<pre style="margin: 0;">+<span id="LC1312" class="line" lang="cpp"></span>
</pre>
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1313
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<pre style="margin: 0;">+<span id="LC1313" class="line" lang="cpp"><span class="n" style="color: #333;">std</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;">bool</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;">BAMPatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">get_alignments</span><span class="p">(</span><span class="n" style="color: #333;">PerThreadReadBuf</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">batch_a</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">readi</span><span class="p">)</span> <span class="p">{</span></span>
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1314
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<pre style="margin: 0;">+<span id="LC1314" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</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="n" style="color: #333;">bam_batch_indexes_</span><span class="p">[</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">tid_</span><span class="p">];</span></span>
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1216
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1315
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<pre style="margin: 0;"> <span id="LC1315" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">done</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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1217
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1316
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<pre style="margin: 0;"> <span id="LC1316" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">read1</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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1218
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1317
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<pre style="margin: 0;"> <span id="LC1317" class="line" lang="cpp"></span>
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1219
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1318
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<pre style="margin: 0;"> <span id="LC1318" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">readi</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">max_buf_</span><span class="p">)</span> <span class="p">{</span></span>
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1220
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<pre style="margin: 0;">-<span id="LC1220" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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1319
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<pre style="margin: 0;">+<span id="LC1319" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">bam_batches_</span><span class="p">[</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">tid_</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="p">{</span></span>
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1320
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<pre style="margin: 0;">+<span id="LC1320" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">readi</span><span class="p">);</span></span>
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1321
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<pre style="margin: 0;">+<span id="LC1321" class="line" lang="cpp"> <span class="p">}</span></span>
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1322
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<pre style="margin: 0;">+<span id="LC1322" class="line" lang="cpp"></span>
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1221
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1323
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<pre style="margin: 0;"> <span id="LC1323" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">flag</span><span class="p">;</span></span>
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1222
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1324
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<pre style="margin: 0;"> <span id="LC1324" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">block_size</span><span class="p">;</span></span>
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1223
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<td class="diff-line-num new_line" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1325
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<pre style="margin: 0;"> <span id="LC1325" class="line" lang="cpp"> <span class="n" style="color: #333;">EList</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="n" style="color: #333;">readbuf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pp_</span><span class="p">.</span><span class="n" style="color: #333;">align_paired_reads</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">read1</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">bufb_</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">bufa_</span><span class="p">;</span></span>
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1224
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1326
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<pre style="margin: 0;"> <span id="LC1326" class="line" lang="cpp"></span>
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<td class="diff-line-num new_line old" data-linenumber="1327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1225" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">zread</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">block_size</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">block_size</span><span class="p">)))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">block_size</span><span class="p">))</span> <span class="p">{</span></span>
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1226
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<pre style="margin: 0;">-<span id="LC1226" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="n" style="color: #333;">readi</span><span class="p">);</span></span>
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1227
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<pre style="margin: 0;">-<span id="LC1227" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1228
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<td class="diff-line-num new_line old" data-linenumber="1327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1228" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBuf</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="n" style="color: #333;">block_size</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1229
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<pre style="margin: 0;">-<span id="LC1229" class="line" lang="cpp"> <span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">block_size</span><span class="p">);</span></span>
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1230
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<pre style="margin: 0;">-<span id="LC1230" class="line" lang="cpp"> <span class="p">}</span></span>
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1231
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<pre style="margin: 0;">-<span id="LC1231" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">zread</span><span class="p">(</span><span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">.</span><span class="n" style="color: #333;">wbuf</span><span class="p">(),</span> <span class="n" style="color: #333;">block_size</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">block_size</span><span class="p">)</span> <span class="p">{</span></span>
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1232
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<td class="diff-line-num new_line old" data-linenumber="1327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1232" class="line" lang="cpp"> <span class="n" style="color: #333;">done</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 old old_line" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1233
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<td class="diff-line-num new_line old" data-linenumber="1327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1233" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1327
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<pre style="margin: 0;">+<span id="LC1327" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">block_size</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bam_batches_</span><span class="p">[</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">tid_</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;">i</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">block_size</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1328
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<pre style="margin: 0;">+<span id="LC1328" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">block_size</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="diff-line-num new new_line" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1329
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<pre style="margin: 0;">+<span id="LC1329" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">done</span><span class="p">,</span> <span class="n" style="color: #333;">readi</span><span class="p">);</span></span>
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1234
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<td class="diff-line-num new_line" data-linenumber="1330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1330
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<pre style="margin: 0;"> <span id="LC1330" class="line" lang="cpp"> <span class="p">}</span></span>
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1235
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<td class="diff-line-num new_line old" data-linenumber="1331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1235" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">.</span><span class="n" style="color: #333;">buf</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span><span class="p">[</span><span class="n" style="color: #333;">BAMField</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">flag</span><span class="p">],</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">flag</span><span class="p">));</span></span>
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1331
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<pre style="margin: 0;">+<span id="LC1331" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">block_size</span><span class="p">);</span></span>
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1332
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<pre style="margin: 0;">+<span id="LC1332" class="line" lang="cpp"></span>
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1333
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<pre style="margin: 0;">+<span id="LC1333" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bam_batches_</span><span class="p">[</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">tid_</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;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span><span class="p">[</span><span class="n" style="color: #333;">BAMField</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">flag</span><span class="p">],</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">flag</span><span class="p">));</span></span>
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1236
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<td class="diff-line-num new_line" data-linenumber="1334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1334
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<pre style="margin: 0;"> <span id="LC1334" 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;">pp_</span><span class="p">.</span><span class="n" style="color: #333;">align_paired_reads</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x40</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="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x80</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="diff-line-num old_line" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1237
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<td class="diff-line-num new_line" data-linenumber="1335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1335
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<pre style="margin: 0;"> <span id="LC1335" class="line" lang="cpp"> <span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1336
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<pre style="margin: 0;">+<span id="LC1336" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">block_size</span><span class="p">;</span></span>
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1238
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1337
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<pre style="margin: 0;"> <span id="LC1337" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1239
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1338
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<pre style="margin: 0;"> <span id="LC1338" class="line" lang="cpp"> <span class="p">}</span></span>
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1339
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<pre style="margin: 0;">+<span id="LC1339" class="line" lang="cpp"></span>
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1240
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1340
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<pre style="margin: 0;"> <span id="LC1340" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pp_</span><span class="p">.</span><span class="n" style="color: #333;">align_paired_reads</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x40</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="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x80</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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1241
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1341
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<pre style="margin: 0;"> <span id="LC1341" class="line" lang="cpp"> <span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC1342" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">block_size</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1343" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1344" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1244" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pp_</span><span class="p">.</span><span class="n" style="color: #333;">align_paired_reads</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">read1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x40</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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1245
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<pre style="margin: 0;">-<span id="LC1245" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Paired reads are out of order"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1246
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<pre style="margin: 0;">-<span id="LC1246" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="n" style="color: #333;">readi</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;">readi</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">readi</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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<pre style="margin: 0;">+<span id="LC1345" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC1346" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pp_</span><span class="p">.</span><span class="n" style="color: #333;">align_paired_reads</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(((</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x40</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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<pre style="margin: 0;">+<span id="LC1347" class="line" lang="cpp"> <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="n" style="color: #333;">block_size</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bam_batches_</span><span class="p">[</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">tid_</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC1348" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">||</span> <span class="p">((</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x80</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;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">block_size</span><span class="p">))))</span></span>
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<pre style="margin: 0;">+<span id="LC1349" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1350" class="line" lang="cpp"> <span class="n" style="color: #333;">ThreadSafe</span> <span class="n" style="color: #333;">ts</span><span class="p">(</span><span class="n" style="color: #333;">orphan_mates_mutex_</span><span class="p">);</span></span>
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1351
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<pre style="margin: 0;">+<span id="LC1351" class="line" lang="cpp"> <span class="n" style="color: #333;">store_orphan_mate</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bam_batches_</span><span class="p">[</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">tid_</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;">i</span><span class="p">,</span> <span class="n" style="color: #333;">block_size</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1352" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">block_size</span><span class="p">;</span></span>
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1353
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<pre style="margin: 0;">+<span id="LC1353" class="line" lang="cpp"> <span class="n" style="color: #333;">get_orphaned_pairs</span><span class="p">(</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">bufa_</span><span class="p">,</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">bufb_</span><span class="p">,</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">max_buf_</span><span class="p">,</span> <span class="n" style="color: #333;">readi</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1354" 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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<pre style="margin: 0;">+<span id="LC1355" class="line" lang="cpp"> <span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">block_size</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1356" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC1357" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">.</span><span class="n" style="color: #333;">wbuf</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bam_batches_</span><span class="p">[</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">tid_</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;">i</span><span class="p">,</span> <span class="n" style="color: #333;">block_size</span><span class="p">);</span></span>
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1358
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<pre style="margin: 0;">+<span id="LC1358" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">block_size</span><span class="p">;</span></span>
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1359
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<pre style="margin: 0;">+<span id="LC1359" class="line" lang="cpp"></span>
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1360
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<pre style="margin: 0;">+<span id="LC1360" class="line" lang="cpp"> <span class="n" style="color: #333;">read1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">read1</span><span class="p">;</span></span>
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1361
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<pre style="margin: 0;">+<span id="LC1361" class="line" lang="cpp"> <span class="n" style="color: #333;">readi</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">pp_</span><span class="p">.</span><span class="n" style="color: #333;">align_paired_reads</span></span>
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1362
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<pre style="margin: 0;">+<span id="LC1362" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">bufb_</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBuf</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="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">readi</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">readi</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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1247
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1363
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<pre style="margin: 0;"> <span id="LC1363" class="line" lang="cpp"> <span class="p">}</span></span>
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1248
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<pre style="margin: 0;">-<span id="LC1248" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pp_</span><span class="p">.</span><span class="n" style="color: #333;">align_paired_reads</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">read1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x80</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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1249
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<pre style="margin: 0;">-<span id="LC1249" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Paired reads are out of order"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1250
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<pre style="margin: 0;">-<span id="LC1250" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="n" style="color: #333;">readi</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;">readi</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">readi</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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<pre style="margin: 0;">+<span id="LC1364" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1365" class="line" lang="cpp"></span>
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1366
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<pre style="margin: 0;">+<span id="LC1366" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">done</span><span class="p">,</span> <span class="n" style="color: #333;">readi</span><span class="p">);</span></span>
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1367
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<pre style="margin: 0;">+<span id="LC1367" class="line" lang="cpp"><span class="p">}</span></span>
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1368
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<pre style="margin: 0;">+<span id="LC1368" class="line" lang="cpp"></span>
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1369
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<pre style="margin: 0;">+<span id="LC1369" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">BAMPatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">store_orphan_mate</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">read_len</span><span class="p">)</span> <span class="p">{</span></span>
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1370
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<pre style="margin: 0;">+<span id="LC1370" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">flag</span><span class="p">;</span></span>
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1371
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<pre style="margin: 0;">+<span id="LC1371" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">flag</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;">offset</span><span class="p">[</span><span class="n" style="color: #333;">BAMField</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">flag</span><span class="p">],</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">flag</span><span class="p">));</span></span>
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1372
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<pre style="margin: 0;">+<span id="LC1372" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC1373" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">orphan_mate_t</span><span class="o" style="font-weight: 600;">>&</span></span>
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1374
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<pre style="margin: 0;">+<span id="LC1374" class="line" lang="cpp"> <span class="n" style="color: #333;">orphan_mates</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x40</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;">orphan_mate1s</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">orphan_mate2s</span><span class="p">;</span></span>
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1375
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<pre style="margin: 0;">+<span id="LC1375" class="line" lang="cpp"></span>
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1376
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<pre style="margin: 0;">+<span id="LC1376" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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1377
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<pre style="margin: 0;">+<span id="LC1377" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</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;">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;">orphan_mates</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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">orphan_mates</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">empty</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 class="p">;</span></span>
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1378
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<pre style="margin: 0;">+<span id="LC1378" class="line" lang="cpp"></span>
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1379
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<pre style="margin: 0;">+<span id="LC1379" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">orphan_mates</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="p">{</span></span>
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1380
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<pre style="margin: 0;">+<span id="LC1380" class="line" lang="cpp"> <span class="n" style="color: #333;">orphan_mates</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">orphan_mates</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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1381
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<pre style="margin: 0;">+<span id="LC1381" class="line" lang="cpp"> <span class="p">}</span></span>
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1382
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<pre style="margin: 0;">+<span id="LC1382" class="line" lang="cpp"></span>
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1383
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<pre style="margin: 0;">+<span id="LC1383" class="line" lang="cpp"> <span class="n" style="color: #333;">orphan_mate_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">mate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">orphan_mates</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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1384
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<pre style="margin: 0;">+<span id="LC1384" class="line" lang="cpp"></span>
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1385
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<pre style="margin: 0;">+<span id="LC1385" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mate</span><span class="p">.</span><span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">mate</span><span class="p">.</span><span class="n" style="color: #333;">cap</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">read_len</span><span class="p">)</span> <span class="p">{</span></span>
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1386
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<pre style="margin: 0;">+<span id="LC1386" class="line" lang="cpp"> <span class="n" style="color: #333;">mate</span><span class="p">.</span><span class="n" style="color: #333;">data</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;">uint8_t</span><span class="p">[</span><span class="n" style="color: #333;">read_len</span><span class="p">];</span></span>
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1387
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<pre style="margin: 0;">+<span id="LC1387" class="line" lang="cpp"> <span class="n" style="color: #333;">mate</span><span class="p">.</span><span class="n" style="color: #333;">cap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_len</span><span class="p">;</span></span>
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1388
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<pre style="margin: 0;">+<span id="LC1388" class="line" lang="cpp"> <span class="p">}</span></span>
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1389
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<pre style="margin: 0;">+<span id="LC1389" class="line" lang="cpp"></span>
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1390
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<pre style="margin: 0;">+<span id="LC1390" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mate</span><span class="p">.</span><span class="n" style="color: #333;">cap</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">read_len</span><span class="p">)</span> <span class="p">{</span></span>
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1391
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<pre style="margin: 0;">+<span id="LC1391" class="line" lang="cpp"> <span class="n" style="color: #333;">mate</span><span class="p">.</span><span class="n" style="color: #333;">data</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;">uint8_t</span><span class="p">[</span><span class="n" style="color: #333;">read_len</span><span class="p">];</span></span>
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1392
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<pre style="margin: 0;">+<span id="LC1392" class="line" lang="cpp"> <span class="n" style="color: #333;">mate</span><span class="p">.</span><span class="n" style="color: #333;">cap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_len</span><span class="p">;</span></span>
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1393
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<pre style="margin: 0;">+<span id="LC1393" class="line" lang="cpp"> <span class="p">}</span></span>
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1394
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<pre style="margin: 0;">+<span id="LC1394" class="line" lang="cpp"></span>
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1395
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<pre style="margin: 0;">+<span id="LC1395" class="line" lang="cpp"> <span class="n" style="color: #333;">mate</span><span class="p">.</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_len</span><span class="p">;</span></span>
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1396
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<pre style="margin: 0;">+<span id="LC1396" class="line" lang="cpp"></span>
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1397
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<pre style="margin: 0;">+<span id="LC1397" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">mate</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">read_len</span><span class="p">);</span></span>
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1398
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<pre style="margin: 0;">+<span id="LC1398" class="line" lang="cpp"><span class="p">}</span></span>
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1399
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<pre style="margin: 0;">+<span id="LC1399" class="line" lang="cpp"></span>
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1400
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<pre style="margin: 0;">+<span id="LC1400" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">BAMPatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">compare_read_names</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m2</span><span class="p">)</span> <span class="p">{</span></span>
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1401
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<pre style="margin: 0;">+<span id="LC1401" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">orphan_mate_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mate1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">orphan_mate_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">m1</span><span class="p">;</span></span>
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1402
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<pre style="margin: 0;">+<span id="LC1402" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">orphan_mate_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mate2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">orphan_mate_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">m2</span><span class="p">;</span></span>
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1403
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<pre style="margin: 0;">+<span id="LC1403" class="line" lang="cpp"></span>
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1404
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<pre style="margin: 0;">+<span id="LC1404" 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;">r1</span> <span class="o" style="font-weight: 600;">=</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="n" style="color: #333;">mate1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span><span class="p">[</span><span class="n" style="color: #333;">BAMField</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">read_name</span><span class="p">]);</span></span>
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1405
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<pre style="margin: 0;">+<span id="LC1405" 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;">r2</span> <span class="o" style="font-weight: 600;">=</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="n" style="color: #333;">mate2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span><span class="p">[</span><span class="n" style="color: #333;">BAMField</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">read_name</span><span class="p">]);</span></span>
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1406
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<pre style="margin: 0;">+<span id="LC1406" class="line" lang="cpp"></span>
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1407
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<pre style="margin: 0;">+<span id="LC1407" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">);</span></span>
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1408
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<pre style="margin: 0;">+<span id="LC1408" class="line" lang="cpp"><span class="p">}</span></span>
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1409
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<pre style="margin: 0;">+<span id="LC1409" class="line" lang="cpp"></span>
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1410
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<pre style="margin: 0;">+<span id="LC1410" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">BAMPatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">compare_read_names2</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">orphan_mate_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">m1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">orphan_mate_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">m2</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1411
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<pre style="margin: 0;">+<span id="LC1411" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">m1</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="diff-line-num new new_line" data-linenumber="1412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1412
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<pre style="margin: 0;">+<span id="LC1412" 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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1413
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<pre style="margin: 0;">+<span id="LC1413" class="line" lang="cpp"> <span class="p">}</span></span>
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1414
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<pre style="margin: 0;">+<span id="LC1414" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1415
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<pre style="margin: 0;">+<span id="LC1415" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">m2</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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1416
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<pre style="margin: 0;">+<span id="LC1416" 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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1417
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<pre style="margin: 0;">+<span id="LC1417" class="line" lang="cpp"> <span class="p">}</span></span>
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1418
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<pre style="margin: 0;">+<span id="LC1418" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1419
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<pre style="margin: 0;">+<span id="LC1419" 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;">r1</span> <span class="o" style="font-weight: 600;">=</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="n" style="color: #333;">m1</span><span class="p">.</span><span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span><span class="p">[</span><span class="n" style="color: #333;">BAMField</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">read_name</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1420
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<pre style="margin: 0;">+<span id="LC1420" 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;">r2</span> <span class="o" style="font-weight: 600;">=</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="n" style="color: #333;">m2</span><span class="p">.</span><span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span><span class="p">[</span><span class="n" style="color: #333;">BAMField</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">read_name</span><span class="p">]);</span></span>
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1421
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<pre style="margin: 0;">+<span id="LC1421" class="line" lang="cpp"></span>
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1422
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<pre style="margin: 0;">+<span id="LC1422" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">);</span></span>
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1423
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<pre style="margin: 0;">+<span id="LC1423" class="line" lang="cpp"><span class="p">}</span></span>
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1424
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<pre style="margin: 0;">+<span id="LC1424" class="line" lang="cpp"></span>
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1425
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<pre style="margin: 0;">+<span id="LC1425" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">BAMPatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">get_orphaned_pairs</span><span class="p">(</span><span class="n" style="color: #333;">EList</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="n" style="color: #333;">buf_a</span><span class="p">,</span> <span class="n" style="color: #333;">EList</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="n" style="color: #333;">buf_b</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">max_buf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">readi</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1426
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<pre style="margin: 0;">+<span id="LC1426" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">orphan_mate1s</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">orphan_mate1s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">BAMPatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">compare_read_names2</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1427
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<pre style="margin: 0;">+<span id="LC1427" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">orphan_mate2s</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">orphan_mate2s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">BAMPatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">compare_read_names2</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1428
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<pre style="margin: 0;">+<span id="LC1428" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1429
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<pre style="margin: 0;">+<span id="LC1429" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">lim1</span><span class="p">,</span> <span class="n" style="color: #333;">lim2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1430
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<pre style="margin: 0;">+<span id="LC1430" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">lim1</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;">lim1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">orphan_mate1s</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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">orphan_mate1s</span><span class="p">[</span><span class="n" style="color: #333;">lim1</span><span class="p">].</span><span class="n" style="color: #333;">empty</span><span class="p">();</span> <span class="n" style="color: #333;">lim1</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">;</span></span>
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1431
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<pre style="margin: 0;">+<span id="LC1431" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">lim2</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;">lim2</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">orphan_mate2s</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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">orphan_mate2s</span><span class="p">[</span><span class="n" style="color: #333;">lim2</span><span class="p">].</span><span class="n" style="color: #333;">empty</span><span class="p">();</span> <span class="n" style="color: #333;">lim2</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">;</span></span>
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1432
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<pre style="margin: 0;">+<span id="LC1432" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1433
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<pre style="margin: 0;">+<span id="LC1433" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">lim2</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="diff-line-num new new_line" data-linenumber="1434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1434
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<pre style="margin: 0;">+<span id="LC1434" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1435
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<pre style="margin: 0;">+<span id="LC1435" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1436
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<pre style="margin: 0;">+<span id="LC1436" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1437
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<pre style="margin: 0;">+<span id="LC1437" 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="n" style="color: #333;">lim1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">readi</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">max_buf</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 class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1438
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<pre style="margin: 0;">+<span id="LC1438" class="line" lang="cpp"> <span class="n" style="color: #333;">orphan_mate_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mate1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">orphan_mate1s</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1439
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<pre style="margin: 0;">+<span id="LC1439" class="line" lang="cpp"> <span class="n" style="color: #333;">orphan_mate_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mate2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">orphan_mate_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">bsearch</span><span class="p">(</span><span class="n" style="color: #333;">mate1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">orphan_mate2s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">lim2</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1440
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<pre style="margin: 0;">+<span id="LC1440" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">orphan_mate2s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]),</span> <span class="n" style="color: #333;">compare_read_names</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1441
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<pre style="margin: 0;">+<span id="LC1441" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1442
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<pre style="margin: 0;">+<span id="LC1442" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mate2</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 new new_line" data-linenumber="1443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1443
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<pre style="margin: 0;">+<span id="LC1443" class="line" lang="cpp"> <span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ra</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf_a</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1444
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<pre style="margin: 0;">+<span id="LC1444" class="line" lang="cpp"> <span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf_b</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">];</span></span>
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1445
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<pre style="margin: 0;">+<span id="LC1445" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1446
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<pre style="margin: 0;">+<span id="LC1446" class="line" lang="cpp"> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">mate1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1447
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<pre style="margin: 0;">+<span id="LC1447" class="line" lang="cpp"> <span class="n" style="color: #333;">rb</span><span class="p">.</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">mate2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1448
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<pre style="margin: 0;">+<span id="LC1448" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1449
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<pre style="margin: 0;">+<span id="LC1449" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">.</span><span class="n" style="color: #333;">wbuf</span><span class="p">(),</span> <span class="n" style="color: #333;">mate1</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;">mate1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">);</span></span>
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1450
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<pre style="margin: 0;">+<span id="LC1450" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">rb</span><span class="p">.</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">.</span><span class="n" style="color: #333;">wbuf</span><span class="p">(),</span> <span class="n" style="color: #333;">mate2</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;">mate2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1451" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC1452" class="line" lang="cpp"> <span class="n" style="color: #333;">mate1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC1453" class="line" lang="cpp"> <span class="n" style="color: #333;">mate2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC1454" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC1455" class="line" lang="cpp"> <span class="n" style="color: #333;">readi</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1456
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<pre style="margin: 0;"> <span id="LC1456" class="line" lang="cpp"> <span class="p">}</span></span>
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1457
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<pre style="margin: 0;">+<span id="LC1457" class="line" lang="cpp"> <span class="p">}</span></span>
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1458
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<pre style="margin: 0;">+<span id="LC1458" class="line" lang="cpp"><span class="p">}</span></span>
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1459
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<pre style="margin: 0;"> <span id="LC1459" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1253" class="line" lang="cpp"> <span class="n" style="color: #333;">read1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">read1</span><span class="p">;</span></span>
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1254
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<pre style="margin: 0;">-<span id="LC1254" class="line" lang="cpp"> <span class="n" style="color: #333;">readi</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">pp_</span><span class="p">.</span><span class="n" style="color: #333;">align_paired_reads</span></span>
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1255
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<pre style="margin: 0;">-<span id="LC1255" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">bufb_</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBuf</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="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">readi</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">readi</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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<pre style="margin: 0;">+<span id="LC1460" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">BAMPatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">decompress_bgzf_block</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dst</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">dst_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">src_len</span><span class="p">)</span> <span class="p">{</span></span>
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1461
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<pre style="margin: 0;">+<span id="LC1461" class="line" lang="cpp"> <span class="n" style="color: #333;">z_stream</span> <span class="n" style="color: #333;">strm</span><span class="p">;</span></span>
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1462
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<pre style="margin: 0;">+<span id="LC1462" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC1463" class="line" lang="cpp"> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">zalloc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z_NULL</span><span class="p">;</span></span>
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1464
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<pre style="margin: 0;">+<span id="LC1464" class="line" lang="cpp"> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">zfree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z_NULL</span><span class="p">;</span></span>
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1465
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<pre style="margin: 0;">+<span id="LC1465" class="line" lang="cpp"> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">opaque</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z_NULL</span><span class="p">;</span></span>
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1466
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<pre style="margin: 0;">+<span id="LC1466" class="line" lang="cpp"></span>
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1467
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<pre style="margin: 0;">+<span id="LC1467" class="line" lang="cpp"> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">avail_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src_len</span><span class="p">;</span></span>
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1468
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<pre style="margin: 0;">+<span id="LC1468" class="line" lang="cpp"> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">next_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src</span><span class="p">;</span></span>
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1469
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<pre style="margin: 0;">+<span id="LC1469" class="line" lang="cpp"> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">avail_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dst_len</span><span class="p">;</span></span>
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1470
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<pre style="margin: 0;">+<span id="LC1470" class="line" lang="cpp"> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">next_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dst</span><span class="p">;</span></span>
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1471
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<pre style="margin: 0;">+<span id="LC1471" class="line" lang="cpp"></span>
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1472
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<pre style="margin: 0;">+<span id="LC1472" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inflateInit2</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">strm</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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1473
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<pre style="margin: 0;">+<span id="LC1473" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">Z_OK</span><span class="p">)</span> <span class="p">{</span></span>
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1474
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<pre style="margin: 0;">+<span id="LC1474" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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1256
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1475
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<pre style="margin: 0;"> <span id="LC1475" class="line" lang="cpp"> <span class="p">}</span></span>
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1257
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<pre style="margin: 0;">-<span id="LC1257" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">done</span><span class="p">,</span> <span class="n" style="color: #333;">readi</span><span class="p">);</span></span>
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1476
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<pre style="margin: 0;">+<span id="LC1476" class="line" lang="cpp"></span>
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1477
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<pre style="margin: 0;">+<span id="LC1477" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inflate</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">strm</span><span class="p">,</span> <span class="n" style="color: #333;">Z_FINISH</span><span class="p">);</span></span>
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1478
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<pre style="margin: 0;">+<span id="LC1478" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">Z_STREAM_END</span><span class="p">)</span> <span class="p">{</span></span>
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1479
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<pre style="margin: 0;">+<span id="LC1479" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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1480
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<pre style="margin: 0;">+<span id="LC1480" class="line" lang="cpp"> <span class="p">}</span></span>
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1481
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<pre style="margin: 0;">+<span id="LC1481" class="line" lang="cpp"></span>
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1482
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<pre style="margin: 0;">+<span id="LC1482" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">inflateEnd</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">strm</span><span class="p">);</span></span>
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1258
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1483
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<pre style="margin: 0;"> <span id="LC1483" class="line" lang="cpp"><span class="p">}</span></span>
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1259
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1484
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<pre style="margin: 0;"> <span id="LC1484" class="line" lang="cpp"></span>
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1260
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1485
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<pre style="margin: 0;"> <span id="LC1485" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">BAMPatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ra</span><span class="p">,</span> <span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rb</span><span class="p">,</span> <span class="n" style="color: #333;">TReadId</span> <span class="n" style="color: #333;">rdid</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/compare/b5fd5c31d9d324d1c724e965365932c64231f2db...7596be203863526cfedcc8e03063d5632c9ea907#6c8922e214bc665a49b5acea11b505cbd36446c5"><strong>pat.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,6 +26,7 @@</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <cassert></span></span>
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27
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string></span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <ctype.h></span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "alphabet.h"</span></span>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "assert_helpers.h"</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "random_source.h"</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,6 +55,7 @@ struct PatternParams {</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"> <span class="n" style="color: #333;">PatternParams</span><span class="p">(</span></span>
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">format_</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">interleaved_</span><span class="p">,</span></span>
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">fileParallel_</span><span class="p">,</span></span>
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">seed_</span><span class="p">,</span></span>
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">max_buf_</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -71,6 +73,7 @@ struct PatternParams {</td>
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71
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">preserve_sam_tags_</span><span class="p">,</span></span>
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72
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">align_paired_reads_</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="c"> <span class="n" style="color: #333;">format</span><span class="p">(</span><span class="n" style="color: #333;">format_</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"> <span class="n" style="color: #333;">interleaved</span><span class="p">(</span><span class="n" style="color: #333;">interleaved_</span><span class="p">),</span></span>
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74
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"> <span class="n" style="color: #333;">fileParallel</span><span class="p">(</span><span class="n" style="color: #333;">fileParallel_</span><span class="p">),</span></span>
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75
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="c"> <span class="n" style="color: #333;">seed</span><span class="p">(</span><span class="n" style="color: #333;">seed_</span><span class="p">),</span></span>
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="c"> <span class="n" style="color: #333;">max_buf</span><span class="p">(</span><span class="n" style="color: #333;">max_buf_</span><span class="p">),</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -89,6 +92,7 @@ struct PatternParams {</td>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="c"> <span class="n" style="color: #333;">align_paired_reads</span><span class="p">(</span><span class="n" style="color: #333;">align_paired_reads_</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">format</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// file format</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">interleaved</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// some or all of the FASTQ reads are interleaved</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">fileParallel</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// true -> wrap files with separate PatternComposers</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">seed</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// pseudo-random seed</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">max_buf</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// number of reads to buffer in one read</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -112,11 +116,12 @@ struct PatternParams {</td>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">PerThreadReadBuf</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="c"> <span class="n" style="color: #333;">PerThreadReadBuf</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">max_buf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="c"> <span class="n" style="color: #333;">PerThreadReadBuf</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">max_buf</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tid</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c"> <span class="n" style="color: #333;">max_buf_</span><span class="p">(</span><span class="n" style="color: #333;">max_buf</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"> <span class="n" style="color: #333;">bufa_</span><span class="p">(</span><span class="n" style="color: #333;">max_buf</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="c"> <span class="n" style="color: #333;">bufb_</span><span class="p">(</span><span class="n" style="color: #333;">max_buf</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="c"> <span class="n" style="color: #333;">rdid_</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="c"> <span class="n" style="color: #333;">rdid_</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="c"> <span class="n" style="color: #333;">tid_</span><span class="p">(</span><span class="n" style="color: #333;">tid</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="c"> <span class="n" style="color: #333;">bufa_</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">max_buf</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="c"> <span class="n" style="color: #333;">bufb_</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">max_buf</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -185,6 +190,7 @@ struct PerThreadReadBuf {</td>
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185
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="c"> <span class="n" style="color: #333;">EList</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="n" style="color: #333;">bufb_</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Read buffer for mate bs</span></span>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">cur_buf_</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Read buffer currently active</span></span>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="c"> <span class="n" style="color: #333;">TReadId</span> <span class="n" style="color: #333;">rdid_</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// index of read at offset 0 of bufa_/bufb_</span></span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tid_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">wrongQualityFormat</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BTString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read_name</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -682,7 +688,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC688" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC689" class="line" lang="c"> <span class="n" style="color: #333;">FastqPatternSource</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC690" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</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;">infiles</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC685" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PatternParams</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;">bool</span> <span class="n" style="color: #333;">interleaved</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">false</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PatternParams</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;">bool</span> <span class="n" style="color: #333;">interleaved</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="c"> <span class="n" style="color: #333;">CFilePatternSource</span><span class="p">(</span><span class="n" style="color: #333;">infiles</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">),</span></span>
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687
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693
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<pre style="margin: 0;"> <span id="LC693" class="line" lang="c"> <span class="n" style="color: #333;">first_</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">),</span></span>
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694
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="c"> <span class="n" style="color: #333;">interleaved_</span><span class="p">(</span><span class="n" style="color: #333;">interleaved</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -719,6 +725,63 @@ protected:</td>
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<pre style="margin: 0;"> <span id="LC725" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">BAMPatternSource</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">public</span> <span class="n" style="color: #333;">CFilePatternSource</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">hdr_t</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">id1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">id2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">cm</span><span class="p">;</span></span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">flg</span><span class="p">;</span></span>
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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">mtime</span><span class="p">;</span></span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">xfl</span><span class="p">;</span></span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">os</span><span class="p">;</span></span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">xlen</span><span class="p">;</span></span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="c"> <span class="p">};</span></span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="c"></span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">ftr_t</span> <span class="p">{</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">crc32</span><span class="p">;</span></span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">isize</span><span class="p">;</span></span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="c"> <span class="p">};</span></span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="c"></span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">BGZF</span> <span class="p">{</span></span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="c"> <span class="n" style="color: #333;">hdr_t</span> <span class="n" style="color: #333;">hdr</span><span class="p">;</span></span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">cdata</span><span class="p">[</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">16</span><span class="p">];</span></span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="c"> <span class="n" style="color: #333;">ftr_t</span> <span class="n" style="color: #333;">ftr</span><span class="p">;</span></span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="c"> <span class="p">};</span></span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="c"></span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">orphan_mate_t</span> <span class="p">{</span></span>
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751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="c"> <span class="n" style="color: #333;">orphan_mate_t</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span></span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="c"> <span class="n" style="color: #333;">data</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">),</span></span>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="c"> <span class="n" style="color: #333;">size</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span></span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="c"> <span class="n" style="color: #333;">cap</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{}</span></span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="c"></span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">reset</span><span class="p">()</span> <span class="p">{</span></span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="c"> <span class="n" style="color: #333;">size</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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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="c"> <span class="p">}</span></span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="c"></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">size</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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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="c"> <span class="p">}</span></span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="c"></span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">cap</span><span class="p">;</span></span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="c"> <span class="p">};</span></span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="c"></span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">BAMField</span> <span class="p">{</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="c"> <span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">aln_rec_field_name</span> <span class="p">{</span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="c"> <span class="n" style="color: #333;">refID</span><span class="p">,</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="c"> <span class="n" style="color: #333;">pos</span><span class="p">,</span></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="c"> <span class="n" style="color: #333;">l_read_name</span><span class="p">,</span></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="c"> <span class="n" style="color: #333;">mapq</span><span class="p">,</span></span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="c"> <span class="n" style="color: #333;">bin</span><span class="p">,</span></span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="c"> <span class="n" style="color: #333;">n_cigar_op</span><span class="p">,</span></span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="c"> <span class="n" style="color: #333;">flag</span><span class="p">,</span></span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="c"> <span class="n" style="color: #333;">l_seq</span><span class="p">,</span></span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="c"> <span class="n" style="color: #333;">next_refID</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="c"> <span class="n" style="color: #333;">next_pos</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="c"> <span class="n" style="color: #333;">tlen</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="c"> <span class="n" style="color: #333;">read_name</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="c"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="c"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC785" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC786" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC787" class="line" lang="c"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -726,7 +789,19 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</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;">infiles</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC790" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PatternParams</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>
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="c"> <span class="n" style="color: #333;">CFilePatternSource</span><span class="p">(</span><span class="n" style="color: #333;">infiles</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC729" class="line" lang="c"> <span class="n" style="color: #333;">first_</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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<pre style="margin: 0;">+<span id="LC792" class="line" lang="c"> <span class="n" style="color: #333;">first_</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="c"> <span class="n" style="color: #333;">blocks_</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">nthreads</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="c"> <span class="n" style="color: #333;">bam_batches_</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">nthreads</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="c"> <span class="n" style="color: #333;">bam_batch_indexes_</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">nthreads</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="c"> <span class="n" style="color: #333;">orphan_mate1s</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">nthreads</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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<pre style="margin: 0;">+<span id="LC797" class="line" lang="c"> <span class="n" style="color: #333;">orphan_mate2s</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">nthreads</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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<pre style="margin: 0;">+<span id="LC798" class="line" lang="c"> <span class="n" style="color: #333;">orphan_mates_mutex_</span><span class="p">(),</span></span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="c"> <span class="n" style="color: #333;">pp_</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// uncompressed size of BGZF block is limited to 2**16 bytes</span></span>
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="c"> <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="n" style="color: #333;">bam_batches_</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;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="c"> <span class="n" style="color: #333;">bam_batches_</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">16</span><span class="p">);</span></span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="c"> <span class="p">}</span></span>
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805
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<pre style="margin: 0;"> <span id="LC805" class="line" lang="c"></span>
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806
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">reset</span><span class="p">()</span> <span class="p">{</span></span>
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807
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<pre style="margin: 0;"> <span id="LC807" class="line" lang="c"> <span class="n" style="color: #333;">first_</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -738,14 +813,27 @@ public:</td>
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813
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<pre style="margin: 0;"> <span id="LC813" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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814
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ra</span><span class="p">,</span> <span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rb</span><span class="p">,</span> <span class="n" style="color: #333;">TReadId</span> <span class="n" style="color: #333;">rdid</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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815
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<pre style="margin: 0;"> <span id="LC815" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="c"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">BAMPatternSource</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// only temporary until c++11</span></span>
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="c"> <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="n" style="color: #333;">orphan_mate1s</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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<pre style="margin: 0;">+<span id="LC819" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">orphan_mate1s</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">data</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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<pre style="margin: 0;">+<span id="LC820" class="line" lang="c"> <span class="n" style="color: #333;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">orphan_mate1s</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="c"> <span class="p">}</span></span>
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822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="c"> <span class="p">}</span></span>
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823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="c"></span>
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824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="c"> <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="n" style="color: #333;">orphan_mate2s</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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825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">orphan_mate2s</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">data</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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<pre style="margin: 0;">+<span id="LC826" class="line" lang="c"> <span class="n" style="color: #333;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">orphan_mate2s</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC832" class="line" lang="c"><span class="n" style="color: #333;">protected</span><span class="o" style="font-weight: 600;">:</span></span>
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833
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<pre style="margin: 0;"> <span id="LC833" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC743" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC744" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Light-parse a batch into the given buffer.</span></span>
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<pre style="margin: 0;">-<span id="LC745" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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746
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<pre style="margin: 0;">-<span id="LC746" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="n" style="color: #333;">std</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;">bool</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;">nextBatchFromFile</span><span class="p">(</span><span class="n" style="color: #333;">PerThreadReadBuf</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pt</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">batch_a</span><span class="p">,</span></span>
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747
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<pre style="margin: 0;">-<span id="LC747" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">readi</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="n" style="color: #333;">std</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;">bool</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;">nextBatch</span><span class="p">(</span><span class="n" style="color: #333;">PerThreadReadBuf</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pt</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">batch_a</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">lock</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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748
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835
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<pre style="margin: 0;"> <span id="LC835" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">nextBGZFBlockFromFile</span><span class="p">(</span><span class="n" style="color: #333;">BGZF</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">block</span><span class="p">);</span></span>
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837
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<pre style="margin: 0;"> <span id="LC837" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC838" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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839
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<pre style="margin: 0;"> <span id="LC839" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Reset state to be ready for the next file.</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -760,24 +848,36 @@ private:</td>
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<pre style="margin: 0;"> <span id="LC848" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC849" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">parse_bam_header</span><span class="p">();</span></span>
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850
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<pre style="margin: 0;"> <span id="LC850" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC763" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">BAMField</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC764" class="line" lang="c"> <span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">aln_rec_field_name</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC765" class="line" lang="c"> <span class="n" style="color: #333;">refID</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC766" class="line" lang="c"> <span class="n" style="color: #333;">pos</span><span class="p">,</span></span>
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767
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<pre style="margin: 0;">-<span id="LC767" class="line" lang="c"> <span class="n" style="color: #333;">l_read_name</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC768" class="line" lang="c"> <span class="n" style="color: #333;">mapq</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC769" class="line" lang="c"> <span class="n" style="color: #333;">bin</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC770" class="line" lang="c"> <span class="n" style="color: #333;">n_cigar_op</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC771" class="line" lang="c"> <span class="n" style="color: #333;">flag</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC772" class="line" lang="c"> <span class="n" style="color: #333;">l_seq</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC773" class="line" lang="c"> <span class="n" style="color: #333;">next_refID</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC774" class="line" lang="c"> <span class="n" style="color: #333;">next_pos</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC775" class="line" lang="c"> <span class="n" style="color: #333;">tlen</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC776" class="line" lang="c"> <span class="n" style="color: #333;">read_name</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC777" class="line" lang="c"> <span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC778" class="line" lang="c"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="n" style="color: #333;">std</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;">bool</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;">nextBatchFromFile</span><span class="p">(</span><span class="n" style="color: #333;">PerThreadReadBuf</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="c"> <span class="p">}</span></span>
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854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="c"></span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">decompress_bgzf_block</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dst</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">dst_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">src_len</span><span class="p">);</span></span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="c"> <span class="n" style="color: #333;">std</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;">bool</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;">get_alignments</span><span class="p">(</span><span class="n" style="color: #333;">PerThreadReadBuf</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pt</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">batch_a</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">readi</span><span class="p">);</span></span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="c"></span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">store_orphan_mate</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">read_len</span><span class="p">);</span></span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="c"></span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">get_orphaned_pairs</span><span class="p">(</span><span class="n" style="color: #333;">EList</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="n" style="color: #333;">buf_a</span><span class="p">,</span> <span class="n" style="color: #333;">EList</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="n" style="color: #333;">buf_b</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">max_buf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">readi</span><span class="p">);</span></span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="c"></span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">get_matching_read</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rec</span><span class="p">);</span></span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="c"></span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">compare_read_names</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m2</span><span class="p">);</span></span>
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866
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">compare_read_names2</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">orphan_mate_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">m1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">orphan_mate_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">m2</span><span class="p">);</span></span>
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779
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868
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<pre style="margin: 0;"> <span id="LC868" class="line" lang="c"></span>
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780
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869
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<pre style="margin: 0;"> <span id="LC869" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <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;">offset</span><span class="p">[];</span></span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">EOF_MARKER</span><span class="p">[];</span></span>
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871
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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BGZF</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">blocks_</span><span class="p">;</span></span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</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;">uint8_t</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bam_batches_</span><span class="p">;</span></span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</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;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bam_batch_indexes_</span><span class="p">;</span></span>
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875
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">orphan_mate_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">orphan_mate1s</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">orphan_mate_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">orphan_mate2s</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="c"> <span class="n" style="color: #333;">MUTEX_T</span> <span class="n" style="color: #333;">orphan_mates_mutex_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="c"> <span class="n" style="color: #333;">PatternParams</span> <span class="n" style="color: #333;">pp_</span><span class="p">;</span></span>
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881
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<pre style="margin: 0;"> <span id="LC881" class="line" lang="c"><span class="p">};</span></span>
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882
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<pre style="margin: 0;"> <span id="LC882" class="line" lang="c"></span>
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883
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<pre style="margin: 0;"> <span id="LC883" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -861,7 +961,7 @@ public:</td>
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861
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961
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<pre style="margin: 0;"> <span id="LC961" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</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;">q</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// qualities associated with singles</span></span>
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862
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962
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<pre style="margin: 0;"> <span id="LC962" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</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;">q1</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// qualities associated with m1</span></span>
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863
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963
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<pre style="margin: 0;"> <span id="LC963" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</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;">q2</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// qualities associated with m2</span></span>
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864
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<pre style="margin: 0;">-<span id="LC864" class="line" lang="c"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">PatternParams</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// read-in params</span></span>
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="c"> <span class="n" style="color: #333;">PatternParams</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// read-in params</span></span>
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865
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965
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<pre style="margin: 0;"> <span id="LC965" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// be talkative?</span></span>
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866
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966
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<pre style="margin: 0;"> <span id="LC966" class="line" lang="c"> </span>
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867
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967
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<pre style="margin: 0;"> <span id="LC967" class="line" lang="c"><span class="n" style="color: #333;">protected</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1017,9 +1117,9 @@ public:</td>
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1017
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1117
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<pre style="margin: 0;"> <span id="LC1117" class="line" lang="c"> </span>
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1018
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1118
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<pre style="margin: 0;"> <span id="LC1118" class="line" lang="c"> <span class="n" style="color: #333;">PatternSourcePerThread</span><span class="p">(</span></span>
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1019
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1119
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<pre style="margin: 0;"> <span id="LC1119" class="line" lang="c"> <span class="n" style="color: #333;">PatternComposer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">composer</span><span class="p">,</span></span>
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1020
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<pre style="margin: 0;">-<span id="LC1020" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PatternParams</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pp</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC1120" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PatternParams</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pp</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tid</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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1121
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<pre style="margin: 0;"> <span id="LC1121" class="line" lang="c"> <span class="n" style="color: #333;">composer_</span><span class="p">(</span><span class="n" style="color: #333;">composer</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC1022" class="line" lang="c"> <span class="n" style="color: #333;">buf_</span><span class="p">(</span><span class="n" style="color: #333;">pp</span><span class="p">.</span><span class="n" style="color: #333;">max_buf</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC1122" class="line" lang="c"> <span class="n" style="color: #333;">buf_</span><span class="p">(</span><span class="n" style="color: #333;">pp</span><span class="p">.</span><span class="n" style="color: #333;">max_buf</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tid</span></span><span class="p">),</span></span>
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1123
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<pre style="margin: 0;"> <span id="LC1123" class="line" lang="c"> <span class="n" style="color: #333;">pp_</span><span class="p">(</span><span class="n" style="color: #333;">pp</span><span class="p">),</span></span>
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1124
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<pre style="margin: 0;"> <span id="LC1124" class="line" lang="c"> <span class="n" style="color: #333;">last_batch_</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>
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1125
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<pre style="margin: 0;"> <span id="LC1125" class="line" lang="c"> <span class="n" style="color: #333;">last_batch_size_</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1107,15 +1207,16 @@ class PatternSourcePerThreadFactory {</td>
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1207
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<pre style="margin: 0;"> <span id="LC1207" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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1208
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<pre style="margin: 0;"> <span id="LC1208" class="line" lang="c"> <span class="n" style="color: #333;">PatternSourcePerThreadFactory</span><span class="p">(</span></span>
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1209
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<pre style="margin: 0;"> <span id="LC1209" class="line" lang="c"> <span class="n" style="color: #333;">PatternComposer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">composer</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1110" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PatternParams</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pp</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC1210" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PatternParams</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pp</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tid</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC1211" class="line" lang="c"> <span class="n" style="color: #333;">composer_</span><span class="p">(</span><span class="n" style="color: #333;">composer</span><span class="p">),</span></span>
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1112
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<pre style="margin: 0;">-<span id="LC1112" class="line" lang="c"> <span class="n" style="color: #333;">pp_</span><span class="p">(</span><span class="n" style="color: #333;">pp</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1212" class="line" lang="c"> <span class="n" style="color: #333;">pp_</span><span class="p">(</span><span class="n" style="color: #333;">pp</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC1213" class="line" lang="c"> <span class="n" style="color: #333;">tid_</span><span class="p">(</span><span class="n" style="color: #333;">tid</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span></span>
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1214
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<pre style="margin: 0;"> <span id="LC1214" class="line" lang="c"> </span>
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1215
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<pre style="margin: 0;"> <span id="LC1215" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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1216
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<pre style="margin: 0;"> <span id="LC1216" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Create a new heap-allocated PatternSourcePerThreads.</span></span>
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1217
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<pre style="margin: 0;"> <span id="LC1217" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1218
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<pre style="margin: 0;"> <span id="LC1218" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="n" style="color: #333;">PatternSourcePerThread</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">create</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1118" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">PatternSourcePerThread</span><span class="p">(</span><span class="n" style="color: #333;">composer_</span><span class="p">,</span> <span class="n" style="color: #333;">pp_</span><span class="p">);</span></span>
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1219
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<pre style="margin: 0;">+<span id="LC1219" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">PatternSourcePerThread</span><span class="p">(</span><span class="n" style="color: #333;">composer_</span><span class="p">,</span> <span class="n" style="color: #333;">pp_</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tid_</span></span><span class="p">);</span></span>
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1119
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1220
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<pre style="margin: 0;"> <span id="LC1220" class="line" lang="c"> <span class="p">}</span></span>
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1120
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1221
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<pre style="margin: 0;"> <span id="LC1221" class="line" lang="c"> </span>
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1121
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1222
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<pre style="margin: 0;"> <span id="LC1222" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1125,7 +1226,7 @@ public:</td>
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1125
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<td class="diff-line-num new_line" data-linenumber="1226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1226
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<pre style="margin: 0;"> <span id="LC1226" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="n" style="color: #333;">EList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">PatternSourcePerThread</span><span class="o" style="font-weight: 600;">*>*</span> <span class="n" style="color: #333;">create</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">n</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="diff-line-num old_line" data-linenumber="1126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1126
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<td class="diff-line-num new_line" data-linenumber="1227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1227
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<pre style="margin: 0;"> <span id="LC1227" class="line" lang="c"> <span class="n" style="color: #333;">EList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">PatternSourcePerThread</span><span class="o" style="font-weight: 600;">*>*</span> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">EList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">PatternSourcePerThread</span><span class="o" style="font-weight: 600;">*></span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1127
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<td class="diff-line-num new_line" data-linenumber="1228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1228
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<pre style="margin: 0;"> <span id="LC1228" class="line" lang="c"> <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="n" style="color: #333;">n</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="diff-line-num old old_line" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1128
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<td class="diff-line-num new_line old" data-linenumber="1229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1128" class="line" lang="c"> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">PatternSourcePerThread</span><span class="p">(</span><span class="n" style="color: #333;">composer_</span><span class="p">,</span> <span class="n" style="color: #333;">pp_</span><span class="p">));</span></span>
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1229
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<pre style="margin: 0;">+<span id="LC1229" class="line" lang="c"> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">PatternSourcePerThread</span><span class="p">(</span><span class="n" style="color: #333;">composer_</span><span class="p">,</span> <span class="n" style="color: #333;">pp_</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tid_</span></span><span class="p">));</span></span>
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1129
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<td class="diff-line-num new_line" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1230
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<pre style="margin: 0;"> <span id="LC1230" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">back</span><span class="p">()</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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1130
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<td class="diff-line-num new_line" data-linenumber="1231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1231
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<pre style="margin: 0;"> <span id="LC1231" class="line" lang="c"> <span class="p">}</span></span>
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1131
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1232
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<pre style="margin: 0;"> <span id="LC1232" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">v</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1135,6 +1236,7 @@ private:</td>
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1135
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1236
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<pre style="margin: 0;"> <span id="LC1236" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">/// Container for obtaining paired reads from PatternSources</span></span>
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1136
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<td class="diff-line-num new_line" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1237
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<pre style="margin: 0;"> <span id="LC1237" class="line" lang="c"> <span class="n" style="color: #333;">PatternComposer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">composer_</span><span class="p">;</span></span>
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1137
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<td class="diff-line-num new_line" data-linenumber="1238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1238
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<pre style="margin: 0;"> <span id="LC1238" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PatternParams</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pp_</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1239
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<pre style="margin: 0;">+<span id="LC1239" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tid_</span><span class="p">;</span></span>
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1138
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1240
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<pre style="margin: 0;"> <span id="LC1240" class="line" lang="c"><span class="p">};</span></span>
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1139
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1241
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<pre style="margin: 0;"> <span id="LC1241" class="line" lang="c"></span>
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1140
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1242
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<pre style="margin: 0;"> <span id="LC1242" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif </span><span class="cm" style="color: #998; font-style: italic;">/*PAT_H_*/</span></span></pre>
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