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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/ivar">Debian Med / ivar</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ivar/-/commit/701a9ea32e3c15bf4d0fb7adeacea2451c117c82">701a9ea3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-10-14T09:15:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.3+dfsg</pre>
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</ul>
<h4>29 changed files:</h4>
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<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
</a>
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<li class="file-stats">
<a href="#8916d3ac534a031cc7ced8d92b33d84445db312c">
data/pair_information.tsv
</a>
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<li class="file-stats">
<a href="#f90d77509d9d998ba68e6c318915da545505db09">
docs/MANUAL.md
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<li class="file-stats">
<a href="#a1b23abed2f2622cdcfbf7ebdd9df3514e8d39d2">
docs/html/index.html
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<li class="file-stats">
<a href="#70d5543a879678fcc424b9ff82a56e4e3bdd9028">
docs/html/manualpage.html
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<li class="file-stats">
<a href="#6f57b2efe88d413dc666fa3f8ec3b655bffc3c21">
docs/latex/index.tex
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<li class="file-stats">
<a href="#5c221b94259c045c60e5cb232a9a20f2a1fb946b">
docs/latex/manualpage.tex
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<li class="file-stats">
<a href="#b4b22c75d1bae589f3ca348869da5660ee3502c3">
docs/man/man3/cookbookpage.3
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<li class="file-stats">
<a href="#b370cc115adb1c2f71c50b3503571c0bbb6f8b98">
docs/man/man3/installpage.3
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<li class="file-stats">
<a href="#0fe496c5ff26325c2cc39ab33e934b42a4627563">
docs/man/man3/manualpage.3
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<li class="file-stats">
<a href="#f5ebd8700f07940a7e8a330865aaddad865be30d">
src/call_consensus_pileup.cpp
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<li class="file-stats">
<a href="#a90b501c7e9fd000f6912d38c32f6642d84586df">
src/call_consensus_pileup.h
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<li class="file-stats">
<a href="#d83847628f25144468f590d3395f6e53e3cde440">
src/call_variants.cpp
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<li class="file-stats">
<a href="#4a466c890bfc12a03440f5824d0cf9d098ba880f">
src/get_masked_amplicons.cpp
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<li class="file-stats">
<a href="#1ed56bc299f4a6bb415bcf995da6bf4ba876e7a4">
src/ivar.cpp
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<li class="file-stats">
<a href="#866d85bf13e1fa8b98ce1b6c3d29af2e31287c2c">
src/primer_bed.cpp
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<li class="file-stats">
<a href="#827c933f78896247082ec5f587c9bb8d23762f1f">
src/ref_seq.cpp
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<li class="file-stats">
<a href="#4644266bab7fcf61e2c44b911c9afd8ddac65d26">
src/ref_seq.h
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<li class="file-stats">
<a href="#00b6081be5179b8efd2e37aec59ecf773a10c3ed">
src/trim_primer_quality.cpp
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<li class="file-stats">
<a href="#fdbb3539733405317eca774fe99c6ab1d8306beb">
src/trim_primer_quality.h
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<li class="file-stats">
<a href="#cd4a49a19da4998db914e7cb10b78953338a4273">
tests/Makefile.am
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<li class="file-stats">
<a href="#75bffbb11d25186dd3d2c6aa35d85c3bf441a4d0">
tests/check_quality_trim.cpp
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<li class="file-stats">
<a href="#cc537d8192ad73764985b8cb628b4e7371a78a18">
tests/test_consensus_min_depth.cpp
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<li class="file-stats">
<a href="#a5cd08d01d59b4eef27e30105aa8893394a12cad">
<span class="new-file">
+
tests/test_consensus_seq_id.cpp
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<li class="file-stats">
<a href="#e0b2f123a81564bf31738653c669118954480d42">
tests/test_getmasked.cpp
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<li class="file-stats">
<a href="#5e14845d439307e7a73e85d110f0b545b6265fa9">
tests/test_primer_trim.cpp
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<li class="file-stats">
<a href="#bc53edf1aafd372a6a2ab1583c4dce2eb60702a7">
tests/test_primer_trim_edge_cases.cpp
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<li class="file-stats">
<a href="#72cf1548681e3cd27df54db6d2a928d482a578e9">
<span class="new-file">
+
tests/test_trim.cpp
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<li class="file-stats">
<a href="#3493333b4fffcb1202514aaf222d6f12b362eeea">
tests/test_unpaired_trim.cpp
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</ul>
<h4>Changes:</h4>
<li id="87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
<a href="https://salsa.debian.org/med-team/ivar/-/commit/701a9ea32e3c15bf4d0fb7adeacea2451c117c82#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2" 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="2" 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">@@ -2,7 +2,7 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"># Process this file with autoconf to produce a configure script.</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">AC_PREREQ([2.63])</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">AC_INIT([ivar], [1.2.<span class="idiff left right">2</span>], [gkarthik@scripps.edu])</span>
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<td class="diff-line-num new old_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="diff-line-num new new_line" data-linenumber="5" 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="LC5" class="line" lang="plaintext">AC_INIT([ivar], [1.2.<span class="idiff left right">3</span>], [gkarthik@scripps.edu])</span>
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<td class="diff-line-num old_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext">AM_INIT_AUTOMAKE([foreign subdir-objects])</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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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">AC_CONFIG_HEADERS([config.h])</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<li id="8916d3ac534a031cc7ced8d92b33d84445db312c">
<a href="https://salsa.debian.org/med-team/ivar/-/commit/701a9ea32e3c15bf4d0fb7adeacea2451c117c82#8916d3ac534a031cc7ced8d92b33d84445db312c"><strong>data/pair_information.tsv</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">WNV_400_1_LEFT WNV_400_1_RIGHT</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">WNV_400_2_LEFT WNV_400_2_RIGHT</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">WNV_400_3_LEFT WNV_400_3_RIGHT</span></pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">WNV_400_3_LEFT WNV_400_3_RIGHT</span></pre>
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<a href="https://salsa.debian.org/med-team/ivar/-/commit/701a9ea32e3c15bf4d0fb7adeacea2451c117c82#f90d77509d9d998ba68e6c318915da545505db09"><strong>docs/MANUAL.md</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">@@ -27,7 +27,9 @@ Trim primer sequences with iVar</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown">iVar uses primer positions supplied in a BED file to soft clip primer sequences from an aligned and sorted BAM file. Following this, the reads are trimmed based on a quality threshold(Default: 20). To do the quality trimming, iVar uses a sliding window approach(Default: 4). The windows slides from the 5' end to the 3' end and if at any point the average base quality in the window falls below the threshold, the remaining read is soft clipped. If after trimming, the length of the read is greater than the minimum length specified(Default: 30), the read is written to the new trimmed BAM file.</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="markdown">To sort and index an aligned BAM file, the following command can be used,</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown">Please note that the strand is taken into account while doing the trimming so forward primers are trimmed only from forward strand and reverse primers are trimmed from reverse strand.</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown">To sort and index an aligned BAM file (OPTIONAL, if index is not present iVar will create one), the following command can be used,</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"># Input file - test.bam</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">@@ -115,7 +117,7 @@ Output Options Description</td>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="markdown">Example Usage:</span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="markdown">samtools mpileup -A -d 600000 -B -Q 0 test.trimmed.bam | ivar variants -p test -q 20 -t 0.03 -r test_reference.fa -g test.gff</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="markdown">samtools mpileup -<span class="idiff left right">aa -</span>A -d 600000 -B -Q 0 test.trimmed.bam | ivar variants -p test -q 20 -t 0.03 -r test_reference.fa -g test.gff</span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="markdown">The command above will generate a test.tsv file.</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">@@ -262,12 +264,14 @@ If there are two nucleotides at the same frequency, both nucleotides are used to</td>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="markdown">The output of the command is a fasta file with the consensus sequence and a .txt file with the average quality of every base used to generate the consensus at each position. <span class="ge" style="font-style: italic;">*For insertions, the quality is set to be the minimum quality threshold since mpileup doesn't give the quality of bases in insertions.*</span></span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="markdown">Command:</span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="markdown">ivar consensus</span>
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="markdown">Usage: samtools mpileup -aa -A -d 0 -Q 0 <input.bam> | ivar consensus -p <prefix> </span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="markdown">Note : samtools mpileup output must be piped into <span class="idiff left right">`ivar consensus`</span></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="markdown">Note : samtools mpileup output must be piped into <span class="idiff left right">ivar consensus</span></span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="markdown">Input Options Description</span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="markdown"> -q Minimum quality score threshold to count base (Default: 20)</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="html"><span class="nt" style="color: #000080;"><li><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"el"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"manualpage.html"</span><span class="nt" style="color: #000080;">></span>Manual<span class="nt" style="color: #000080;"></a></li></span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="html"><span class="nt" style="color: #000080;"><h1><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"anchor"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"autotoc_md2<span class="idiff left right">1</span>"</span><span class="nt" style="color: #000080;">></a></span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="html"><span class="nt" style="color: #000080;"><h1><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"anchor"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"autotoc_md2<span class="idiff left right">3</span>"</span><span class="nt" style="color: #000080;">></a></span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="html">Publication<span class="nt" style="color: #000080;"></h1></span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="html"><span class="nt" style="color: #000080;"><p><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://doi.org/10.1186/s13059-018-1618-7"</span><span class="nt" style="color: #000080;">></span>An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar<span class="nt" style="color: #000080;"></a></p></span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="html"><span class="nt" style="color: #000080;"><p><em></span>Genome Biology<span class="nt" style="color: #000080;"></em></span> 2019 <span class="nt" style="color: #000080;"><b></span>20<span class="nt" style="color: #000080;"></b></span>:8<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="html"><span class="nt" style="color: #000080;"><li</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"level2"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#autotoc_md17"</span><span class="nt" style="color: #000080;">></span>Call variants with iVar<span class="nt" style="color: #000080;"></a></li></span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="html"><span class="nt" style="color: #000080;"><li</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"level2"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#autotoc_md20"</span><span class="nt" style="color: #000080;">></span>(Experimental) trimadapter<span class="nt" style="color: #000080;"></a></li></span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="html"><span class="nt" style="color: #000080;"><li</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"level2"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#autotoc_md20"</span><span class="nt" style="color: #000080;">></span>Get primers with mismatches to the reference sequence<span class="nt" style="color: #000080;"></a></li></span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="html"><span class="nt" style="color: #000080;"><li</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"level2"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#autotoc_md21"</span><span class="nt" style="color: #000080;">></span>Remove reads associated with mismatched primer indices<span class="nt" style="color: #000080;"></a></li></span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="html"><span class="nt" style="color: #000080;"><li</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"level2"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#autotoc_md22"</span><span class="nt" style="color: #000080;">></span>(Experimental) trimadapter<span class="nt" style="color: #000080;"></a></li></span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></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">@@ -108,7 +110,8 @@ Description of commands</h1></td>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="html"><span class="nt" style="color: #000080;"><h2><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"anchor"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"autotoc_md16"</span><span class="nt" style="color: #000080;">></a></span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="html">Trim primer sequences with iVar<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>iVar uses primer positions supplied in a BED file to soft clip primer sequences from an aligned and sorted BAM file. Following this, the reads are trimmed based on a quality threshold(Default: 20). To do the quality trimming, iVar uses a sliding window approach(Default: 4). The windows slides from the 5' end to the 3' end and if at any point the average base quality in the window falls below the threshold, the remaining read is soft clipped. If after trimming, the length of the read is greater than the minimum length specified(Default: 30), the read is written to the new trimmed BAM file.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>To sort and index an aligned BAM file, the following command can be used,<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Please note that the strand is taken into account while doing the trimming so forward primers are trimmed only from forward strand and reverse primers are trimmed from reverse strand.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>To sort and index an aligned BAM file (OPTIONAL, if index is not present iVar will create one), the following command can be used,<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span># Input file - test.bam<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>samtools sort -o test.sorted.bam test.bam <span class="ni" style="color: #800080;">&&</span> samtools index test.sorted.bam.<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p><b></span>Note<span class="nt" style="color: #000080;"></b></span>: All the trimming in iVar is done by soft-clipping reads in an aligned BAM file. This information is lost if reads are extracted in fastq or fasta format from the trimmed BAM file.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Command: <span class="nt" style="color: #000080;"></p><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>ivar trim<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Usage: ivar trim -i <span class="ni" style="color: #800080;"><</span>input.bam<span class="ni" style="color: #800080;">></span> -b <span class="ni" style="color: #800080;"><</span>primers.bed<span class="ni" style="color: #800080;">></span> -p <span class="ni" style="color: #800080;"><</span>prefix<span class="ni" style="color: #800080;">></span> [-m <span class="ni" style="color: #800080;"><</span>min-length<span class="ni" style="color: #800080;">></span>] [-q <span class="ni" style="color: #800080;"><</span>min-quality<span class="ni" style="color: #800080;">></span>] [-s <span class="ni" style="color: #800080;"><</span>sliding-window-width<span class="ni" style="color: #800080;">></span>]<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Input Options Description<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -i (Required) Sorted bam file, with aligned reads, to trim primers and quality<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -b (Required) BED file with primer sequences and positions<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -m Minimum length of read to retain after trimming (Default: 30)<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -q Minimum quality threshold for sliding window to pass (Default: 20)<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -s Width of sliding window (Default: 4)<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -e Include reads with no primers. By default, reads with no primers are excluded<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Output Options Description<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -p (Required) Prefix for the output BAM file<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span>Example Usage: <span class="nt" style="color: #000080;"></p><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>ivar trim -b test_primers.bed -p test.trimmed -i test.bam -q 15 -m 50 -s 4<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span>The command above will produce a trimmed BAM file test.trimmed.bam after trimming the aligned reads in test.bam using the primer positions specified in test_primers.bed and a minimum quality threshold of <span class="nt" style="color: #000080;"><b></span>15<span class="nt" style="color: #000080;"></b></span>, minimum read length of <span class="nt" style="color: #000080;"><b></span>50<span class="nt" style="color: #000080;"></b></span> and a sliding window of <span class="nt" style="color: #000080;"><b></span>4<span class="nt" style="color: #000080;"></b></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Example BED file<span class="nt" style="color: #000080;"></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">@@ -120,7 +123,7 @@ Call variants with iVar</h2></td>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="html"><span class="nt" style="color: #000080;"><h4></span>Account for RNA editing through polymerase slippage<span class="nt" style="color: #000080;"></h4></span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Some RNA viruses such as Ebola virus, might have polymerase slippage causing the insertion of a couple of nucleotides. More details can be found <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://viralzone.expasy.org/857?outline=all_by_protein"</span><span class="nt" style="color: #000080;">></span>here<span class="nt" style="color: #000080;"></a></span>. iVar can account for this editing and identify the correct open reading frames. The user will have to specify two additional parameters, <span class="nt" style="color: #000080;"><b></span>EditPosition<span class="nt" style="color: #000080;"></b></span>: Position at which edit occurs and <span class="nt" style="color: #000080;"><b></span>EditSequence<span class="nt" style="color: #000080;"></b></span>: The sequence tht is inserted at the given positon, in the "attributes" column of the GFF file to account for this. A test example is given below,<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>test Genbank CDS 2 292 . + . ID=id-testedit1;Note=PinkFloyd;EditPosition=100;EditSequence=A<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>test Genbank CDS 2 292 . + . ID=id-testedit2;Note=AnotherBrickInTheWall;EditPosition=102;EditSequence=AA<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span>If a certain base is present in multiple CDSs, iVar will add a new row for each CDS frame and distinguish the rows by adding the ID (specified in attributes of GFF) of the GFF feature used for the translation. This is shown for position 42 in the example output below. There are two rows with two different GFF features: id-test3 and id-test4.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Command: <span class="nt" style="color: #000080;"></p><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Usage: samtools mpileup -aa -A -d 0 -B -Q 0 --reference [<span class="ni" style="color: #800080;"><</span>reference-fasta] <span class="ni" style="color: #800080;"><</span>input.bam<span class="ni" style="color: #800080;">></span> | ivar variants -p <span class="ni" style="color: #800080;"><</span>prefix<span class="ni" style="color: #800080;">></span> [-q <span class="ni" style="color: #800080;"><</span>min-quality<span class="ni" style="color: #800080;">></span>] [-t <span class="ni" style="color: #800080;"><</span>min-frequency-threshold<span class="ni" style="color: #800080;">></span>] [-m <span class="ni" style="color: #800080;"><</span>minimum depth<span class="ni" style="color: #800080;">></span>] [-r <span class="ni" style="color: #800080;"><</span>reference-fasta<span class="ni" style="color: #800080;">></span>] [-g GFF file]<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Note : samtools mpileup output must be piped into ivar variants<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Input Options Description<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -q Minimum quality score threshold to count base (Default: 20)<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -t Minimum frequency threshold(0 - 1) to call variants (Default: 0.03)<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -m Minimum read depth to call variants (Default: 0)<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -r Reference file used for alignment. This is used to translate the nucleotide sequences and identify intra host single nucleotide variants<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -g A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done.<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Output Options Description<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -p (Required) Prefix for the output tsv variant file<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span>Example Usage: <span class="nt" style="color: #000080;"></p><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>samtools mpileup -A -d 600000 -B -Q 0 test.trimmed.bam | ivar variants -p test -q 20 -t 0.03 -r test_reference.fa -g test.gff<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span>The command above will generate a test.tsv file.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Command: <span class="nt" style="color: #000080;"></p><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Usage: samtools mpileup -aa -A -d 0 -B -Q 0 --reference [<span class="ni" style="color: #800080;"><</span>reference-fasta] <span class="ni" style="color: #800080;"><</span>input.bam<span class="ni" style="color: #800080;">></span> | ivar variants -p <span class="ni" style="color: #800080;"><</span>prefix<span class="ni" style="color: #800080;">></span> [-q <span class="ni" style="color: #800080;"><</span>min-quality<span class="ni" style="color: #800080;">></span>] [-t <span class="ni" style="color: #800080;"><</span>min-frequency-threshold<span class="ni" style="color: #800080;">></span>] [-m <span class="ni" style="color: #800080;"><</span>minimum depth<span class="ni" style="color: #800080;">></span>] [-r <span class="ni" style="color: #800080;"><</span>reference-fasta<span class="ni" style="color: #800080;">></span>] [-g GFF file]<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Note : samtools mpileup output must be piped into ivar variants<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Input Options Description<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -q Minimum quality score threshold to count base (Default: 20)<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -t Minimum frequency threshold(0 - 1) to call variants (Default: 0.03)<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -m Minimum read depth to call variants (Default: 0)<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -r Reference file used for alignment. This is used to translate the nucleotide sequences and identify intra host single nucleotide variants<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -g A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done.<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Output Options Description<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -p (Required) Prefix for the output tsv variant file<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span>Example Usage: <span class="nt" style="color: #000080;"></p><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>samtools mpileup -<span class="idiff left right">aa -</span>A -d 600000 -B -Q 0 test.trimmed.bam | ivar variants -p test -q 20 -t 0.03 -r test_reference.fa -g test.gff<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span>The command above will generate a test.tsv file.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Example of output .tsv file.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>REGION POS REF ALT REF_DP REF_RV REF_QUAL ALT_DP ALT_RV ALT_QUAL ALT_FREQ TOTAL_DP PVAL PASS GFF_FEATURE REF_CODON REF_AA ALT_CODON ALT_AA<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>test 42 G T 0 0 0 1 0 49 1 1 1 FALSE id-test3 AGG R ATG M<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>test 42 G T 0 0 0 1 0 49 1 1 1 FALSE id-test4 CAG Q CAT H<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>test 320 A T 1 1 35 1 1 46 0.5 2 0.666667 FALSE NA NA NA NA NA<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>test 365 A T 0 0 0 1 1 27 1 1 1 FALSE NA NA NA NA NA<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span>Description<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="html"><span class="nt" style="color: #000080;"><table</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTable"</span><span class="nt" style="color: #000080;">></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">@@ -255,33 +258,19 @@ Generate a consensus sequences from an aligned BAM file</h2></td>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="html"><span class="nt" style="color: #000080;"><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableBodyLeft"</span><span class="nt" style="color: #000080;">></span>1 <span class="nt" style="color: #000080;"></td><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableBodyNone"</span><span class="nt" style="color: #000080;">></span>D(A or T or G) <span class="nt" style="color: #000080;"></td></tr></span></span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="html"><span class="nt" style="color: #000080;"></table></span></span>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The output of the command is a fasta file with the consensus sequence and a .txt file with the average quality of every base used to generate the consensus at each position. <span class="nt" style="color: #000080;"><em></span>For insertions, the quality is set to be the minimum quality threshold since mpileup doesn't give the quality of bases in insertions.<span class="nt" style="color: #000080;"></em></p></span></span>
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Command: ``` ivar consensus<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Usage: samtools mpileup -aa -A -d 0 -Q 0 <span class="ni" style="color: #800080;"><</span>input.bam<span class="ni" style="color: #800080;">></span> | ivar consensus -p <span class="ni" style="color: #800080;"><</span>prefix<span class="ni" style="color: #800080;">></span><span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Note : samtools mpileup output must be piped into <span class="nt" style="color: #000080;"><code></span>ivar consensus<span class="nt" style="color: #000080;"></code></p></span></span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Input Options Description -q Minimum quality score threshold to count base (Default: 20) -t Minimum frequency threshold(0 - 1) to call consensus. (Default: 0) <span class="nt" style="color: #000080;"></p><table</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTable"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="html"><span class="nt" style="color: #000080;"><tr</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableHead"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="html"><span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableHeadNone"</span><span class="nt" style="color: #000080;">></span>Frequently used thresholds <span class="nt" style="color: #000080;"></th><th</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableHeadNone"</span><span class="nt" style="color: #000080;">></span>Description <span class="nt" style="color: #000080;"></th></tr></span></span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="html"><span class="nt" style="color: #000080;"><tr</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableBody"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableRowOdd"</span><span class="nt" style="color: #000080;">></span></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="html"><span class="nt" style="color: #000080;"><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableBodyNone"</span><span class="nt" style="color: #000080;">></span>0 <span class="nt" style="color: #000080;"></td><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableBodyNone"</span><span class="nt" style="color: #000080;">></span>Majority or most common base <span class="nt" style="color: #000080;"></td></tr></span></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="html"><span class="nt" style="color: #000080;"><tr</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableBody"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableRowEven"</span><span class="nt" style="color: #000080;">></span></span>
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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="html"><span class="nt" style="color: #000080;"><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableBodyNone"</span><span class="nt" style="color: #000080;">></span>0.2 <span class="nt" style="color: #000080;"></td><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableBodyNone"</span><span class="nt" style="color: #000080;">></span>Bases that make up atleast 20% of the depth at a position <span class="nt" style="color: #000080;"></td></tr></span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="html"><span class="nt" style="color: #000080;"><tr</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableBody"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableRowOdd"</span><span class="nt" style="color: #000080;">></span></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="html"><span class="nt" style="color: #000080;"><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableBodyNone"</span><span class="nt" style="color: #000080;">></span>0.5 <span class="nt" style="color: #000080;"></td><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableBodyNone"</span><span class="nt" style="color: #000080;">></span>Strict or bases that make up atleast 50% of the depth at a position <span class="nt" style="color: #000080;"></td></tr></span></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="html"><span class="nt" style="color: #000080;"><tr</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableBody"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableRowEven"</span><span class="nt" style="color: #000080;">></span></span>
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271
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<td class="diff-line-num new_line old" data-linenumber="261" 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="LC271" class="line" lang="html"><span class="nt" style="color: #000080;"><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableBodyNone"</span><span class="nt" style="color: #000080;">></span>0.9 <span class="nt" style="color: #000080;"></td><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableBodyNone"</span><span class="nt" style="color: #000080;">></span>Strict or bases that make up atleast 90% of the depth at a position <span class="nt" style="color: #000080;"></td></tr></span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="html"><span class="nt" style="color: #000080;"><tr</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableBody"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableRowOdd"</span><span class="nt" style="color: #000080;">></span></span>
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273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="html"><span class="nt" style="color: #000080;"><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableBodyNone"</span><span class="nt" style="color: #000080;">></span>1 <span class="nt" style="color: #000080;"></td><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"markdownTableBodyNone"</span><span class="nt" style="color: #000080;">></span>Identical or bases that make up 100% of the depth at a position. Will have highest ambiguities <span class="nt" style="color: #000080;"></td></tr></span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="html"><span class="nt" style="color: #000080;"></table></span></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>-m Minimum depth to call consensus(Default: 10) -k If '-k' flag is added, regions with depth less than minimum depth will not be added to the consensus sequence. Using '-k' will override any option specified using -n -n (N/-) Character to print in regions with less than minimum coverage(Default: N)<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Output Options Description -p (Required) Prefix for the output fasta file and quality file <span class="nt" style="color: #000080;"></p><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Example Usage:<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span> samtools mpileup -d 1000 -A -Q 0 test.bam | ivar consensus -p test -q 20 -t 0 <span class="nt" style="color: #000080;"></p><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>The command above will produce a test.fa fasta file with the consensus sequence and a test.qual.txt with the average quality of each base in the consensus sequence.<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Get primers with mismatches to the reference sequence<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>----<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>iVar uses a .tsv file with variants to get the zero based indices(based on the BED file) of mismatched primers. This command requires another .tsv file with each line containing the left and right primer names separated by a tab. This is used to get both the primers for an amplicon with a single mismatched primer. The output is a text file with the zero based primer indices delimited by a space. The output is written to a a text file using the prefix provided.<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Command:<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span> ivar getmasked Usage: ivar getmasked -i <span class="ni" style="color: #800080;"><</span>input-filtered.tsv<span class="ni" style="color: #800080;">></span> -b <span class="ni" style="color: #800080;"><</span>primers.bed<span class="ni" style="color: #800080;">></span> -f <span class="ni" style="color: #800080;"><</span>primer_pairs.tsv<span class="ni" style="color: #800080;">></span> -p <span class="ni" style="color: #800080;"><</span>prefix<span class="ni" style="color: #800080;">></span> Note: This step is used only for amplicon-based sequencing.<span class="nt" style="color: #000080;"></p></span></span>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Input Options Description -i (Required) Input filtered variants tsv generated from 'ivar filtervariants' -b (Required) BED file with primer sequences and positions -f (Required) Primer pair information file containing left and right primer names for the same amplicon separated by a tab Output Options Description -p (Required) Prefix for the output text file<span class="nt" style="color: #000080;"></p></span></span>
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278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Example BED file<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span> Puerto 28 52 400_1_out_L 60 + Puerto 482 504 400_1_out_R 60 - Puerto 359 381 400_2_out_L 60 + Puerto 796 818 400_2_out_R 60 - Puerto 658 680 400_3_out_L* 60 + Puerto 1054 1076 400_3_out_R* 60 -<span class="nt" style="color: #000080;"></p><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Example primer pair information file<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span> 400_1_out_L 400_1_out_R 400_2_out_L 400_2_out_R 400_3_out_L 400_3_out_R<span class="nt" style="color: #000080;"></p><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Example Usage:<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span> ivar getmasked -i test.filtered.tsv -b primers.bed -f pair_information.tsv -p test.masked.txt <span class="nt" style="color: #000080;"></p><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>The command above produces an output file - test.masked.txt.<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Example Output:<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span> 1 2 7 8 <span class="nt" style="color: #000080;"></p><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Remove reads associated with mismatched primer indices<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>----<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>This command accepts an aligned and sorted BAM file trimmed using `ivar trim` and removes the reads corresponding to the supplied primer indices, which is the output of `ivar getmasked` command. Under the hood, `ivar trim` adds the zero based primer index(based on the BED file) to the BAM auxillary data for every read. Hence, ivar removereads will only work on BAM files that have been trimmed using `ivar trim`.<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Command:<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span> ivar removereads<span class="nt" style="color: #000080;"></p></span></span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Usage: ivar removereads -i <span class="ni" style="color: #800080;"><</span>input.trimmed.bam<span class="ni" style="color: #800080;">></span> -p <span class="ni" style="color: #800080;"><</span>prefix<span class="ni" style="color: #800080;">></span> -t <span class="ni" style="color: #800080;"><</span>text-file-with-primer-indices<span class="ni" style="color: #800080;">></span> Note: This step is used only for amplicon-based sequencing.<span class="nt" style="color: #000080;"></p></span></span>
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280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Input Options Description -i (Required) Input BAM file trimmed with ivar trim. Must be sorted and indexed, which can be done using sort_index_bam.sh -t (Required) Text file with primer indices separated by spaces. This is the output of getmasked command.<span class="nt" style="color: #000080;"></p></span></span>
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281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Output Options Description -p (Required) Prefix for the output filtered BAM file<span class="nt" style="color: #000080;"></p></span></span>
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282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Example Usage:<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span> ivar trim -i test.bam -p test.trimmed ivar removereads -i test.trimmed.bam -p test.trimmed.masked.bam -t test.masked.txt ```<span class="nt" style="color: #000080;"></p></span></span>
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<td class="diff-line-num old old_line" data-linenumber="283" 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">
283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The <span class="nt" style="color: #000080;"><code></span>ivar trim<span class="nt" style="color: #000080;"></code></span> command above trims test.bam and produced test.trimmed.bam with the primer indice data added. The <span class="nt" style="color: #000080;"><code></span>ivar removereads<span class="nt" style="color: #000080;"></code></span> command produces an output file - test.trimmed.masked.bam after removing all the reads corresponding to primer indices - 1,2,7 and 8.<span class="nt" style="color: #000080;"></p></span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Command:<span class="nt" style="color: #000080;"></p></span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>ivar consensus<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Usage: samtools mpileup -aa -A -d 0 -Q 0 <span class="ni" style="color: #800080;"><</span>input.bam<span class="ni" style="color: #800080;">></span> | ivar consensus -p <span class="ni" style="color: #800080;"><</span>prefix<span class="ni" style="color: #800080;">></span> <span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Note : samtools mpileup output must be piped into ivar consensus<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Input Options Description<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -q Minimum quality score threshold to count base (Default: 20)<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -t Minimum frequency threshold(0 - 1) to call consensus. (Default: 0)<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> Frequently used thresholds | Description<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> ---------------------------|------------<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> 0 | Majority or most common base<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> 0.2 | Bases that make up atleast 20% of the depth at a position<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> 0.5 | Strict or bases that make up atleast 50% of the depth at a position<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> 0.9 | Strict or bases that make up atleast 90% of the depth at a position<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> 1 | Identical or bases that make up 100% of the depth at a position. Will have highest ambiguities<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -m Minimum depth to call consensus(Default: 10)<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -k If <span class="ni" style="color: #800080;">'</span>-k<span class="ni" style="color: #800080;">'</span> flag is added, regions with depth less than minimum depth will not be added to the consensus sequence. Using <span class="ni" style="color: #800080;">'</span>-k<span class="ni" style="color: #800080;">'</span> will override any option specified using -n <span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -n (N/-) Character to print in regions with less than minimum coverage(Default: N)<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Output Options Description<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -p (Required) Prefix for the output fasta file and quality file<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span>Example Usage: <span class="nt" style="color: #000080;"></p><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>samtools mpileup -d 1000 -A -Q 0 test.bam | ivar consensus -p test -q 20 -t 0<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span>The command above will produce a test.fa fasta file with the consensus sequence and a test.qual.txt with the average quality of each base in the consensus sequence.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="html"><span class="nt" style="color: #000080;"><h2><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"anchor"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"autotoc_md20"</span><span class="nt" style="color: #000080;">></a></span></span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="html">Get primers with mismatches to the reference sequence<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>iVar uses a .tsv file with variants to get the zero based indices(based on the BED file) of mismatched primers. This command requires another .tsv file with each line containing the left and right primer names separated by a tab. This is used to get both the primers for an amplicon with a single mismatched primer. The output is a text file with the zero based primer indices delimited by a space. The output is written to a a text file using the prefix provided.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Command: <span class="nt" style="color: #000080;"></p><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>ivar getmasked<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Usage: ivar getmasked -i <span class="ni" style="color: #800080;"><</span>input-filtered.tsv<span class="ni" style="color: #800080;">></span> -b <span class="ni" style="color: #800080;"><</span>primers.bed<span class="ni" style="color: #800080;">></span> -f <span class="ni" style="color: #800080;"><</span>primer_pairs.tsv<span class="ni" style="color: #800080;">></span> -p <span class="ni" style="color: #800080;"><</span>prefix<span class="ni" style="color: #800080;">></span><span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Note: This step is used only for amplicon-based sequencing.<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Input Options Description<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -i (Required) Input filtered variants tsv generated from <span class="ni" style="color: #800080;">'</span>ivar filtervariants<span class="ni" style="color: #800080;">'</span><span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -b (Required) BED file with primer sequences and positions<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -f (Required) Primer pair information file containing left and right primer names for the same amplicon separated by a tab<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Output Options Description<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -p (Required) Prefix for the output text file<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span>Example BED file<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Puerto 28 52 400_1_out_L 60 +<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Puerto 482 504 400_1_out_R 60 -<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Puerto 359 381 400_2_out_L 60 +<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Puerto 796 818 400_2_out_R 60 -<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Puerto 658 680 400_3_out_L* 60 +<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Puerto 1054 1076 400_3_out_R* 60 -<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>.<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>.<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>.<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>.<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span>Example primer pair information file <span class="nt" style="color: #000080;"></p><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>400_1_out_L 400_1_out_R<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>400_2_out_L 400_2_out_R<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>400_3_out_L 400_3_out_R<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>.<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>.<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>.<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>.<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span>Example Usage: <span class="nt" style="color: #000080;"></p><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>ivar getmasked -i test.filtered.tsv -b primers.bed -f pair_information.tsv -p test.masked.txt<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span>The command above produces an output file - test.masked.txt.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Example Output:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>1 2 7 8<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><h2><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"anchor"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"autotoc_md21"</span><span class="nt" style="color: #000080;">></a></span></span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="html">Remove reads associated with mismatched primer indices<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>This command accepts an aligned and sorted BAM file trimmed using <span class="nt" style="color: #000080;"><code></span>ivar trim<span class="nt" style="color: #000080;"></code></span> and removes the reads corresponding to the supplied primer indices, which is the output of <span class="nt" style="color: #000080;"><code></span>ivar getmasked<span class="nt" style="color: #000080;"></code></span> command. Under the hood, <span class="nt" style="color: #000080;"><code></span>ivar trim<span class="nt" style="color: #000080;"></code></span> adds the zero based primer index(based on the BED file) to the BAM auxillary data for every read. Hence, ivar removereads will only work on BAM files that have been trimmed using <span class="nt" style="color: #000080;"><code></span>ivar trim<span class="nt" style="color: #000080;"></code></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Command: <span class="nt" style="color: #000080;"></p><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>ivar removereads<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Usage: ivar removereads -i <span class="ni" style="color: #800080;"><</span>input.trimmed.bam<span class="ni" style="color: #800080;">></span> -p <span class="ni" style="color: #800080;"><</span>prefix<span class="ni" style="color: #800080;">></span> -t <span class="ni" style="color: #800080;"><</span>text-file-with-primer-indices<span class="ni" style="color: #800080;">></span><span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Note: This step is used only for amplicon-based sequencing.<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Input Options Description<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -i (Required) Input BAM file trimmed with ivar trim. Must be sorted and indexed, which can be done using sort_index_bam.sh<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -t (Required) Text file with primer indices separated by spaces. This is the output of getmasked command.<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>Output Options Description<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span> -p (Required) Prefix for the output filtered BAM file<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span>Example Usage: <span class="nt" style="color: #000080;"></p><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fragment"</span><span class="nt" style="color: #000080;">><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>ivar trim -i test.bam -p test.trimmed<span class="nt" style="color: #000080;"></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"line"</span><span class="nt" style="color: #000080;">></span>ivar removereads -i test.trimmed.bam -p test.trimmed.masked.bam -t test.masked.txt<span class="nt" style="color: #000080;"></div></div></span><span class="c" style="color: #998; font-style: italic;"><!-- fragment --></span><span class="nt" style="color: #000080;"><p></span>The <span class="nt" style="color: #000080;"><code></span>ivar trim<span class="nt" style="color: #000080;"></code></span> command above trims test.bam and produced test.trimmed.bam with the primer indice data added. The <span class="nt" style="color: #000080;"><code></span>ivar removereads<span class="nt" style="color: #000080;"></code></span> command produces an output file - test.trimmed.masked.bam after removing all the reads corresponding to primer indices - 1,2,7 and 8.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="html"><span class="nt" style="color: #000080;"><h2><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"anchor"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"autotoc_md22"</span><span class="nt" style="color: #000080;">></a></span></span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="html">(Experimental) trimadapter<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="html"><span class="nt" style="color: #000080;"><p><b></span>Note: This feature is under active development and not completely validated yet.<span class="nt" style="color: #000080;"></b></p></span></span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>trimadapter in iVar can be used to trim adapter sequences from fastq files using a supplied fasta file. <span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span> <span class="k" style="font-weight: 600;">\mbox</span><span class="p">{</span><span class="k" style="font-weight: 600;">\hyperlink</span><span class="p">{</span>installpage<span class="p">}{</span>Installation<span class="p">}}</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span> <span class="k" style="font-weight: 600;">\mbox</span><span class="p">{</span><span class="k" style="font-weight: 600;">\hyperlink</span><span class="p">{</span>manualpage<span class="p">}{</span>Manual<span class="p">}}</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span> <span class="k" style="font-weight: 600;">\mbox</span><span class="p">{</span><span class="k" style="font-weight: 600;">\hyperlink</span><span class="p">{</span>cookbookpage<span class="p">}{</span>Cookbook<span class="p">}}</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{DoxyItemize}</span><span class="k" style="font-weight: 600;">\hypertarget</span><span class="p">{</span>index<span class="p">_</span>autotoc<span class="p">_</span>md2<span class="idiff left">1</span><span class="p"><span class="idiff">}{}</span></span><span class="k" style="font-weight: 600;"><span class="idiff">\section</span></span><span class="p"><span class="idiff">{</span></span><span class="idiff">Publication</span><span class="p"><span class="idiff">}</span></span><span class="k" style="font-weight: 600;"><span class="idiff">\label</span></span><span class="p"><span class="idiff">{</span></span><span class="idiff">index</span><span class="p"><span class="idiff">_</span></span><span class="idiff">autotoc</span><span class="p"><span class="idiff">_</span></span><span class="idiff right">md21</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{DoxyItemize}</span><span class="k" style="font-weight: 600;">\hypertarget</span><span class="p">{</span>index<span class="p">_</span>autotoc<span class="p">_</span>md2<span class="idiff left">3</span><span class="p"><span class="idiff">}{}</span></span><span class="k" style="font-weight: 600;"><span class="idiff">\section</span></span><span class="p"><span class="idiff">{</span></span><span class="idiff">Publication</span><span class="p"><span class="idiff">}</span></span><span class="k" style="font-weight: 600;"><span class="idiff">\label</span></span><span class="p"><span class="idiff">{</span></span><span class="idiff">index</span><span class="p"><span class="idiff">_</span></span><span class="idiff">autotoc</span><span class="p"><span class="idiff">_</span></span><span class="idiff right">md23</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="tex"><span class="k" style="font-weight: 600;">\href</span><span class="p">{</span>https://doi.org/10.1186/s13059-018-1618-7<span class="p">}{</span><span class="k" style="font-weight: 600;">\tt</span> An amplicon-<span class="k" style="font-weight: 600;">\/</span>based sequencing framework for accurately measuring intrahost virus diversity using Primal<span class="k" style="font-weight: 600;">\+</span>Seq and i<span class="k" style="font-weight: 600;">\+</span>Var<span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="tex"><span class="p">{</span><span class="k" style="font-weight: 600;">\itshape</span> Genome Biology<span class="p">}</span> 2019 <span class="p">{</span><span class="k" style="font-weight: 600;">\bfseries</span> 20<span class="p">}</span><span class="k" style="font-weight: 600;">\+</span>:8</span>
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<a href="https://salsa.debian.org/med-team/ivar/-/commit/701a9ea32e3c15bf4d0fb7adeacea2451c117c82#5c221b94259c045c60e5cb232a9a20f2a1fb946b"><strong>docs/latex/manualpage.tex</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">@@ -24,7 +24,9 @@ To view detailed usage for each command type {\ttfamily ivar $<$command$>$} Note</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="tex"><span class="k" style="font-weight: 600;">\hypertarget</span><span class="p">{</span>manualpage<span class="p">_</span>autotoc<span class="p">_</span>md16<span class="p">}{}</span><span class="k" style="font-weight: 600;">\subsection</span><span class="p">{</span>Trim primer sequences with i<span class="k" style="font-weight: 600;">\+</span>Var<span class="p">}</span><span class="k" style="font-weight: 600;">\label</span><span class="p">{</span>manualpage<span class="p">_</span>autotoc<span class="p">_</span>md16<span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="tex">i<span class="k" style="font-weight: 600;">\+</span>Var uses primer positions supplied in a B<span class="k" style="font-weight: 600;">\+</span>ED file to soft clip primer sequences from an aligned and sorted B<span class="k" style="font-weight: 600;">\+</span>AM file. Following this, the reads are trimmed based on a quality threshold(<span class="k" style="font-weight: 600;">\+</span>Default<span class="k" style="font-weight: 600;">\+</span>: 20). To do the quality trimming, i<span class="k" style="font-weight: 600;">\+</span>Var uses a sliding window approach(<span class="k" style="font-weight: 600;">\+</span>Default<span class="k" style="font-weight: 600;">\+</span>: 4). The windows slides from the 5<span class="k" style="font-weight: 600;">\textquotesingle</span><span class="p">{}</span> end to the 3<span class="k" style="font-weight: 600;">\textquotesingle</span><span class="p">{}</span> end and if at any point the average base quality in the window falls below the threshold, the remaining read is soft clipped. If after trimming, the length of the read is greater than the minimum length specified(<span class="k" style="font-weight: 600;">\+</span>Default<span class="k" style="font-weight: 600;">\+</span>: 30), the read is written to the new trimmed B<span class="k" style="font-weight: 600;">\+</span>AM file.</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="tex"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="tex">To sort and index an aligned B<span class="k" style="font-weight: 600;">\+</span>AM file, the following command can be used,</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="tex">Please note that the strand is taken into account while doing the trimming so forward primers are trimmed only from forward strand and reverse primers are trimmed from reverse strand.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="tex"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="tex">To sort and index an aligned B<span class="k" style="font-weight: 600;">\+</span>AM file (O<span class="k" style="font-weight: 600;">\+</span>P<span class="k" style="font-weight: 600;">\+</span>T<span class="k" style="font-weight: 600;">\+</span>I<span class="k" style="font-weight: 600;">\+</span>O<span class="k" style="font-weight: 600;">\+</span>N<span class="k" style="font-weight: 600;">\+</span>AL, if index is not present i<span class="k" style="font-weight: 600;">\+</span>Var will create one), the following command can be used,</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="tex"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="tex"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{DoxyCode}</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">@@ -123,7 +125,7 @@ Output Options Description</td>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="tex"></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="tex">Example Usage<span class="k" style="font-weight: 600;">\+</span>: </span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{DoxyCode}</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="tex">samtools mpileup -A -d 600000 -B -Q 0 test.trimmed.bam | ivar variants -p test -q 20 -t 0.03 -r</span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="tex">samtools mpileup -<span class="idiff left right">aa -</span>A -d 600000 -B -Q 0 test.trimmed.bam | ivar variants -p test -q 20 -t 0.03 -r</span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="tex"> test<span class="k" style="font-weight: 600;">\_</span>reference.fa -g test.gff</span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{DoxyCode}</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="tex"></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">@@ -326,99 +328,136 @@ If there are two nucleotides at the same frequency, both nucleotides are used to</td>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="tex"></span>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="tex">The output of the command is a fasta file with the consensus sequence and a .txt file with the average quality of every base used to generate the consensus at each position. <span class="p">{</span><span class="k" style="font-weight: 600;">\itshape</span> For insertions, the quality is set to be the minimum quality threshold since mpileup doesn<span class="k" style="font-weight: 600;">\textquotesingle</span><span class="p">{}</span>t give the quality of bases in insertions.<span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="tex">Command<span class="k" style="font-weight: 600;">\+</span>:<span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">\`</span></span><span class="p"><span class="idiff">{}</span></span><span class="k" style="font-weight: 600;"><span class="idiff">\`</span></span><span class="p"><span class="idiff">{}</span></span><span class="k" style="font-weight: 600;"><span class="idiff">\`</span></span><span class="p"><span class="idiff">{}</span></span><span class="idiff right"> ivar consensus</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="tex">Command<span class="k" style="font-weight: 600;">\+</span>:</span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="tex"></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="tex">Usage<span class="k" style="font-weight: 600;">\+</span>: samtools mpileup -<span class="k" style="font-weight: 600;">\/</span>aa -<span class="k" style="font-weight: 600;">\/</span>A -<span class="k" style="font-weight: 600;">\/</span>d 0 -<span class="k" style="font-weight: 600;">\/</span>Q 0 <span class="p">$</span><span class="nb" style="color: #0086b3;"><</span><span class="p">$</span>input.<span class="k" style="font-weight: 600;">\+</span>bam<span class="p">$</span><span class="nb" style="color: #0086b3;">></span><span class="p">$</span> <span class="p">$</span><span class="nv" style="color: #008080;">\vert</span><span class="p">$</span> ivar consensus -<span class="k" style="font-weight: 600;">\/</span>p <span class="p">$</span><span class="nb" style="color: #0086b3;"><</span><span class="p">$</span>prefix<span class="p">$</span><span class="nb" style="color: #0086b3;">></span><span class="p">$</span></span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="tex"></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="tex">Note <span class="k" style="font-weight: 600;">\+</span>: samtools mpileup output must be piped into <span class="p">{</span><span class="k" style="font-weight: 600;">\ttfamily</span> ivar consensus<span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{DoxyCode}</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="tex">ivar consensus</span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="tex"></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="tex">Input Options Description -<span class="k" style="font-weight: 600;">\/</span>q Minimum quality score threshold to count base (Default<span class="k" style="font-weight: 600;">\+</span>: 20) -<span class="k" style="font-weight: 600;">\/</span>t Minimum frequency threshold(0 -<span class="k" style="font-weight: 600;">\/</span> 1) to call consensus. (Default<span class="k" style="font-weight: 600;">\+</span>: 0) <span class="k" style="font-weight: 600;">\tabulinesep</span>=1mm</span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{longtabu}</span> spread 0pt [c]<span class="p">{</span>*<span class="p">{</span>2<span class="p">}{</span>|X[-1]<span class="p">}</span>|<span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="tex"><span class="k" style="font-weight: 600;">\hline</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="tex"><span class="k" style="font-weight: 600;">\rowcolor</span><span class="p">{</span><span class="k" style="font-weight: 600;">\tableheadbgcolor</span><span class="p">}</span><span class="k" style="font-weight: 600;">\textbf</span><span class="p">{</span> Frequently used thresholds <span class="p">}&</span><span class="k" style="font-weight: 600;">\textbf</span><span class="p">{</span> Description <span class="p">}</span><span class="k" style="font-weight: 600;">\\\cline</span><span class="p">{</span>1-2<span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="tex"><span class="k" style="font-weight: 600;">\endfirsthead</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="tex"><span class="k" style="font-weight: 600;">\hline</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="tex"><span class="k" style="font-weight: 600;">\endfoot</span></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="tex"><span class="k" style="font-weight: 600;">\hline</span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="tex"><span class="k" style="font-weight: 600;">\rowcolor</span><span class="p">{</span><span class="k" style="font-weight: 600;">\tableheadbgcolor</span><span class="p">}</span><span class="k" style="font-weight: 600;">\textbf</span><span class="p">{</span> Frequently used thresholds <span class="p">}&</span><span class="k" style="font-weight: 600;">\textbf</span><span class="p">{</span> Description <span class="p">}</span><span class="k" style="font-weight: 600;">\\\cline</span><span class="p">{</span>1-2<span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="tex"><span class="k" style="font-weight: 600;">\endhead</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="tex">0 <span class="p">&</span>Majority or most common base <span class="k" style="font-weight: 600;">\\\cline</span><span class="p">{</span>1-2<span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="tex">0.<span class="k" style="font-weight: 600;">\+</span>2 <span class="p">&</span>Bases that make up atleast 20<span class="k" style="font-weight: 600;">\%</span> of the depth at a position <span class="k" style="font-weight: 600;">\\\cline</span><span class="p">{</span>1-2<span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="tex">0.<span class="k" style="font-weight: 600;">\+</span>5 <span class="p">&</span>Strict or bases that make up atleast 50<span class="k" style="font-weight: 600;">\%</span> of the depth at a position <span class="k" style="font-weight: 600;">\\\cline</span><span class="p">{</span>1-2<span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="tex">0.<span class="k" style="font-weight: 600;">\+</span>9 <span class="p">&</span>Strict or bases that make up atleast 90<span class="k" style="font-weight: 600;">\%</span> of the depth at a position <span class="k" style="font-weight: 600;">\\\cline</span><span class="p">{</span>1-2<span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="tex">1 <span class="p">&</span>Identical or bases that make up 100<span class="k" style="font-weight: 600;">\%</span> of the depth at a position. Will have highest ambiguities <span class="k" style="font-weight: 600;">\\\cline</span><span class="p">{</span>1-2<span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{longtabu}</span></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="tex">-<span class="k" style="font-weight: 600;">\/</span>m Minimum depth to call consensus(<span class="k" style="font-weight: 600;">\+</span>Default<span class="k" style="font-weight: 600;">\+</span>: 10) -<span class="k" style="font-weight: 600;">\/</span>k If <span class="k" style="font-weight: 600;">\textquotesingle</span><span class="p">{}</span>-<span class="k" style="font-weight: 600;">\/</span>k<span class="k" style="font-weight: 600;">\textquotesingle</span><span class="p">{}</span> flag is added, regions with depth less than minimum depth will not be added to the consensus sequence. Using <span class="k" style="font-weight: 600;">\textquotesingle</span><span class="p">{}</span>-<span class="k" style="font-weight: 600;">\/</span>k<span class="k" style="font-weight: 600;">\textquotesingle</span><span class="p">{}</span> will override any option specified using -<span class="k" style="font-weight: 600;">\/</span>n -<span class="k" style="font-weight: 600;">\/</span>n (N/-<span class="k" style="font-weight: 600;">\/</span>) Character to print in regions with less than minimum coverage(<span class="k" style="font-weight: 600;">\+</span>Default<span class="k" style="font-weight: 600;">\+</span>: N)</span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="tex">Usage: samtools mpileup -aa -A -d 0 -Q 0 <input.bam> | ivar consensus -p <prefix> </span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="tex"></span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="tex">Output Options Description -<span class="k" style="font-weight: 600;">\/</span>p (Required) Prefix for the output fasta file and quality file </span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{DoxyCode}</span></span>
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="tex">Example Usage:</span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="tex">Note : samtools mpileup output must be piped into ivar consensus</span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="tex"></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="tex">Input Options Description</span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="tex"> -q Minimum quality score threshold to count base (Default: 20)</span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="tex"> -t Minimum frequency threshold(0 - 1) to call consensus. (Default: 0)</span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="tex"> Frequently used thresholds | Description</span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="tex"> ---------------------------|------------</span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="tex"> 0 | Majority or most common base</span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="tex"> 0.2 | Bases that make up atleast 20<span class="c" style="color: #998; font-style: italic;">% of the depth at a position</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="tex"> 0.5 | Strict or bases that make up atleast 50<span class="c" style="color: #998; font-style: italic;">% of the depth at a</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="tex"> position</span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="tex"> 0.9 | Strict or bases that make up atleast 90<span class="c" style="color: #998; font-style: italic;">% of the depth at a</span></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="tex"> position</span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="tex"> 1 | Identical or bases that make up 100<span class="c" style="color: #998; font-style: italic;">% of the depth at a</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="tex"> position. Will have highest ambiguities</span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="tex"> -m Minimum depth to call consensus(Default: 10)</span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="tex"> -k If '-k' flag is added, regions with depth less than minimum depth will not be added to the</span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="tex"> consensus sequence. Using '-k' will override any option specified using -n </span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="tex"> -n (N/-) Character to print in regions with less than minimum coverage(Default: N)</span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="tex"></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="tex">Output Options Description</span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="tex"> -p (Required) Prefix for the output fasta file and quality file</span>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{DoxyCode}</span></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="tex"> samtools mpileup -<span class="k" style="font-weight: 600;">\/</span>d 1000 -<span class="k" style="font-weight: 600;">\/</span>A -<span class="k" style="font-weight: 600;">\/</span>Q 0 test.<span class="k" style="font-weight: 600;">\+</span>bam <span class="p">$</span><span class="nv" style="color: #008080;">\vert</span><span class="p">$</span> ivar consensus -<span class="k" style="font-weight: 600;">\/</span>p test -<span class="k" style="font-weight: 600;">\/</span>q 20 -<span class="k" style="font-weight: 600;">\/</span>t 0 </span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="tex"></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="tex">Example Usage<span class="k" style="font-weight: 600;">\+</span>: </span>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{DoxyCode}</span></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="tex"><span class="idiff left right">The command above will produce a test.fa fasta file with the consensus sequence and a test.qual.txt with</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="tex"><span class="idiff left right"> the average quality of each base in the consensus sequence.</span></span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="tex"><span class="idiff left right">samtools mpileup -d 1000 -A -Q 0 test.bam | ivar consensus -p test -q 20 -t 0</span></span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="tex"><span class="nt" style="color: #000080;"><span class="idiff left right">\end{DoxyCode}</span></span></span>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="tex"></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="tex">Get primers with mismatches to the reference sequence</span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="tex">----</span>
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="tex"></span>
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="tex">iVar uses a .tsv file with variants to get the zero based indices(based on the BED file) of mismatched</span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="tex"> primers. This command requires another .tsv file with each line containing the left and right primer names</span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="tex"> separated by a tab. This is used to get both the primers for an amplicon with a single mismatched primer. The</span>
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="tex"> output is a text file with the zero based primer indices delimited by a space. The output is written to a a</span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="tex"> text file using the prefix provided.</span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="tex">The command above will produce a test.<span class="k" style="font-weight: 600;">\+</span>fa fasta file with the consensus sequence and a test.<span class="k" style="font-weight: 600;">\+</span>qual.<span class="k" style="font-weight: 600;">\+</span>txt with the average quality of each base in the consensus sequence.<span class="k" style="font-weight: 600;">\hypertarget</span><span class="p">{</span>manualpage<span class="p">_</span>autotoc<span class="p">_</span>md20<span class="p">}{}</span><span class="k" style="font-weight: 600;">\subsection</span><span class="p">{</span>Get primers with mismatches to the reference sequence<span class="p">}</span><span class="k" style="font-weight: 600;">\label</span><span class="p">{</span>manualpage<span class="p">_</span>autotoc<span class="p">_</span>md20<span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="tex">i<span class="k" style="font-weight: 600;">\+</span>Var uses a .tsv file with variants to get the zero based indices(based on the B<span class="k" style="font-weight: 600;">\+</span>E<span class="k" style="font-weight: 600;">\+</span>D file) of mismatched primers. This command requires another .tsv file with each line containing the left and right primer names separated by a tab. This is used to get both the primers for an amplicon with a single mismatched primer. The output is a text file with the zero based primer indices delimited by a space. The output is written to a a text file using the prefix provided.</span>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="tex"></span>
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="tex">Command:</span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="tex">Command<span class="k" style="font-weight: 600;">\+</span>: </span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{DoxyCode}</span></span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="tex">ivar getmasked</span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="tex">Usage: ivar getmasked -i <input-filtered.tsv> -b <primers.bed> -f <primer<span class="k" style="font-weight: 600;">\_</span>pairs.tsv> -p <prefix></span>
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="tex">Note: This step is used only for amplicon-based sequencing.</span>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="tex"></span>
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="tex">Input Options Description</span>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="tex"> -i (Required) Input filtered variants tsv generated from 'ivar filtervariants'</span>
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="tex"> -b (Required) BED file with primer sequences and positions</span>
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="tex"> -f (Required) Primer pair information file containing left and right primer names for the</span>
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="tex"> same amplicon separated by a tab</span>
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="tex">Output Options Description</span>
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="tex"> -p (Required) Prefix for the output text file</span>
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372
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{DoxyCode}</span></span>
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373
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="tex"> ivar getmasked Usage<span class="k" style="font-weight: 600;">\+</span>: ivar getmasked -<span class="k" style="font-weight: 600;">\/</span>i <span class="p">$</span><span class="nb" style="color: #0086b3;"><</span><span class="p">$</span>input-<span class="k" style="font-weight: 600;">\/</span>filtered.<span class="k" style="font-weight: 600;">\+</span>tsv<span class="p">$</span><span class="nb" style="color: #0086b3;">></span><span class="p">$</span> -<span class="k" style="font-weight: 600;">\/</span>b <span class="p">$</span><span class="nb" style="color: #0086b3;"><</span><span class="p">$</span>primers.<span class="k" style="font-weight: 600;">\+</span>bed<span class="p">$</span><span class="nb" style="color: #0086b3;">></span><span class="p">$</span> -<span class="k" style="font-weight: 600;">\/</span>f <span class="p">$</span><span class="nb" style="color: #0086b3;"><</span><span class="p">$</span>primer<span class="k" style="font-weight: 600;">\+\_\+</span>pairs.<span class="k" style="font-weight: 600;">\+</span>tsv<span class="p">$</span><span class="nb" style="color: #0086b3;">></span><span class="p">$</span> -<span class="k" style="font-weight: 600;">\/</span>p <span class="p">$</span><span class="nb" style="color: #0086b3;"><</span><span class="p">$</span>prefix<span class="p">$</span><span class="nb" style="color: #0086b3;">></span><span class="p">$</span> Note<span class="k" style="font-weight: 600;">\+</span>: This step is used only for amplicon-<span class="k" style="font-weight: 600;">\/</span>based sequencing.</span>
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374
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="tex"></span>
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="tex">Input Options Description -<span class="k" style="font-weight: 600;">\/</span>i (Required) Input filtered variants tsv generated from <span class="k" style="font-weight: 600;">\textquotesingle</span><span class="p">{}</span>ivar filtervariants<span class="k" style="font-weight: 600;">\textquotesingle</span><span class="p">{}</span> -<span class="k" style="font-weight: 600;">\/</span>b (Required) B<span class="k" style="font-weight: 600;">\+</span>ED file with primer sequences and positions -<span class="k" style="font-weight: 600;">\/</span>f (Required) Primer pair information file containing left and right primer names for the same amplicon separated by a tab Output Options Description -<span class="k" style="font-weight: 600;">\/</span>p (Required) Prefix for the output text file</span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="tex"></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="tex">Example B<span class="k" style="font-weight: 600;">\+</span>ED file</span>
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376
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="tex"></span>
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377
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391
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="tex"></span>
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378
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392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{DoxyCode}</span></span>
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379
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="tex">Example BED file</span>
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="tex">Puerto 28 52 400<span class="k" style="font-weight: 600;">\_</span>1<span class="k" style="font-weight: 600;">\_</span>out<span class="k" style="font-weight: 600;">\_</span>L 60 +</span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="tex">Puerto 482 504 400<span class="k" style="font-weight: 600;">\_</span>1<span class="k" style="font-weight: 600;">\_</span>out<span class="k" style="font-weight: 600;">\_</span>R 60 -</span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="tex">Puerto 359 381 400<span class="k" style="font-weight: 600;">\_</span>2<span class="k" style="font-weight: 600;">\_</span>out<span class="k" style="font-weight: 600;">\_</span>L 60 +</span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="tex">Puerto 796 818 400<span class="k" style="font-weight: 600;">\_</span>2<span class="k" style="font-weight: 600;">\_</span>out<span class="k" style="font-weight: 600;">\_</span>R 60 -</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="tex">Puerto 658 680 400<span class="k" style="font-weight: 600;">\_</span>3<span class="k" style="font-weight: 600;">\_</span>out<span class="k" style="font-weight: 600;">\_</span>L* 60 +</span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="tex">Puerto 1054 1076 400<span class="k" style="font-weight: 600;">\_</span>3<span class="k" style="font-weight: 600;">\_</span>out<span class="k" style="font-weight: 600;">\_</span>R* 60 -</span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="tex">.</span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="tex">.</span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="tex">.</span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="tex">.</span>
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380
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{DoxyCode}</span></span>
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381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="tex"> Puerto 28 52 400<span class="k" style="font-weight: 600;">\+\_\+</span>1<span class="k" style="font-weight: 600;">\+\_\+</span>out<span class="k" style="font-weight: 600;">\+\_\+</span>L 60 + Puerto 482 504 400<span class="k" style="font-weight: 600;">\+\_\+</span>1<span class="k" style="font-weight: 600;">\+\_\+</span>out<span class="k" style="font-weight: 600;">\+\_\+</span>R 60 -<span class="k" style="font-weight: 600;">\/</span> Puerto 359 381 400<span class="k" style="font-weight: 600;">\+\_\+</span>2<span class="k" style="font-weight: 600;">\+\_\+</span>out<span class="k" style="font-weight: 600;">\+\_\+</span>L 60 + Puerto 796 818 400<span class="k" style="font-weight: 600;">\+\_\+</span>2<span class="k" style="font-weight: 600;">\+\_\+</span>out<span class="k" style="font-weight: 600;">\+\_\+</span>R 60 -<span class="k" style="font-weight: 600;">\/</span> Puerto 658 680 400<span class="k" style="font-weight: 600;">\+\_\+</span>3<span class="k" style="font-weight: 600;">\+\_\+</span>out<span class="k" style="font-weight: 600;">\+\_\+\+</span>L<span class="p">$</span><span class="nv" style="color: #008080;">\ast</span><span class="p">$</span> 60 + Puerto 1054 1076 400<span class="k" style="font-weight: 600;">\+\_\+</span>3<span class="k" style="font-weight: 600;">\+\_\+</span>out<span class="k" style="font-weight: 600;">\+\_\+\+</span>R<span class="p">$</span><span class="nv" style="color: #008080;">\ast</span><span class="p">$</span> 60 -<span class="k" style="font-weight: 600;">\/</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="tex"></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="tex"></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="tex">Example primer pair information file </span>
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{DoxyCode}</span></span>
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="tex">Example primer pair information file</span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="tex">400<span class="k" style="font-weight: 600;">\_</span>1<span class="k" style="font-weight: 600;">\_</span>out<span class="k" style="font-weight: 600;">\_</span>L 400<span class="k" style="font-weight: 600;">\_</span>1<span class="k" style="font-weight: 600;">\_</span>out<span class="k" style="font-weight: 600;">\_</span>R</span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="tex">400<span class="k" style="font-weight: 600;">\_</span>2<span class="k" style="font-weight: 600;">\_</span>out<span class="k" style="font-weight: 600;">\_</span>L 400<span class="k" style="font-weight: 600;">\_</span>2<span class="k" style="font-weight: 600;">\_</span>out<span class="k" style="font-weight: 600;">\_</span>R</span>
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="tex">400<span class="k" style="font-weight: 600;">\_</span>3<span class="k" style="font-weight: 600;">\_</span>out<span class="k" style="font-weight: 600;">\_</span>L 400<span class="k" style="font-weight: 600;">\_</span>3<span class="k" style="font-weight: 600;">\_</span>out<span class="k" style="font-weight: 600;">\_</span>R</span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="tex">.</span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="tex">.</span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="tex">.</span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="tex">.</span>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{DoxyCode}</span></span>
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="tex"> 400<span class="k" style="font-weight: 600;">\+\_\+</span>1<span class="k" style="font-weight: 600;">\+\_\+</span>out<span class="k" style="font-weight: 600;">\+\_\+</span>L 400<span class="k" style="font-weight: 600;">\+\_\+</span>1<span class="k" style="font-weight: 600;">\+\_\+</span>out<span class="k" style="font-weight: 600;">\+\_\+</span>R 400<span class="k" style="font-weight: 600;">\+\_\+</span>2<span class="k" style="font-weight: 600;">\+\_\+</span>out<span class="k" style="font-weight: 600;">\+\_\+</span>L 400<span class="k" style="font-weight: 600;">\+\_\+</span>2<span class="k" style="font-weight: 600;">\+\_\+</span>out<span class="k" style="font-weight: 600;">\+\_\+</span>R 400<span class="k" style="font-weight: 600;">\+\_\+</span>3<span class="k" style="font-weight: 600;">\+\_\+</span>out<span class="k" style="font-weight: 600;">\+\_\+</span>L 400<span class="k" style="font-weight: 600;">\+\_\+</span>3<span class="k" style="font-weight: 600;">\+\_\+</span>out<span class="k" style="font-weight: 600;">\+\_\+</span>R</span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="tex"></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="tex"></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="tex">Example Usage<span class="k" style="font-weight: 600;">\+</span>: </span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{DoxyCode}</span></span>
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="tex"><span class="idiff left right">Example Usage:</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="tex"><span class="idiff left">ivar getmasked -i test.filtered.tsv -b primers.bed -f pair</span><span class="k" style="font-weight: 600;"><span class="idiff">\_</span></span><span class="idiff right">information.tsv -p test.masked.txt</span></span>
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388
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{DoxyCode}</span></span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="tex"> ivar getmasked -<span class="k" style="font-weight: 600;">\/</span>i test.<span class="k" style="font-weight: 600;">\+</span>filtered.<span class="k" style="font-weight: 600;">\+</span>tsv -<span class="k" style="font-weight: 600;">\/</span>b primers.<span class="k" style="font-weight: 600;">\+</span>bed -<span class="k" style="font-weight: 600;">\/</span>f pair<span class="k" style="font-weight: 600;">\+\_\+</span>information.<span class="k" style="font-weight: 600;">\+</span>tsv -<span class="k" style="font-weight: 600;">\/</span>p test.<span class="k" style="font-weight: 600;">\+</span>masked.<span class="k" style="font-weight: 600;">\+</span>txt </span>
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390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{DoxyCode}</span></span>
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391
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="tex">The command above produces an output file - test.masked.txt.</span>
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392
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="tex"></span>
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393
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="tex">Example Output:</span>
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{DoxyCode}</span></span>
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="tex"> 1 2 7 8 </span>
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{DoxyCode}</span></span>
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="tex">Remove reads associated with mismatched primer indices</span>
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="tex">----</span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="tex"></span>
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="tex">This command accepts an aligned and sorted BAM file trimmed using `ivar trim` and removes the reads</span>
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="tex"> corresponding to the supplied primer indices, which is the output of `ivar getmasked` command. Under the hood,</span>
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="tex"> `ivar trim` adds the zero based primer index(based on the BED file) to the BAM auxillary data for every read.</span>
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="tex"> Hence, ivar removereads will only work on BAM files that have been trimmed using `ivar trim`.</span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="tex">The command above produces an output file -<span class="k" style="font-weight: 600;">\/</span> test.<span class="k" style="font-weight: 600;">\+</span>masked.<span class="k" style="font-weight: 600;">\+</span>txt.</span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="tex"></span>
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="tex">Command:</span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="tex">Example Output<span class="k" style="font-weight: 600;">\+</span>:</span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="tex"></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="tex"></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{DoxyCode}</span></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="tex">1 2 7 8</span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{DoxyCode}</span></span>
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="tex"> ivar removereads</span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="tex"><span class="k" style="font-weight: 600;">\hypertarget</span><span class="p">{</span>manualpage<span class="p">_</span>autotoc<span class="p">_</span>md21<span class="p">}{}</span><span class="k" style="font-weight: 600;">\subsection</span><span class="p">{</span>Remove reads associated with mismatched primer indices<span class="p">}</span><span class="k" style="font-weight: 600;">\label</span><span class="p">{</span>manualpage<span class="p">_</span>autotoc<span class="p">_</span>md21<span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="tex">This command accepts an aligned and sorted B<span class="k" style="font-weight: 600;">\+</span>AM file trimmed using <span class="p">{</span><span class="k" style="font-weight: 600;">\ttfamily</span> ivar trim<span class="p">}</span> and removes the reads corresponding to the supplied primer indices, which is the output of <span class="p">{</span><span class="k" style="font-weight: 600;">\ttfamily</span> ivar getmasked<span class="p">}</span> command. Under the hood, <span class="p">{</span><span class="k" style="font-weight: 600;">\ttfamily</span> ivar trim<span class="p">}</span> adds the zero based primer index(based on the B<span class="k" style="font-weight: 600;">\+</span>E<span class="k" style="font-weight: 600;">\+</span>D file) to the B<span class="k" style="font-weight: 600;">\+</span>AM auxillary data for every read. Hence, ivar removereads will only work on B<span class="k" style="font-weight: 600;">\+</span>AM files that have been trimmed using <span class="p">{</span><span class="k" style="font-weight: 600;">\ttfamily</span> ivar trim<span class="p">}</span>.</span>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="tex"></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="tex">Usage<span class="k" style="font-weight: 600;">\+</span>: ivar removereads -<span class="k" style="font-weight: 600;">\/</span>i <span class="p">$</span><span class="nb" style="color: #0086b3;"><</span><span class="p">$</span>input.<span class="k" style="font-weight: 600;">\+</span>trimmed.<span class="k" style="font-weight: 600;">\+</span>bam<span class="p">$</span><span class="nb" style="color: #0086b3;">></span><span class="p">$</span> -<span class="k" style="font-weight: 600;">\/</span>p <span class="p">$</span><span class="nb" style="color: #0086b3;"><</span><span class="p">$</span>prefix<span class="p">$</span><span class="nb" style="color: #0086b3;">></span><span class="p">$</span> -<span class="k" style="font-weight: 600;">\/</span>t <span class="p">$</span><span class="nb" style="color: #0086b3;"><</span><span class="p">$</span>text-<span class="k" style="font-weight: 600;">\/</span>file-<span class="k" style="font-weight: 600;">\/</span>with-<span class="k" style="font-weight: 600;">\/</span>primer-<span class="k" style="font-weight: 600;">\/</span>indices<span class="p">$</span><span class="nb" style="color: #0086b3;">></span><span class="p">$</span> Note<span class="k" style="font-weight: 600;">\+</span>: This step is used only for amplicon-<span class="k" style="font-weight: 600;">\/</span>based sequencing.</span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="tex">Command<span class="k" style="font-weight: 600;">\+</span>: </span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{DoxyCode}</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="tex">ivar removereads</span>
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438
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="tex"></span>
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411
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="tex">Input Options Description -<span class="k" style="font-weight: 600;">\/</span>i (Required) Input B<span class="k" style="font-weight: 600;">\+</span>AM file trimmed with ivar trim. Must be sorted and indexed, which can be done using sort<span class="k" style="font-weight: 600;">\+\_\+</span>index<span class="k" style="font-weight: 600;">\+\_\+</span>bam.<span class="k" style="font-weight: 600;">\+</span>sh -<span class="k" style="font-weight: 600;">\/</span>t (Required) Text file with primer indices separated by spaces. This is the output of getmasked command.</span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="tex">Usage: ivar removereads -i <input.trimmed.bam> -p <prefix> -t <text-file-with-primer-indices></span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="tex">Note: This step is used only for amplicon-based sequencing.</span>
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412
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="tex"></span>
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="tex">Output Options Description -<span class="k" style="font-weight: 600;">\/</span>p (Required) Prefix for the output filtered B<span class="k" style="font-weight: 600;">\+</span>AM file</span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="tex">Input Options Description</span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="tex"> -i (Required) Input BAM file trimmed with ivar trim. Must be sorted and indexed, which can</span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="tex"> be done using sort<span class="k" style="font-weight: 600;">\_</span>index<span class="k" style="font-weight: 600;">\_</span>bam.sh</span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="tex"> -t (Required) Text file with primer indices separated by spaces. This is the output of</span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="tex"> getmasked command.</span>
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="tex"></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="tex">Output Options Description</span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="tex"> -p (Required) Prefix for the output filtered BAM file</span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{DoxyCode}</span></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="tex"></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="tex"></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="tex">Example Usage<span class="k" style="font-weight: 600;">\+</span>: </span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{DoxyCode}</span></span>
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="tex">Example Usage:</span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="tex">ivar trim -i test.bam -p test.trimmed</span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="tex">ivar removereads -i test.trimmed.bam -p test.trimmed.masked.bam -t test.masked.txt</span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{DoxyCode}</span></span>
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="tex"> ivar trim -<span class="k" style="font-weight: 600;">\/</span>i test.<span class="k" style="font-weight: 600;">\+</span>bam -<span class="k" style="font-weight: 600;">\/</span>p test.<span class="k" style="font-weight: 600;">\+</span>trimmed ivar removereads -<span class="k" style="font-weight: 600;">\/</span>i test.<span class="k" style="font-weight: 600;">\+</span>trimmed.<span class="k" style="font-weight: 600;">\+</span>bam -<span class="k" style="font-weight: 600;">\/</span>p test.<span class="k" style="font-weight: 600;">\+</span>trimmed.<span class="k" style="font-weight: 600;">\+</span>masked.<span class="k" style="font-weight: 600;">\+</span>bam -<span class="k" style="font-weight: 600;">\/</span>t test.<span class="k" style="font-weight: 600;">\+</span>masked.<span class="k" style="font-weight: 600;">\+</span>txt <span class="k" style="font-weight: 600;">\`</span><span class="p">{}</span><span class="k" style="font-weight: 600;">\`</span><span class="p">{}</span><span class="k" style="font-weight: 600;">\`</span><span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="tex"></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="tex">The <span class="p">{</span><span class="k" style="font-weight: 600;">\ttfamily</span> ivar trim<span class="p">}</span> command above trims test.<span class="k" style="font-weight: 600;">\+</span>bam and produced test.<span class="k" style="font-weight: 600;">\+</span>trimmed.<span class="k" style="font-weight: 600;">\+</span>bam with the primer indice data added. The <span class="p">{</span><span class="k" style="font-weight: 600;">\ttfamily</span> ivar removereads<span class="p">}</span> command produces an output file -<span class="k" style="font-weight: 600;">\/</span> test.<span class="k" style="font-weight: 600;">\+</span>trimmed.<span class="k" style="font-weight: 600;">\+</span>masked.<span class="k" style="font-weight: 600;">\+</span>bam after removing all the reads corresponding to primer indices -<span class="k" style="font-weight: 600;">\/</span> 1,2,7 and 8.<span class="k" style="font-weight: 600;">\hypertarget</span><span class="p">{</span>manualpage<span class="p">_</span>autotoc<span class="p">_</span>md20<span class="p">}{}</span><span class="k" style="font-weight: 600;">\subsection</span><span class="p">{</span>(<span class="k" style="font-weight: 600;">\+</span>Experimental) trimadapter<span class="p">}</span><span class="k" style="font-weight: 600;">\label</span><span class="p">{</span>manualpage<span class="p">_</span>autotoc<span class="p">_</span>md20<span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="tex"></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="tex">The <span class="p">{</span><span class="k" style="font-weight: 600;">\ttfamily</span> ivar trim<span class="p">}</span> command above trims test.<span class="k" style="font-weight: 600;">\+</span>bam and produced test.<span class="k" style="font-weight: 600;">\+</span>trimmed.<span class="k" style="font-weight: 600;">\+</span>bam with the primer indice data added. The <span class="p">{</span><span class="k" style="font-weight: 600;">\ttfamily</span> ivar removereads<span class="p">}</span> command produces an output file -<span class="k" style="font-weight: 600;">\/</span> test.<span class="k" style="font-weight: 600;">\+</span>trimmed.<span class="k" style="font-weight: 600;">\+</span>masked.<span class="k" style="font-weight: 600;">\+</span>bam after removing all the reads corresponding to primer indices -<span class="k" style="font-weight: 600;">\/</span> 1,2,7 and 8.<span class="k" style="font-weight: 600;">\hypertarget</span><span class="p">{</span>manualpage<span class="p">_</span>autotoc<span class="p">_</span>md22<span class="p">}{}</span><span class="k" style="font-weight: 600;">\subsection</span><span class="p">{</span>(<span class="k" style="font-weight: 600;">\+</span>Experimental) trimadapter<span class="p">}</span><span class="k" style="font-weight: 600;">\label</span><span class="p">{</span>manualpage<span class="p">_</span>autotoc<span class="p">_</span>md22<span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="tex"><span class="p">{</span><span class="k" style="font-weight: 600;">\bfseries</span> Note<span class="k" style="font-weight: 600;">\+</span>: This feature is under active development and not completely validated yet.<span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="tex"></span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="tex">trimadapter in i<span class="k" style="font-weight: 600;">\+</span>Var can be used to trim adapter sequences from fastq files using a supplied fasta file. </span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.TH "cookbookpage" 3 "Fri <span class="idiff left right">Apr 3</span> 2020" "iVar" \" -*- nroff -*-</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH "cookbookpage" 3 "Fri <span class="idiff left right">Jun 19</span> 2020" "iVar" \" -*- nroff -*-</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">.ad l</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.nh</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.TH "installpage" 3 "Fri <span class="idiff left right">Apr 3</span> 2020" "iVar" \" -*- nroff -*-</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH "installpage" 3 "Fri <span class="idiff left right">Jun 19</span> 2020" "iVar" \" -*- nroff -*-</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">.ad l</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.nh</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.TH "manualpage" 3 "Fri <span class="idiff left right">Apr 3</span> 2020" "iVar" \" -*- nroff -*-</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH "manualpage" 3 "Fri <span class="idiff left right">Jun 19</span> 2020" "iVar" \" -*- nroff -*-</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">.ad l</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.nh</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">.SH NAME</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">@@ -14,7 +14,9 @@ To view detailed usage for each command type \fCivar <command>\fP Note : Command</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">.SS "Trim primer sequences with iVar"</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">iVar uses primer positions supplied in a BED file to soft clip primer sequences from an aligned and sorted BAM file\&. Following this, the reads are trimmed based on a quality threshold(Default: 20)\&. To do the quality trimming, iVar uses a sliding window approach(Default: 4)\&. The windows slides from the 5' end to the 3' end and if at any point the average base quality in the window falls below the threshold, the remaining read is soft clipped\&. If after trimming, the length of the read is greater than the minimum length specified(Default: 30), the read is written to the new trimmed BAM file\&.</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">To sort and index an aligned BAM file, the following command can be used,</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Please note that the strand is taken into account while doing the trimming so forward primers are trimmed only from forward strand and reverse primers are trimmed from reverse strand\&.</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">To sort and index an aligned BAM file (OPTIONAL, if index is not present iVar will create one), the following command can be used,</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">.nf</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">@@ -115,7 +117,7 @@ Output Options Description</td>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext">Example Usage: </span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext">.nf</span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="plaintext">samtools mpileup -A -d 600000 -B -Q 0 test\&.trimmed\&.bam | ivar variants -p test -q 20 -t 0\&.03 -r test_reference\&.fa -g test\&.gff</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">samtools mpileup -<span class="idiff left right">aa -</span>A -d 600000 -B -Q 0 test\&.trimmed\&.bam | ivar variants -p test -q 20 -t 0\&.03 -r test_reference\&.fa -g test\&.gff</span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext">.fi</span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="plaintext">.PP</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">@@ -216,93 +218,141 @@ Minimum frequency threshold Consensus 0 T 0\&.5 T 0\&.6 T 0\&.7 D(A</td>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="plaintext">The output of the command is a fasta file with the consensus sequence and a \&.txt file with the average quality of every base used to generate the consensus at each position\&. \fIFor insertions, the quality is set to be the minimum quality threshold since mpileup doesn't give the quality of bases in insertions\&.\fP</span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="plaintext">Command:<span class="idiff left right"> ``` ivar consensus</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext">Command:</span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="plaintext">Usage: samtools mpileup -aa -A -d 0 -Q 0 <input\&.bam> | ivar consensus -p <prefix></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="plaintext">Note : samtools mpileup output must be piped into \fCivar consensus\fP</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext">.nf</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext">ivar consensus</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext">Usage: samtools mpileup -aa -A -d 0 -Q 0 <input\&.bam> | ivar consensus -p <prefix> </span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext">Note : samtools mpileup output must be piped into ivar consensus</span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">Input Options Description</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext"> -q Minimum quality score threshold to count base (Default: 20)</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext"> -t Minimum frequency threshold(0 - 1) to call consensus\&. (Default: 0)</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext"> Frequently used thresholds | Description</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext"> ---------------------------|------------</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext"> 0 | Majority or most common base</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext"> 0\&.2 | Bases that make up atleast 20% of the depth at a position</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext"> 0\&.5 | Strict or bases that make up atleast 50% of the depth at a position</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext"> 0\&.9 | Strict or bases that make up atleast 90% of the depth at a position</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext"> 1 | Identical or bases that make up 100% of the depth at a position\&. Will have highest ambiguities</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext"> -m Minimum depth to call consensus(Default: 10)</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext"> -k If '-k' flag is added, regions with depth less than minimum depth will not be added to the consensus sequence\&. Using '-k' will override any option specified using -n </span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext"> -n (N/-) Character to print in regions with less than minimum coverage(Default: N)</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext">Output Options Description</span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext"> -p (Required) Prefix for the output fasta file and quality file</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext">.fi</span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="plaintext">Input Options Description -q Minimum quality score threshold to count base (Default: 20) -t Minimum frequency threshold(0 - 1) to call consensus\&. (Default: 0) Frequently used thresholds Description 0 Majority or most common base 0\&.2 Bases that make up atleast 20% of the depth at a position 0\&.5 Strict or bases that make up atleast 50% of the depth at a position 0\&.9 Strict or bases that make up atleast 90% of the depth at a position 1 Identical or bases that make up 100% of the depth at a position\&. Will have highest ambiguities -m Minimum depth to call consensus(Default: 10) -k If '-k' flag is added, regions with depth less than minimum depth will not be added to the consensus sequence\&. Using '-k' will override any option specified using -n -n (N/-) Character to print in regions with less than minimum coverage(Default: N)</span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="plaintext"><span class="idiff left right">Output Options Description -p (Required) Prefix for the output fasta file and quality file</span> </span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext"><span class="idiff left right">Example Usage:</span> </span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="plaintext">.nf</span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="plaintext"><span class="idiff left right">Example Usage:</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext"><span class="idiff left right">samtools mpileup -d 1000 -A -Q 0 test\&.bam | ivar consensus -p test -q 20 -t 0</span></span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="plaintext">.fi</span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="plaintext"> samtools mpileup -d 1000 -A -Q 0 test\&.bam | ivar consensus -p test -q 20 -t 0 </span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="plaintext">.nf</span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="plaintext">The command above will produce a test\&.fa fasta file with the consensus sequence and a test\&.qual\&.txt with the average quality of each base in the consensus sequence\&.</span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="plaintext">Get primers with mismatches to the reference sequence</span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="plaintext">----</span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext">.SS "Get primers with mismatches to the reference sequence"</span>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="plaintext">iVar uses a \&.tsv file with variants to get the zero based indices(based on the BED file) of mismatched primers\&. This command requires another \&.tsv file with each line containing the left and right primer names separated by a tab\&. This is used to get both the primers for an amplicon with a single mismatched primer\&. The output is a text file with the zero based primer indices delimited by a space\&. The output is written to a a text file using the prefix provided\&.</span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext">Command: </span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext">.nf</span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext">ivar getmasked</span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext">Usage: ivar getmasked -i <input-filtered\&.tsv> -b <primers\&.bed> -f <primer_pairs\&.tsv> -p <prefix></span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext">Note: This step is used only for amplicon-based sequencing\&.</span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="plaintext">Command:</span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext">Input Options Description</span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext"> -i (Required) Input filtered variants tsv generated from 'ivar filtervariants'</span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext"> -b (Required) BED file with primer sequences and positions</span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext"> -f (Required) Primer pair information file containing left and right primer names for the same amplicon separated by a tab</span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext">Output Options Description</span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext"> -p (Required) Prefix for the output text file</span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="plaintext">.fi</span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="plaintext"> ivar getmasked Usage: ivar getmasked -i <input-filtered\&.tsv> -b <primers\&.bed> -f <primer_pairs\&.tsv> -p <prefix> Note: This step is used only for amplicon-based sequencing\&.</span>
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249
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="plaintext"><span class="idiff left right">Input Options Description -i (Required) Input filtered variants tsv generated from 'ivar filtervariants' -b (Required) BED file with primer sequences and positions -f (Required) Primer pair information file containing left and right primer names for the same amplicon separated by a tab Output Options Description -p (Required) Prefix for the output text</span> file</span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext"><span class="idiff left right">Example BED</span> file</span>
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251
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280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="plaintext">.PP</span>
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252
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="plaintext">.PP</span>
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253
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="plaintext">.nf</span>
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254
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="plaintext">Example BED file</span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext">Puerto 28 52 400_1_out_L 60 +</span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext">Puerto 482 504 400_1_out_R 60 -</span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext">Puerto 359 381 400_2_out_L 60 +</span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext">Puerto 796 818 400_2_out_R 60 -</span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext">Puerto 658 680 400_3_out_L* 60 +</span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext">Puerto 1054 1076 400_3_out_R* 60 -</span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext">\&.</span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext">\&.</span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext">\&.</span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext">\&.</span>
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="plaintext">.fi</span>
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256
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="plaintext"> Puerto 28 52 400_1_out_L 60 + Puerto 482 504 400_1_out_R 60 - Puerto 359 381 400_2_out_L 60 + Puerto 796 818 400_2_out_R 60 - Puerto 658 680 400_3_out_L* 60 + Puerto 1054 1076 400_3_out_R* 60 -</span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext">.PP</span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext">Example primer pair information file </span>
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258
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="plaintext">.PP</span>
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259
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="plaintext">.nf</span>
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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="plaintext">Example primer pair information file</span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext">400_1_out_L 400_1_out_R</span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext">400_2_out_L 400_2_out_R</span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext">400_3_out_L 400_3_out_R</span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext">\&.</span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext">\&.</span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext">\&.</span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext">\&.</span>
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261
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306
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="plaintext"></span>
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262
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="plaintext">.fi</span>
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263
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="plaintext">.PP</span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="plaintext"> 400_1_out_L 400_1_out_R 400_2_out_L 400_2_out_R 400_3_out_L 400_3_out_R</span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext">.PP</span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext">Example Usage: </span>
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265
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311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="plaintext">.PP</span>
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266
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312
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="plaintext">.nf</span>
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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="plaintext"><span class="idiff left right">Example Usage:</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext"><span class="idiff left right">ivar getmasked -i test\&.filtered\&.tsv -b primers\&.bed -f pair_information\&.tsv -p test\&.masked\&.txt</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="plaintext"></span>
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315
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="plaintext">.fi</span>
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270
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="plaintext"> ivar getmasked -i test\&.filtered\&.tsv -b primers\&.bed -f pair_information\&.tsv -p test\&.masked\&.txt </span>
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272
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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="plaintext">.PP</span>
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273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="plaintext">.nf</span>
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274
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="plaintext">The command above produces an output file - test\&.masked\&.txt\&.</span>
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275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="plaintext"></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext">.PP</span>
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276
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="plaintext">Example Output:</span>
</pre>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext">.nf</span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext">1 2 7 8</span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="plaintext">.fi</span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="plaintext"> 1 2 7 8 </span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext">.SS "Remove reads associated with mismatched primer indices"</span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="plaintext">This command accepts an aligned and sorted BAM file trimmed using \fCivar trim\fP and removes the reads corresponding to the supplied primer indices, which is the output of \fCivar getmasked\fP command\&. Under the hood, \fCivar trim\fP adds the zero based primer index(based on the BED file) to the BAM auxillary data for every read\&. Hence, ivar removereads will only work on BAM files that have been trimmed using \fCivar trim\fP\&.</span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="plaintext">Command: </span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="plaintext">.nf</span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="plaintext">Remove reads associated with mismatched primer indices</span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="plaintext">----</span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext">ivar removereads</span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="plaintext">This command accepts an aligned and sorted BAM file trimmed using `ivar trim` and removes the reads corresponding to the supplied primer indices, which is the output of `ivar getmasked` command\&. Under the hood, `ivar trim` adds the zero based primer index(based on the BED file) to the BAM auxillary data for every read\&. Hence, ivar removereads will only work on BAM files that have been trimmed using `ivar trim`\&.</span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="plaintext">Usage: ivar removereads -i <input\&.trimmed\&.bam> -p <prefix> -t <text-file-with-primer-indices></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="plaintext">Note: This step is used only for amplicon-based sequencing\&.</span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="plaintext">Command:</span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="plaintext">Input Options Description</span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="plaintext"> -i (Required) Input BAM file trimmed with ivar trim\&. Must be sorted and indexed, which can be done using sort_index_bam\&.sh</span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="plaintext"> -t (Required) Text file with primer indices separated by spaces\&. This is the output of getmasked command\&.</span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="plaintext">Output Options Description</span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="plaintext"> -p (Required) Prefix for the output filtered BAM file</span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="plaintext">.fi</span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="plaintext"> ivar removereads</span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="plaintext">Usage: ivar removereads -i <input\&.trimmed\&.bam> -p <prefix> -t <text-file-with-primer-indices> Note: This step is used only for amplicon-based sequencing\&.</span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="plaintext">Input Options Description -i (Required) Input BAM file trimmed with ivar trim\&. Must be sorted and indexed, which can be done using sort_index_bam\&.sh -t (Required) Text file with primer indices separated by spaces\&. This is the output of getmasked command\&.</span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="plaintext">Output Options Description -p (Required) Prefix for the output filtered BAM file</span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="plaintext">Example Usage: </span>
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349
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="plaintext">.PP</span>
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350
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="plaintext">.nf</span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="plaintext">Example Usage:</span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="plaintext">ivar trim -i test\&.bam -p test\&.trimmed</span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="plaintext">ivar removereads -i test\&.trimmed\&.bam -p test\&.trimmed\&.masked\&.bam -t test\&.masked\&.txt</span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="plaintext">.fi</span>
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="plaintext"> ivar trim -i test\&.bam -p test\&.trimmed ivar removereads -i test\&.trimmed\&.bam -p test\&.trimmed\&.masked\&.bam -t test\&.masked\&.txt ```</span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="plaintext">The \fCivar trim\fP command above trims test\&.bam and produced test\&.trimmed\&.bam with the primer indice data added\&. The \fCivar removereads\fP command produces an output file - test\&.trimmed\&.masked\&.bam after removing all the reads corresponding to primer indices - 1,2,7 and 8\&.</span>
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358
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="plaintext">.SS "(Experimental) trimadapter"</span>
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<a href="https://salsa.debian.org/med-team/ivar/-/commit/701a9ea32e3c15bf4d0fb7adeacea2451c117c82#f5ebd8700f07940a7e8a330865aaddad865be30d"><strong>src/call_consensus_pileup.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">@@ -130,13 +130,17 @@ ret_t get_consensus_allele(std::vector<allele> ad, uint8_t min_qual, double thre</td>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">t</span><span class="p">;</span></span>
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">call_consensus_from_plup</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cin</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">out_file</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">threshold</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">min_depth</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">min_coverage_flag</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">call_consensus_from_plup</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cin</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;"><span class="idiff left">seq_id</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">out_file</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">threshold</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">min_depth</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">min_coverage_flag</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC134" 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;">string</span> <span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">cell</span><span class="p">;</span></span>
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135
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<pre style="margin: 0;"> <span id="LC135" 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;">ofstream</span> <span class="n" style="color: #333;">fout</span><span class="p">((</span><span class="n" style="color: #333;">out_file</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".fa"</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC136" 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;">ofstream</span> <span class="n" style="color: #333;">tmp_qout</span><span class="p">((</span><span class="n" style="color: #333;">out_file</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".qual.txt"</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">o</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">[</span><span class="n" style="color: #333;">out_file</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">">Consensus_"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"_threshold_"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"_quality_"</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="p">)</span> <span class="n" style="color: #333;">min_qual</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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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">seq_id</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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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">">Consensus_"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"_threshold_"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"_quality_"</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="p">)</span> <span class="n" style="color: #333;">min_qual</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="LC141" 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="LC142" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">seq_id</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="LC143" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="p">[]</span> <span class="n" style="color: #333;">o</span><span class="p">;</span></span>
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ctr</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;">mdepth</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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142
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">prev_pos</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;">pos</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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<a href="https://salsa.debian.org/med-team/ivar/-/commit/701a9ea32e3c15bf4d0fb7adeacea2451c117c82#a90b501c7e9fd000f6912d38c32f6642d84586df"><strong>src/call_consensus_pileup.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">@@ -19,7 +19,7 @@ struct ret_t {</td>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"><span class="p">};</span></span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">format_alleles</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">allele</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ad</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">call_consensus_from_plup</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cin</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">out_file</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">threshold</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">min_depth</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">min_coverage_flag</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">call_consensus_from_plup</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cin</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;"><span class="idiff left">seq_id</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">out_file</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">threshold</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">min_depth</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">min_coverage_flag</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="n" style="color: #333;">ret_t</span> <span class="nf" style="color: #900; font-weight: 600;">get_consensus_allele</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">allele</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ad</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">threshold</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">gap</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ivar/-/commit/701a9ea32e3c15bf4d0fb7adeacea2451c117c82#d83847628f25144468f590d3395f6e53e3cde440"><strong>src/call_variants.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">@@ -86,12 +86,19 @@ int call_variants_from_plup(std::istream &cin, std::string out_file, uint8_t min</td>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">ctr</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mdepth</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_depth</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// Check for minimum depth</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">ad</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">update_allele_depth</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">bases</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="p">,</span> <span class="n" style="color: #333;">min_qual</span><span class="p">);</span></span>
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90
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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;">ad</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>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">line_stream</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="LC92" 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="LC93" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="cpp"> <span class="n" style="color: #333;">ad</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">update_allele_depth</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">bases</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="p">,</span> <span class="n" style="color: #333;">min_qual</span><span class="p">);</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ad</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>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Get ungapped depth</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">pdepth</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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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">allele</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ad</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">ad</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;">it</span><span class="p">)</span> <span class="p">{</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nuc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'*'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nuc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'+'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nuc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">)</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="n" style="color: #333;">pdepth</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">depth</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="p">}</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pdepth</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_depth</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// Check for minimum depth</span></span>
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"> <span class="n" style="color: #333;">line_stream</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</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="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="105" 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="112" 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">@@ -105,13 +112,6 @@ int call_variants_from_plup(std::istream &cin, std::string out_file, uint8_t min</td>
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105
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">ad</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">);</span></span>
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106
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"> <span class="n" style="color: #333;">ref_it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ad</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Get ungapped coverage</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">pdepth</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="LC110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">allele</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ad</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">ad</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;">it</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nuc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'*'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nuc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'+'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nuc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC112" 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="LC113" class="line" lang="cpp"> <span class="n" style="color: #333;">pdepth</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">depth</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">allele</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ad</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">ad</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;">it</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC116" 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;">it</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_it</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nuc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'*'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC117" 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 unfold js-unfold old_line" data-linenumber="150" 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">@@ -150,6 +150,7 @@ int call_variants_from_plup(std::istream &cin, std::string out_file, uint8_t min</td>
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150
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"> <span class="p">}</span></span>
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151
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp"> <span class="n" style="color: #333;">out_str</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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152
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333;">out_str</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="LC153" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">freq_depth</span><span class="p">;</span></span>
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153
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp"> <span class="p">}</span></span>
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154
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp"> <span class="n" style="color: #333;">line_stream</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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155
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp"> <span class="p">}</span></span>
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<li id="4a466c890bfc12a03440f5824d0cf9d098ba880f">
<a href="https://salsa.debian.org/med-team/ivar/-/commit/701a9ea32e3c15bf4d0fb7adeacea2451c117c82#4a466c890bfc12a03440f5824d0cf9d098ba880f"><strong>src/get_masked_amplicons.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="35" 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="35" 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">@@ -35,12 +35,22 @@ int get_primers_with_mismatches(std::string bed, std::string vpath, std::string</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// 1 based to 0 based</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_primers</span><span class="p">(</span><span class="n" style="color: #333;">primers</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// mismatches_primers.insert(mismatches_primers.end(), tmp.begin(), tmp.end());</span></span>
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<pre style="margin: 0;">+<span id="LC39" 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;">primer</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">tmp_it</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">tmp</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;">it</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC39" 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;">primer</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">tmp_it</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;">find</span><span class="p">(</span><span class="n" style="color: #333;">mismatches_primers</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">mismatches_primers</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;">it</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tmp_it</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">tmp</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_it</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;">find</span><span class="p">(</span><span class="n" style="color: #333;">mismatches_primers</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">mismatches_primers</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;">it</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tmp_it</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">mismatches_primers</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()){</span></span>
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<pre style="margin: 0;">+<span id="LC43" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_name</span><span class="p">()</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="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">mismatches_primers</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Look for primer pair</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_pair_indice</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_it</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;">find</span><span class="p">(</span><span class="n" style="color: #333;">mismatches_primers</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">mismatches_primers</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">primers</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_pair_indice</span><span class="p">()));</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tmp_it</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">mismatches_primers</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()){</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="n" style="color: #333;">mismatches_primers</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">primers</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_pair_indice</span><span class="p">()));</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">mismatches_primers</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">mismatches_primers</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">tmp</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">tmp</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"> <span class="n" style="color: #333;">line_stream</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="LC55" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"> <span class="p">}</span></span>
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<li id="1ed56bc299f4a6bb415bcf995da6bf4ba876e7a4">
<a href="https://salsa.debian.org/med-team/ivar/-/commit/701a9ea32e3c15bf4d0fb7adeacea2451c117c82#1ed56bc299f4a6bb415bcf995da6bf4ba876e7a4"><strong>src/ivar.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">@@ -16,12 +16,13 @@</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "suffix_tree.h"</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "get_common_variants.h"</span></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</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="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.2.<span class="idiff left right">2</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</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="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.2.<span class="idiff left right">3</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">args_t</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC22" 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;">string</span> <span class="n" style="color: #333;">bam</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -i</span></span>
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23
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<pre style="margin: 0;"> <span id="LC23" 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;">string</span> <span class="n" style="color: #333;">bed</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -b</span></span>
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24
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<pre style="margin: 0;"> <span id="LC24" 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;">string</span> <span class="n" style="color: #333;">text</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -t</span></span>
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<pre style="margin: 0;">+<span id="LC25" 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;">string</span> <span class="n" style="color: #333;">seq_id</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -i for consensus</span></span>
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25
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<td class="diff-line-num new_line" data-linenumber="26" 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="LC26" 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;">string</span> <span class="n" style="color: #333;">prefix</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -p</span></span>
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<pre style="margin: 0;"> <span id="LC27" 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;">string</span> <span class="n" style="color: #333;">ref</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -r</span></span>
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<pre style="margin: 0;"> <span id="LC28" 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;">string</span> <span class="n" style="color: #333;">region</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -R</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">@@ -38,6 +39,7 @@ struct args_t {</td>
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38
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<pre style="margin: 0;"> <span id="LC39" 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;">string</span> <span class="n" style="color: #333;">primer_pair_file</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -f</span></span>
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39
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40
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<pre style="margin: 0;"> <span id="LC40" 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;">string</span> <span class="n" style="color: #333;">file_list</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -f</span></span>
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40
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">write_no_primers_flag</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -e</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">mark_qcfail_flag</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -f</span></span>
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41
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43
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<pre style="margin: 0;"> <span id="LC43" 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;">string</span> <span class="n" style="color: #333;">gff</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -g</span></span>
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42
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"><span class="p">}</span> <span class="n" style="color: #333;">g_args</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC45" 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">@@ -66,7 +68,8 @@ void print_trim_usage(){</td>
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -m Minimum length of read to retain after trimming (Default: 30)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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67
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -q Minimum quality threshold for sliding window to pass (Default: 20)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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68
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -s Width of sliding window (Default: 4)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -e Include reads with no primers. By default, reads with no primers are excluded</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -e Include reads with no primers. By default, reads with no primers are excluded</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -f Mark reads as QCFAIL instead of excluding them</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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70
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Output Options Description</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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71
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -p (Required) Prefix for the output BAM file</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC75" 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="114" 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">@@ -114,7 +117,8 @@ void print_consensus_usage(){</td>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -k If '-k' flag is added, regions with depth less than minimum depth will not be added to the consensus sequence. Using '-k' will override any option specified using -n </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -n (N/-) Character to print in regions with less than minimum coverage(Default: N)</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Output Options Description</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -p (Required) Prefix for the output fasta file and quality file</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -p (Required) Prefix for the output fasta file and quality file</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -i (Optional) Name of fasta header. By default, the prefix is used to create the fasta header in the following format, Consensus_<prefix>_threshold_<frequency-threshold>_quality_<minimum-quality></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"><span class="p">}</span></span>
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">print_removereads_usage</span><span class="p">(){</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="158" 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">@@ -158,9 +162,9 @@ void print_version_info(){</td>
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158
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Please raise issues and bug reports at https://github.com/andersen-lab/ivar/</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="cpp"><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;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trim_opt_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"i:b:p:m:q:s:eh?"</span><span class="p">;</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"><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;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trim_opt_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"i:b:p:m:q:s:e<span class="idiff left right">f</span>h?"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp"><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;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">variants_opt_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"p:t:q:m:r:g:h?"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="cpp"><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;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">consensus_opt_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"p:q:t:m:n:kh?"</span><span class="p">;</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"><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;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">consensus_opt_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">i:</span>p:q:t:m:n:kh?"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"><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;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">removereads_opt_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"i:p:t:b:h?"</span><span class="p">;</span></span>
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165
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"><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;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">filtervariants_opt_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"p:t:f:h?"</span><span class="p">;</span></span>
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"><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;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">getmasked_opt_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"i:b:f:p:h?"</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="210" 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="214" 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">@@ -210,6 +214,7 @@ int main(int argc, char* argv[]){</td>
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210
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">sliding_window</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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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">30</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">write_no_primers_flag</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="LC217" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">mark_qcfail_flag</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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213
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">bed</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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214
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219
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt</span><span class="p">(</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="n" style="color: #333;">trim_opt_str</span><span class="p">);</span></span>
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215
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220
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span> <span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="232" 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="237" 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">@@ -232,10 +237,13 @@ int main(int argc, char* argv[]){</td>
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232
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'s'</span><span class="p">:</span></span>
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233
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238
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">sliding_window</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;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>
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234
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<td class="diff-line-num new_line" data-linenumber="239" 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">
239
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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235
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'h'</span><span class="p">:</span></span>
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236
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240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'e'</span><span class="p">:</span></span>
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237
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241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">write_no_primers_flag</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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238
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242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'f'</span><span class="p">:</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">mark_qcfail_flag</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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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'h'</span><span class="p">:</span></span>
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239
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247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'?'</span><span class="p">:</span></span>
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240
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248
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp"> <span class="n" style="color: #333;">print_trim_usage</span><span class="p">();</span></span>
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241
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="248" 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="256" 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">@@ -248,7 +256,7 @@ int main(int argc, char* argv[]){</td>
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248
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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249
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_filename_without_extension</span><span class="p">(</span><span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span><span class="s" style="color: #d14;">".bam"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="251" 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">
251
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<td class="diff-line-num new_line old" data-linenumber="259" 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="LC251" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trim_bam_qual_primer</span><span class="p">(</span><span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">bed</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">region</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">sliding_window</span><span class="p">,</span> <span class="n" style="color: #333;">cl_cmd</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">(),</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">write_no_primers_flag</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_length</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="252" 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="259" 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">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trim_bam_qual_primer</span><span class="p">(</span><span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">bed</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">region</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">sliding_window</span><span class="p">,</span> <span class="n" style="color: #333;">cl_cmd</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">(),</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">write_no_primers_flag</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">m<span class="idiff left">ark_qcfail_flag</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g_args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">m</span>in_length</span><span class="p">);</span></span>
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252
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<td class="diff-line-num new_line" data-linenumber="260" 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">
260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">compare</span><span class="p">(</span><span class="s" style="color: #d14;">"variants"</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 old_line" data-linenumber="253" 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">
253
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<td class="diff-line-num new_line" data-linenumber="261" 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">
261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">20</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="254" 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">
254
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<td class="diff-line-num new_line" data-linenumber="262" 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">
262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_threshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.03</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="307" 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="315" 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">@@ -307,6 +315,7 @@ int main(int argc, char* argv[]){</td>
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<td class="diff-line-num old_line" data-linenumber="307" 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">
307
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<td class="diff-line-num new_line" data-linenumber="315" 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">
315
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">call_variants_from_plup</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cin</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_threshold</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_depth</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">gff</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="308" 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">
308
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<td class="diff-line-num new_line" data-linenumber="316" 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">
316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">compare</span><span class="p">(</span><span class="s" style="color: #d14;">"consensus"</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 old_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">
309
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<td class="diff-line-num new_line" data-linenumber="317" 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">
317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt</span><span class="p">(</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="n" style="color: #333;">consensus_opt_str</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="310" 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="318" 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">
318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">seq_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="310" 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">
310
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<td class="diff-line-num new_line" data-linenumber="319" 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">
319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_threshold</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 old_line" data-linenumber="311" 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">
311
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<td class="diff-line-num new_line" data-linenumber="320" 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">
320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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<td class="diff-line-num 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">
312
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<td class="diff-line-num new_line" data-linenumber="321" 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">
321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="317" 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="326" 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">@@ -317,6 +326,9 @@ int main(int argc, char* argv[]){</td>
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<td class="diff-line-num old_line" data-linenumber="317" 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">
317
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<td class="diff-line-num new_line" data-linenumber="326" 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">
326
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'t'</span><span class="p">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="318" 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">
318
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<td class="diff-line-num new_line" data-linenumber="327" 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">
327
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_threshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atof</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="319" 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">
319
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<td class="diff-line-num new_line" data-linenumber="328" 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">
328
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'i'</span><span class="p">:</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">seq_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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320
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332
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'p'</span><span class="p">:</span></span>
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321
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333
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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322
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334
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="372" 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">@@ -360,7 +372,7 @@ int main(int argc, char* argv[]){</td>
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360
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372
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<pre style="margin: 0;"> <span id="LC372" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Regions with depth less than minimum depth will not added to consensus"</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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361
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373
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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362
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374
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<pre style="margin: 0;"> <span id="LC374" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Regions with depth less than minimum depth covered by: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">gap</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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363
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<td class="diff-line-num new_line old" data-linenumber="375" 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="LC363" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">call_consensus_from_plup</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cin</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_threshold</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_depth</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">keep_min_coverage</span><span class="p">);</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">call_consensus_from_plup</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cin</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">seq_id</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g_args</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_threshold</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_depth</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">keep_min_coverage</span><span class="p">);</span></span>
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364
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">compare</span><span class="p">(</span><span class="s" style="color: #d14;">"removereads"</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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365
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377
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt</span><span class="p">(</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="n" style="color: #333;">removereads_opt_str</span><span class="p">);</span></span>
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366
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378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span> <span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="p">{</span></span>
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<li id="866d85bf13e1fa8b98ce1b6c3d29af2e31287c2c">
<a href="https://salsa.debian.org/med-team/ivar/-/commit/701a9ea32e3c15bf4d0fb7adeacea2451c117c82#866d85bf13e1fa8b98ce1b6c3d29af2e31287c2c"><strong>src/primer_bed.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="80" 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">@@ -80,7 +80,6 @@ void primer::add_read_count(uint32_t rc){</td>
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">read_count</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rc</span><span class="p">;</span></span>
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81
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"><span class="p">}</span></span>
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82
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">print_bed_format</span><span class="p">(){</span></span>
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<pre style="margin: 0;"> <span id="LC84" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"iVar uses the standard 6 column BED format as defined here - https://genome.ucsc.edu/FAQ/FAQformat.html#format1."</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="LC85" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"It requires the following columns delimited by a tab: chrom, chromStart, chromEnd, name, score, strand"</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -96,6 +95,7 @@ std::vector<primer> populate_from_file(std::string path){</td>
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96
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<pre style="margin: 0;"> <span id="LC95" 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;">string</span> <span class="n" style="color: #333;">cell</span><span class="p">;</span></span>
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97
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ctr</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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98
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">primer</span> <span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">set_strand</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Set strand to NULL</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">lineStream</span><span class="p">,</span><span class="n" style="color: #333;">cell</span><span class="p">,</span><span class="sc" style="color: #d14;">'\t'</span><span class="p">)){</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span><span class="n" style="color: #333;">ctr</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="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="126" 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">@@ -126,9 +126,9 @@ std::vector<primer> populate_from_file(std::string path){</td>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">all_of</span><span class="p">(</span><span class="n" style="color: #333;">cell</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">cell</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;">isdigit</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">set_score</span><span class="p">(</span><span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">cell</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC128" 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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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="cpp"> <span class="n" style="color: #333;">print_bed_format</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">primers</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">clear</span></span><span class="p"><span class="idiff right">()</span>;</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">primers</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="n" style="color: #333;">print_bed_format</span><span class="p">();</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// score is missing, send warning but continue populating</span></span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">cout</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">WARNING: The BED file provided did not have the expected score column, but iVar will continue trimming</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><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="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">endl</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"><span class="idiff left"> </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">set_score</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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132
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"> <span class="p">}</span></span>
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133
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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134
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">5</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">@@ -142,16 +142,14 @@ std::vector<primer> populate_from_file(std::string path){</td>
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142
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"> <span class="p">}</span></span>
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143
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"> <span class="n" style="color: #333;">ctr</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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144
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"> <span class="p">}</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">indice</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;">ctr</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">6</span><span class="p">)</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Strand not found in primer BED file so strand will not be considered for trimming"</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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145
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">set_indice</span><span class="p">(</span><span class="n" style="color: #333;">indice</span><span class="p">);</span></span>
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146
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">set_pair_indice</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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147
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">set_read_count</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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148
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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;">primers</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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149
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp"> <span class="n" style="color: #333;">indice</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"> <span class="p">}</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">primers</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>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333;">print_bed_format</span><span class="p">();</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Found 0 primers in BED 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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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC153" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Found "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">primers</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" primers in BED 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="LC154" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">primers</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC155" 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">@@ -217,8 +215,7 @@ primer get_min_start(std::vector<primer> primers){</td>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">minmax_start</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">);</span></span>
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp"><span class="n" style="color: #333;">primer</span> <span class="nf" style="color: #900; font-weight: 600;">get_max_end</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">primers</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">minmax_start</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;">minmax_element</span><span class="p">(</span><span class="n" style="color: #333;">primers</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">primers</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="p">[]</span> <span class="p">(</span><span class="n" style="color: #333;">primer</span> <span class="n" style="color: #333;">lhs</span><span class="p">,</span> <span class="n" style="color: #333;">primer</span> <span class="n" style="color: #333;">rhs</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">lhs</span><span class="p">.</span><span class="n" style="color: #333;">get_end</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">rhs</span><span class="p">.</span><span class="n" style="color: #333;">get_end</span><span class="p">();});</span></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">minmax_start</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="LC224" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"><span class="p">}</span></span></pre>
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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">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/ivar/-/commit/701a9ea32e3c15bf4d0fb7adeacea2451c117c82#827c933f78896247082ec5f587c9bb8d23762f1f"><strong>src/ref_seq.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">@@ -2,12 +2,13 @@</td>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ref_antd</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">get_base</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">region</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;">// 1-based position</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">base</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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5
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6
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<pre style="margin: 0;"> <span id="LC6" 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;">region</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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fai</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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6
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fai_fetch</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fai</span><span class="p">,</span> <span class="n" style="color: #333;">region</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="idiff"> </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">NULL</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="cpp"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">pos</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">1</span></span><span class="p"><span class="idiff right">))</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">base</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">pos</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">1</span></span><span class="p"><span class="idiff right">));</span></span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">free</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">base</span></span><span class="p">;</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ref_antd</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">get_codon</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">region</span><span class="p">,</span> <span class="n" style="color: #333;">gff3_feature</span> <span class="n" style="color: #333;">feature</span><span class="p">){</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="35" 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="36" 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">@@ -35,6 +36,7 @@ char* ref_antd::get_codon(int64_t pos, std::string region, gff3_feature feature)</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">codon</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">codon_start_pos</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;">edit_offset</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="p">}</span></span>
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">codon</span><span class="p">;</span></span>
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"><span class="p">}</span></span>
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="68" 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="70" 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">@@ -68,6 +70,7 @@ char* ref_antd::get_codon(int64_t pos, std::string region, gff3_feature feature,</td>
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68
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"> <span class="p">}</span></span>
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69
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">alt_pos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">edit_offset</span><span class="p">;</span></span>
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70
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">codon</span><span class="p">[</span><span class="n" style="color: #333;">alt_pos</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;">codon_start_pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alt</span><span class="p">;</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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71
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">codon</span><span class="p">;</span></span>
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72
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"><span class="p">}</span></span>
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73
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="101" 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="104" 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">@@ -101,6 +104,11 @@ ref_antd::ref_antd(std::string ref_path, std::string gff_path){</td>
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101
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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;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add_gff</span><span class="p">(</span><span class="n" style="color: #333;">gff_path</span><span class="p">);</span></span>
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102
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"><span class="n" style="color: #333;">ref_antd</span><span class="o" style="font-weight: 600;">::~</span><span class="n" style="color: #333;">ref_antd</span><span class="p">()</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"><span class="p">{</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fai</span><span class="p">)</span> <span class="n" style="color: #333;">fai_destroy</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fai</span><span class="p">);</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"><span class="p">}</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"></span>
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104
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_antd</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">codon_aa_stream</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">region</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostringstream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">line_stream</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ofstream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fout</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">alt</span><span class="p">){</span></span>
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105
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113
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<pre style="margin: 0;"> <span id="LC113" 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;">gff3_feature</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">features</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gff</span><span class="p">.</span><span class="n" style="color: #333;">query_features</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="s" style="color: #d14;">"CDS"</span><span class="p">);</span></span>
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106
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">features</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="c1" style="color: #998; font-style: italic;">// No matching CDS</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="119" 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="127" 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">@@ -119,6 +127,9 @@ int ref_antd::codon_aa_stream(std::string region, std::ostringstream &line_strea</td>
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119
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">alt_codon</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;">alt_codon</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">alt_codon</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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120
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">codon2aa</span><span class="p">(</span><span class="n" style="color: #333;">alt_codon</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">alt_codon</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">alt_codon</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</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="LC130" class="line" lang="cpp"></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">ref_codon</span><span class="p">;</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">alt_codon</span><span class="p">;</span></span>
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122
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"> <span class="p">}</span></span>
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123
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134
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<pre style="margin: 0;"> <span id="LC134" 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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124
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"><span class="p">}</span></span>
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<li id="4644266bab7fcf61e2c44b911c9afd8ddac65d26">
<a href="https://salsa.debian.org/med-team/ivar/-/commit/701a9ea32e3c15bf4d0fb7adeacea2451c117c82#4644266bab7fcf61e2c44b911c9afd8ddac65d26"><strong>src/ref_seq.h</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="15" 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">@@ -15,6 +15,7 @@ class ref_antd{</td>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"><span class="nl">public:</span></span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"> <span class="n" style="color: #333;">ref_antd</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">ref_path</span><span class="p">);</span></span>
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17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"> <span class="n" style="color: #333;">ref_antd</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">ref_path</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">gff_path</span><span class="p">);</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">ref_antd</span><span class="p">();</span></span>
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18
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">get_base</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">region</span><span class="p">);</span></span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">add_gff</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">path</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">add_seq</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">path</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/ivar/-/commit/701a9ea32e3c15bf4d0fb7adeacea2451c117c82#00b6081be5179b8efd2e37aec59ecf773a10c3ed"><strong>src/trim_primer_quality.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">@@ -84,8 +84,13 @@ cigar_ quality_trim(bam1_t* r, uint8_t qual_threshold, uint8_t sliding_window){</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;">del_len</span><span class="p">,</span> <span class="n" style="color: #333;">cig</span><span class="p">,</span> <span class="n" style="color: #333;">temp</span><span class="p">;</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="kt" style="color: #458; font-weight: 600;">uint32_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;">j</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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86
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">cigar_</span> <span class="n" style="color: #333;">t</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">qual_threshold</span> <span class="o" style="font-weight: 600;">&&</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="kt" style="color: #458; font-weight: 600;">uint32_t</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;">core</span><span class="p">.</span><span class="n" style="color: #333;">l_qseq</span><span class="p">)){</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">init_cigar</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">t</span><span class="p">);</span></span>
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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;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">l_qseq</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sliding_window</span><span class="p">)</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">sliding_window</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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;">core</span><span class="p">.</span><span class="n" style="color: #333;">l_qseq</span><span class="p">;</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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;">core</span><span class="p">.</span><span class="n" style="color: #333;">l_qseq</span><span class="p">){</span></span>
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88
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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;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mean_quality</span><span class="p">(</span><span class="n" style="color: #333;">qual</span><span class="p">,</span> <span class="n" style="color: #333;">i</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;">sliding_window</span><span class="p">);</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">qual_threshold</span><span class="p">)</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" 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="LC94" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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90
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95
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<pre style="margin: 0;"> <span id="LC95" 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="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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;">core</span><span class="p">.</span><span class="n" style="color: #333;">l_qseq</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sliding_window</span><span class="p">)</span></span>
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91
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">sliding_window</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="97" 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">@@ -97,7 +102,9 @@ cigar_ quality_trim(bam1_t* r, uint8_t qual_threshold, uint8_t sliding_window){</td>
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97
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"> <span class="n" style="color: #333;">del_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">l_qseq</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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98
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"> <span class="n" style="color: #333;">start_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_pos_on_reference</span><span class="p">(</span><span class="n" style="color: #333;">cigar</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;">core</span><span class="p">.</span><span class="n" style="color: #333;">n_cigar</span><span class="p">,</span> <span class="n" style="color: #333;">del_len</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;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// For reverse reads need to set core->pos.</span></span>
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<td class="diff-line-num old_line" data-linenumber="99" 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">
99
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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;">if</span><span class="p">(</span><span class="n" style="color: #333;">reverse</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">start_pos</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">ncigar</span><span class="p">);</span></span>
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100
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cigar</span><span class="p">;</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">free_cig</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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101
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">nlength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">n_cigar</span><span class="p">;</span></span>
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102
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">start_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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103
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">t</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">@@ -140,6 +147,7 @@ cigar_ quality_trim(bam1_t* r, uint8_t qual_threshold, uint8_t sliding_window){</td>
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140
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"> <span class="p">}</span></span>
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141
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ncigar</span><span class="p">;</span></span>
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142
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">nlength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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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;">t</span><span class="p">.</span><span class="n" style="color: #333;">free_cig</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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143
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp"> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">start_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start_pos</span><span class="p">;</span></span>
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144
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">t</span><span class="p">;</span></span>
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145
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153
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<pre style="margin: 0;"> <span id="LC153" 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="227" 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="235" 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">@@ -227,6 +235,7 @@ cigar_ primer_trim(bam1_t *r, int32_t new_pos, bool unpaired_rev = false){</td>
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227
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235
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp"> <span class="p">}</span></span>
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228
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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;">return</span> <span class="p">{</span></span>
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229
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"> <span class="n" style="color: #333;">ncigar</span><span class="p">,</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span></span>
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230
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239
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp"> <span class="n" style="color: #333;">j</span><span class="p">,</span></span>
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231
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240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"> <span class="n" style="color: #333;">start_pos</span></span>
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232
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241
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<pre style="margin: 0;"> <span id="LC241" 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="259" 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="268" 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">@@ -259,7 +268,7 @@ void get_overlapping_primers(bam1_t* r, std::vector<primer> primers, std::vector</td>
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259
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp"> <span class="n" style="color: #333;">start_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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260
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="cpp"> <span class="p">}</span></span>
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261
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">primers</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">primers</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;">it</span><span class="p">)</span> <span class="p">{</span></span>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">start_pos</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_start</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">start_pos</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_end</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;"><span class="idiff left">strand</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">it</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">get_strand</span></span><span class="p"><span class="idiff right">(</span>))</span></span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">start_pos</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_start</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">start_pos</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_end</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">strand</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">it</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">get_strand</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="n" style="color: #333;"><span class="idiff">it</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">get_strand</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">0</span></span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="cpp"> <span class="n" style="color: #333;">overlapped_primers</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC274" 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">@@ -276,31 +285,27 @@ void get_overlapping_primers(bam1_t* r, std::vector<primer> primers, std::vector</td>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="cpp"> <span class="n" style="color: #333;">start_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">primers</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">primers</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;">it</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">start_pos</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_start</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">start_pos</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_end</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;"><span class="idiff left">strand</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">it</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">get_strand</span></span><span class="p"><span class="idiff right">(</span>))</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">start_pos</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_start</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">start_pos</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_end</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">strand</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">it</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">get_strand</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="n" style="color: #333;"><span class="idiff">it</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">get_strand</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">0</span></span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp"> <span class="n" style="color: #333;">overlapped_primers</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="cpp"><span class="n" style="color: #333;"><span class="idiff left">cigar_</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">condense_cigar</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">cigar</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">n</span></span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">void</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">condense_cigar</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">cigar_</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">t</span></span><span class="p">){</span></span>
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285
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_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;">len</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;">cig</span><span class="p">,</span> <span class="n" style="color: #333;">next_cig</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="cpp"> <span class="n" style="color: #333;">cigar_</span> <span class="n" style="color: #333;">t</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</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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288
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="cpp"> <span class="n" style="color: #333;">cig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_cigar_op</span><span class="p">(</span><span class="n" style="color: #333;">cigar</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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289
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="cpp"> <span class="n" style="color: #333;">next_cig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_cigar_op</span><span class="p">(</span><span class="n" style="color: #333;">cigar</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;">1</span><span class="p">]);</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nlength</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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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"> <span class="n" style="color: #333;">cig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_cigar_op</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cigar</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="297" 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">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"> <span class="n" style="color: #333;">next_cig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_cigar_op</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cigar</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;">1</span><span class="p">]);</span></span>
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290
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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;">if</span><span class="p">(</span><span class="n" style="color: #333;">cig</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">next_cig</span><span class="p">){</span></span>
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291
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="cpp"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_cigar_oplen</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">cigar</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">bam_cigar_oplen</span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">cigar</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;">1</span><span class="p">]);</span></span>
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292
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">cigar</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</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="n" style="color: #333;"><span class="idiff">bam_cigar_gen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">len</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bam_cigar_op</span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">cigar</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]));</span></span>
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293
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<pre style="margin: 0;">-<span id="LC293" 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;">uint32_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff left right">n</span></span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">cigar</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">j</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 right"> </span><span class="n" style="color: #333;">cigar</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="299" 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">
299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_cigar_oplen</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">cigar</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">bam_cigar_oplen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">cigar</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;">1</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="300" 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">
300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">cigar</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</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="n" style="color: #333;"><span class="idiff">bam_cigar_gen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">len</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bam_cigar_op</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">cigar</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="301" 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">
301
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<pre style="margin: 0;">+<span id="LC301" 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;">uint32_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff left">t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">nlength</span></span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</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="LC302" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">cigar</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">j</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="n" style="color: #333;"><span class="idiff">t</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">cigar</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">n</span></span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">nlength</span></span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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297
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305
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<pre style="margin: 0;"> <span id="LC305" 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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306
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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299
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="cpp"> <span class="p">}</span></span>
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="cpp"> <span class="p">}</span></span>
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301
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="cpp"> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cigar</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="cpp"> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">nlength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">t</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">add_pg_line_to_header</span><span class="p">(</span><span class="n" style="color: #333;">bam_hdr_t</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cmd</span><span class="p">){</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="315" 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">@@ -315,16 +320,17 @@ void add_pg_line_to_header(bam_hdr_t** hdr, char *cmd){</td>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hdr</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">l_text</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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316
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">trim_bam_qual_primer</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bed</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam_out</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">region_</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">sliding_window</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">write_no_primer_reads</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">min_length</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">30</span></span><span class="p"><span class="idiff right">)</span>{</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">trim_bam_qual_primer</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bed</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam_out</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">region_</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">sliding_window</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">write_no_primer_reads</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mark_qcfail_flag</span></span><span class="p"><span class="idiff">,</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">min_length</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">30</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC324" 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;">primer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">primers</span><span class="p">;</span></span>
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320
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325
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<pre style="margin: 0;"> <span id="LC325" 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;">bed</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()){</span></span>
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321
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326
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"> <span class="n" style="color: #333;">primers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">populate_from_file</span><span class="p">(</span><span class="n" style="color: #333;">bed</span><span class="p">);</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">primers</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>
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328
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<pre style="margin: 0;">+<span id="LC328" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Exiting."</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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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"> <span class="p">}</span></span>
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322
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331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// if(primers.size() == 0){</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// return 0;</span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()){</span></span>
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<pre style="margin: 0;">-<span id="LC327" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Bam file i<span class="idiff left right">n</span> empty."</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="LC333" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Bam file i<span class="idiff left right">s</span> empty."</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="LC334" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="cpp"> <span class="n" style="color: #333;">bam_out</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">".bam"</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="399" 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="405" 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">@@ -399,6 +405,7 @@ int trim_bam_qual_primer(std::string bam, std::string bed, std::string bam_out,</td>
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="cpp"> <span class="n" style="color: #333;">bam1_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aln</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_init1</span><span class="p">();</span></span>
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406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ctr</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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401
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="cpp"> <span class="n" style="color: #333;">cigar_</span> <span class="n" style="color: #333;">t</span><span class="p">;</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp"> <span class="n" style="color: #333;">init_cigar</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">t</span><span class="p">);</span></span>
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409
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">primer_trim_count</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;">no_primer_counter</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;">low_quality</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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410
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">unmapped_flag</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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411
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">unmapped_counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="423" 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">@@ -423,6 +430,7 @@ int trim_bam_qual_primer(std::string bam, std::string bed, std::string bam_out,</td>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="cpp"> <span class="n" style="color: #333;">aln</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">start_pos</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="cpp"> <span class="n" style="color: #333;">replace_cigar</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">nlength</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Add count to primer</span></span>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="cpp"> <span class="n" style="color: #333;">cit</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;">find</span><span class="p">(</span><span class="n" style="color: #333;">primers</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">primers</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">cand_primer</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cit</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">primers</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="439" 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">@@ -431,7 +439,7 @@ int trim_bam_qual_primer(std::string bam, std::string bed, std::string bam_out,</td>
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431
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="cpp"> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">quality_trim</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">,</span> <span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="n" style="color: #333;">sliding_window</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Quality Trimming</span></span>
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bam_is_rev</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="cpp"> <span class="n" style="color: #333;">aln</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">start_pos</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">t</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">condense_cigar</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">cigar</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">nlength</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">condense_cigar</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">t</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// aln->core.pos += t.start_pos;</span></span>
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="cpp"> <span class="n" style="color: #333;">replace_cigar</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">nlength</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span><span class="p">);</span></span>
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437
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445
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// Unpaired reads: Might be stitched reads</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="461" 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">@@ -461,7 +469,7 @@ int trim_bam_qual_primer(std::string bam, std::string bed, std::string bam_out,</td>
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461
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469
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="cpp"> <span class="n" style="color: #333;">cit</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add_read_count</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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462
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470
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="cpp"> <span class="p">}</span></span>
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463
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471
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="cpp"> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">quality_trim</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">,</span> <span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="n" style="color: #333;">sliding_window</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Quality Trimming</span></span>
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464
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">t</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">condense_cigar</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">cigar</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">nlength</span></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;"><span class="idiff left">condense_cigar</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">t</span></span><span class="p">);</span></span>
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473
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="cpp"> <span class="n" style="color: #333;">replace_cigar</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">nlength</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">cigar</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="p">}</span></span>
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475
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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;">primer_trimmed</span><span class="p">){</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="488" 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="496" 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">@@ -488,6 +496,7 @@ int trim_bam_qual_primer(std::string bam, std::string bed, std::string bam_out,</td>
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488
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496
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="cpp"> <span class="p">}</span></span>
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489
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497
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<pre style="margin: 0;"> <span id="LC497" 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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490
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498
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">primers</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">write_no_primer_reads</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;">unmapped_flag</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;">// Write mapped reads to BAM if -e flag given</span></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mark_qcfail_flag</span><span class="p">)</span> <span class="n" style="color: #333;">aln</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">BAM_FQCFAIL</span><span class="p">;</span></span>
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491
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500
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bam_write1</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">aln</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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492
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501
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<pre style="margin: 0;"> <span id="LC501" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Not able to write to BAM"</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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502
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="cpp"> <span class="n" style="color: #333;">hts_itr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">iter</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="503" 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="512" 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">@@ -503,6 +512,19 @@ int trim_bam_qual_primer(std::string bam, std::string bed, std::string bam_out,</td>
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503
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512
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="cpp"> <span class="p">}</span></span>
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504
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513
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<pre style="margin: 0;"> <span id="LC513" 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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505
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514
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="cpp"> <span class="n" style="color: #333;">low_quality</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mark_qcfail_flag</span><span class="p">)</span> <span class="p">{</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="cpp"> <span class="n" style="color: #333;">aln</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">BAM_FQCFAIL</span><span class="p">;</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bam_write1</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">aln</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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518
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<pre style="margin: 0;">+<span id="LC518" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Not able to write to BAM"</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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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="cpp"> <span class="n" style="color: #333;">hts_itr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">iter</span><span class="p">);</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="cpp"> <span class="n" style="color: #333;">hts_idx_destroy</span><span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">);</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="cpp"> <span class="n" style="color: #333;">bam_destroy1</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">);</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="cpp"> <span class="n" style="color: #333;">bam_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">);</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="cpp"> <span class="n" style="color: #333;">sam_close</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">);</span></span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="cpp"> <span class="n" style="color: #333;">bgzf_close</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="cpp"> <span class="p">}</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="cpp"> <span class="p">}</span></span>
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506
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528
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="cpp"> <span class="p">}</span></span>
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507
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529
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="cpp"> <span class="n" style="color: #333;">ctr</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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508
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530
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ctr</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">log_skip</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -516,9 +538,16 @@ int trim_bam_qual_primer(std::string bam, std::string bed, std::string bam_out,</td>
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516
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538
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<pre style="margin: 0;"> <span id="LC538" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cit</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_name</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cit</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_read_count</span><span class="p">()</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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517
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539
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="cpp"> <span class="p">}</span></span>
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518
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540
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<pre style="margin: 0;"> <span id="LC540" 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;">cout</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="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Trimmed primers from "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">round_int</span><span class="p">(</span><span class="n" style="color: #333;">primer_trim_count</span><span class="p">,</span> <span class="n" style="color: #333;">mapped</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"% ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">primer_trim_count</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">") of reads."</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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519
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<pre style="margin: 0;">-<span id="LC519" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">round_int</span><span class="p">(</span> <span class="n" style="color: #333;">low_quality</span><span class="p">,</span> <span class="n" style="color: #333;">mapped</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"% ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">low_quality</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">") of reads were quality trimmed below the minimum length of "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">min_length</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" bp and were not writen to 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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541
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<pre style="margin: 0;">+<span id="LC541" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">round_int</span><span class="p">(</span> <span class="n" style="color: #333;">low_quality</span><span class="p">,</span> <span class="n" style="color: #333;">mapped</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"% ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">low_quality</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">") of reads were quality trimmed below the minimum length of "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">min_length</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" bp and were "</span><span class="p">;</span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mark_qcfail_flag</span><span class="p">)</span> <span class="p">{</span></span>
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543
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<pre style="margin: 0;">+<span id="LC543" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"marked as failed"</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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544
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<pre style="margin: 0;">+<span id="LC544" 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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545
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<pre style="margin: 0;">+<span id="LC545" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"not written to 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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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="cpp"> <span class="p">}</span></span>
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520
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547
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">write_no_primer_reads</span><span class="p">){</span></span>
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521
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<pre style="margin: 0;">-<span id="LC521" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">round_int</span><span class="p">(</span><span class="n" style="color: #333;">no_primer_counter</span><span class="p">,</span> <span class="n" style="color: #333;">mapped</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"% ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">no_primer_counter</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">") of reads started outside of primer regions. Since the -e flag was given, these reads were written to 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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548
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<pre style="margin: 0;">+<span id="LC548" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">round_int</span><span class="p">(</span><span class="n" style="color: #333;">no_primer_counter</span><span class="p">,</span> <span class="n" style="color: #333;">mapped</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"% ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">no_primer_counter</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">") of reads started outside of primer regions. Since the -e flag was given, these reads were written to file"</span><span class="p">;</span></span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mark_qcfail_flag</span><span class="p">)</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" and the BAM_QCFAIL flag set"</span><span class="p">;</span></span>
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550
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<pre style="margin: 0;">+<span id="LC550" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">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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522
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551
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">primers</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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523
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552
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<pre style="margin: 0;"> <span id="LC552" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">round_int</span><span class="p">(</span><span class="n" style="color: #333;">no_primer_counter</span><span class="p">,</span> <span class="n" style="color: #333;">mapped</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"% ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">no_primer_counter</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">") of reads started outside of primer regions. Since there were no primers found in BED file, these reads were written to 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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524
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553
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<pre style="margin: 0;"> <span id="LC553" 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="LC19" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">cigar_</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cigar</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">free_cig</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">nlength</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">start_pos</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">init_cigar</span><span class="p">(</span><span class="n" style="color: #333;">cigar_</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">t</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cigar</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">free_cig</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nlength</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;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start_pos</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="LC28" class="line" lang="c"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">free_cigar</span><span class="p">(</span><span class="n" style="color: #333;">cigar_</span> <span class="n" style="color: #333;">t</span><span class="p">)</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">free_cig</span><span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span><span class="p">);</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">add_pg_line_to_header</span><span class="p">(</span><span class="n" style="color: #333;">bam_hdr_t</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cmd</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">trim_bam_qual_primer</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bed</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam_out</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">region_</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">sliding_window</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">write_no_primer_reads</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_length</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">trim_bam_qual_primer</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bed</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam_out</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">region_</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">sliding_window</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">write_no_primer_reads</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">mark_qcfail_flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_length</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">free_cigar</span><span class="p">(</span><span class="n" style="color: #333;">cigar_</span> <span class="n" style="color: #333;">t</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="nf" style="color: #900; font-weight: 600;">get_pos_on_query</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cigar</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">ncigar</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">ref_start</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="nf" style="color: #900; font-weight: 600;">get_pos_on_reference</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cigar</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">ncigar</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">ref_start</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">reverse_qual</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;">q</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l</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">@@ -35,7 +41,7 @@ cigar_ quality_trim(bam1_t* r, uint8_t qual_threshold, uint8_t sliding_window);</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">print_cigar</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cigar</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nlength</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"><span class="n" style="color: #333;">cigar_</span> <span class="nf" style="color: #900; font-weight: 600;">primer_trim</span><span class="p">(</span><span class="n" style="color: #333;">bam1_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;">int32_t</span> <span class="n" style="color: #333;">new_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">unpaired_rev</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">replace_cigar</span><span class="p">(</span><span class="n" style="color: #333;">bam1_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">b</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="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cigar</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"><span class="n" style="color: #333;"><span class="idiff left">cigar_</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">condense_cigar</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">cigar</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">n</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">void</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">condense_cigar</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">cigar_</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">t</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">get_overlapping_primers</span><span class="p">(</span><span class="n" style="color: #333;">bam1_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">primers</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">overlapping_primers</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">get_overlapping_primers</span><span class="p">(</span><span class="n" style="color: #333;">bam1_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">primers</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">overlapping_primers</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">unpaired_rev</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC47" 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">@@ -2,14 +2,16 @@ LIBS = -lhts -lz -lpthread</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++11 <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-Wextra</span> <span class="nt" style="color: #000080;">-Werror</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="make"><span class="nv" style="color: #008080;">TESTS</span> <span class="o" style="font-weight: 600;">=</span> check_primer_trim check_<span class="idiff left right">quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth</span> check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="make"><span class="nv" style="color: #008080;">check_PROGRAMS</span> <span class="o" style="font-weight: 600;">=</span> check_primer_trim check_<span class="idiff left right">quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth</span> check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="make"><span class="nv" style="color: #008080;">TESTS</span> <span class="o" style="font-weight: 600;">=</span> check_primer_trim check_<span class="idiff left right">trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id</span> check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="make"><span class="nv" style="color: #008080;">check_PROGRAMS</span> <span class="o" style="font-weight: 600;">=</span> check_primer_trim check_<span class="idiff left right">trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id</span> check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases</span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="make"><span class="nv" style="color: #008080;">check_primer_trim_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> test_primer_trim.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="make"><span class="nv" style="color: #008080;">check_trim_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> test_trim.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp</span>
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8
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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">
9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"><span class="nv" style="color: #008080;">check_quality_trim_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> check_quality_trim.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp</span>
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9
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"><span class="nv" style="color: #008080;">check_consensus_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> test_call_consensus_from_plup.cpp ../src/call_consensus_pileup.cpp ../src/allele_functions.cpp</span>
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10
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"><span class="nv" style="color: #008080;">check_allele_depth_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> test_allele_depth.cpp ../src/allele_functions.cpp</span>
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11
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"><span class="nv" style="color: #008080;">check_consensus_threshold_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> test_consensus_threshold.cpp ../src/call_consensus_pileup.cpp ../src/allele_functions.cpp</span>
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12
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="make"><span class="nv" style="color: #008080;">check_consensus_min_depth_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> test_consensus_min_depth.cpp ../src/call_consensus_pileup.cpp ../src/allele_functions.cpp</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="make"><span class="nv" style="color: #008080;">check_consensus_seq_id_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> test_consensus_seq_id.cpp ../src/call_consensus_pileup.cpp ../src/allele_functions.cpp</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="make"><span class="nv" style="color: #008080;">check_variants_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> test_variants.cpp ../src/call_variants.cpp ../src/allele_functions.cpp ../src/parse_gff.cpp ../src/ref_seq.cpp</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="make"><span class="nv" style="color: #008080;">check_common_variants_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> test_common_variants.cpp ../src/get_common_variants.cpp</span>
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15
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"><span class="nv" style="color: #008080;">check_primer_bed_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> test_primer_bed.cpp ../src/primer_bed.cpp</span>
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<li id="75bffbb11d25186dd3d2c6aa35d85c3bf441a4d0">
<a href="https://salsa.debian.org/med-team/ivar/-/commit/701a9ea32e3c15bf4d0fb7adeacea2451c117c82#75bffbb11d25186dd3d2c6aa35d85c3bf441a4d0"><strong>tests/check_quality_trim.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">@@ -15,8 +15,8 @@ int main(){</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_itr_querys</span><span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">region_</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"> <span class="n" style="color: #333;">bam1_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aln</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_init1</span><span class="p">();</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"> <span class="n" style="color: #333;">cigar_</span> <span class="n" style="color: #333;">t</span><span class="p">;</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">150</span><span class="p">,</span><span class="mi" style="color: #099;"><span class="idiff left">100</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">25</span></span><span class="p">,</span><span class="mi" style="color: #099;">146</span><span class="p">,</span><span class="mi" style="color: #099;">144</span><span class="p">},</span> <span class="n" style="color: #333;">ctr</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="LC19" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start_pos_rev</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">19</span><span class="p">,</span> <span class="mi" style="color: #099;">11<span class="idiff left">3</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">208</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">324</span></span><span class="p">,</span> <span class="mi" style="color: #099;">199</span><span class="p">,</span> <span class="mi" style="color: #099;">231</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">150</span><span class="p">,</span><span class="mi" style="color: #099;"><span class="idiff left">99</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">99</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">24</span></span><span class="p">,</span><span class="mi" style="color: #099;">146</span><span class="p">,</span><span class="mi" style="color: #099;">144</span><span class="p">},</span> <span class="n" style="color: #333;">ctr</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="LC19" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start_pos_rev</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">19</span><span class="p">,</span> <span class="mi" style="color: #099;">11<span class="idiff left">4</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">209</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">325</span></span><span class="p">,</span> <span class="mi" style="color: #099;">199</span><span class="p">,</span> <span class="mi" style="color: #099;">231</span><span class="p">};</span></span>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">sam_itr_next</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">iter</span><span class="p">,</span> <span class="n" style="color: #333;">aln</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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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">quality_trim</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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22
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22
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<pre style="margin: 0;"> <span id="LC22" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">bam_get_qname</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">)</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="27" 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">@@ -27,7 +27,14 @@ int main(){</td>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bam_cigar2rlen</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">nlength</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">ctr</span><span class="p">]){</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"> <span class="n" style="color: #333;">free_cigar</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"> <span class="n" style="color: #333;">ctr</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">bam_destroy1</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"> <span class="n" style="color: #333;">bam_itr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">iter</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">sam_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">hts_idx_destroy</span><span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="n" style="color: #333;">hts_close</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">success</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ivar/-/commit/701a9ea32e3c15bf4d0fb7adeacea2451c117c82#cc537d8192ad73764985b8cb628b4e7371a78a18"><strong>tests/test_consensus_min_depth.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">@@ -4,10 +4,10 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "../src/call_consensus_pileup.h"</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "../src/allele_functions.h"</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">call_cns_check_outfile</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">cns</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">call_min_depth</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_depth</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">call_cns_check_outfile</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;"><span class="idiff left">input_id</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">cns</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">call_min_depth</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_depth</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC8" 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;">string</span> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"../data/test.gap.sorted.mpileup"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC9" 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;">ifstream</span> <span class="n" style="color: #333;">mplp</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="cpp"> <span class="n" style="color: #333;">call_consensus_from_plup</span><span class="p">(</span><span class="n" style="color: #333;">mplp</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">min_depth</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">call_min_depth</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"> <span class="n" style="color: #333;">call_consensus_from_plup</span><span class="p">(</span><span class="n" style="color: #333;">mplp</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">input_id</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">min_depth</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">call_min_depth</span><span class="p">);</span></span>
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11
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<pre style="margin: 0;"> <span id="LC11" 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;">ifstream</span> <span class="n" style="color: #333;">outFile</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".fa"</span><span class="p">);</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" 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;">string</span> <span class="n" style="color: #333;">l</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"> <span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">outFile</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Ignore first line</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,11 +20,11 @@ int main() {</td>
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<pre style="margin: 0;"> <span id="LC20" 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;">string</span> <span class="n" style="color: #333;">c_</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"CTGCTGGGTCATGGGCCCATCATGATGGTCTTGGCGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCATCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAGAAAGAT------------------------------AGGAAGGAGAAGAAGAGACGWGGCGCAGATACTAGTGTCGGAATTGTTGGMCTCCTGCTGACCACAGCTATGGMAGCGGAGGTCACKAGACGTGGGAGTGCATACTATATGTACTTGGACWGAAACGATGCKGGGGAGGCCATATCTTTTCCAACCACATTGGGGTTGAATAAGTG"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC21" 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;">string</span> <span class="n" style="color: #333;">cN</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"CTGCTGGGTCATGGGCCCATCATGATGGTCTTGGCGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCATCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAGAAAGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGAAGGAGAAGAAGAGACGWGGCGCAGATACTAGTGTCGGAATTGTTGGMCTCCTGCTGACCACAGCTATGGMAGCGGAGGTCACKAGACGTGGGAGTGCATACTATATGTACTTGGACWGAAACGATGCKGGGGAGGCCATATCTTTTCCAACCACATTGGGGTTGAATAAGTG"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC22" 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;">string</span> <span class="n" style="color: #333;">ck</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"CTGCTGGGTCATGGGCCCATCATGATGGTCTTGGCGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCATCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAGAAAGATAGGAAGGAGAAGAAGAGACGWGGCGCAGATACTAGTGTCGGAATTGTTGGMCTCCTGCTGACCACAGCTATGGMAGCGGAGGTCACKAGACGTGGGAGTGCATACTATATGTACTTGGACWGAAACGATGCKGGGGAGGCCATATCTTTTCCAACCACATTGGGGTTGAATAAGTG"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"> <span class="n" style="color: #333;">num_success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">call_cns_check_outfile</span><span class="p">(</span><span class="s" style="color: #d14;">"../data/test.gap"</span><span class="p">,</span> <span class="n" style="color: #333;">c_</span><span class="p">,</span> <span class="sc" style="color: #d14;">'-'</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="LC23" class="line" lang="cpp"> <span class="n" style="color: #333;">num_success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">call_cns_check_outfile</span><span class="p">(</span><span class="s" style="color: #d14;">"<span class="idiff left">"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"</span>../data/test.gap"</span><span class="p">,</span> <span class="n" style="color: #333;">c_</span><span class="p">,</span> <span class="sc" style="color: #d14;">'-'</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="LC24" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">num_success</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="LC25" class="line" lang="cpp"> <span class="n" style="color: #333;">num_success</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">call_cns_check_outfile</span><span class="p">(</span><span class="s" style="color: #d14;">"../data/test.gap"</span><span class="p">,</span> <span class="n" style="color: #333;">cN</span><span class="p">,</span> <span class="sc" style="color: #d14;">'N'</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="LC25" class="line" lang="cpp"> <span class="n" style="color: #333;">num_success</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">call_cns_check_outfile</span><span class="p">(</span><span class="s" style="color: #d14;">"<span class="idiff left">TESTID"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"</span>../data/test.gap"</span><span class="p">,</span> <span class="n" style="color: #333;">cN</span><span class="p">,</span> <span class="sc" style="color: #d14;">'N'</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="LC26" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">num_success</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="LC27" class="line" lang="cpp"> <span class="n" style="color: #333;">num_success</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">call_cns_check_outfile</span><span class="p">(</span><span class="s" style="color: #d14;">"../data/test.gap"</span><span class="p">,</span> <span class="n" style="color: #333;">ck</span><span class="p">,</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</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="LC27" class="line" lang="cpp"> <span class="n" style="color: #333;">num_success</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">call_cns_check_outfile</span><span class="p">(</span><span class="s" style="color: #d14;">"<span class="idiff left">TESTID"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"</span>../data/test.gap"</span><span class="p">,</span> <span class="n" style="color: #333;">ck</span><span class="p">,</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</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="LC28" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">num_success</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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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">num_success</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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30
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<pre style="margin: 0;"> <span id="LC30" 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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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include<iostream></span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include<fstream></span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include<string></span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "../src/call_consensus_pileup.h"</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "../src/allele_functions.h"</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">call_cns_check_outfile</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">seq_id</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">call_min_depth</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_depth</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC8" 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;">string</span> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"../data/test.gap.sorted.mpileup"</span><span class="p">;</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" 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;">string</span> <span class="n" style="color: #333;">expctd_hdr</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" 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;">ifstream</span> <span class="n" style="color: #333;">mplp</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">);</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"> <span class="n" style="color: #333;">call_consensus_from_plup</span><span class="p">(</span><span class="n" style="color: #333;">mplp</span><span class="p">,</span> <span class="n" style="color: #333;">seq_id</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">min_depth</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">call_min_depth</span><span class="p">);</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" 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;">ifstream</span> <span class="n" style="color: #333;">outFile</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".fa"</span><span class="p">);</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" 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;">string</span> <span class="n" style="color: #333;">l</span><span class="p">;</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"> <span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">outFile</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// header</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">seq_id</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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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">o</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">[</span><span class="n" style="color: #333;">prefix</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"> <span class="n" style="color: #333;">expctd_hdr</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">">Consensus_"</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="p">(</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"_threshold_0_quality_20"</span><span class="p">;</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"> </span>
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20
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<pre style="margin: 0;">+<span id="LC20" 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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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"> <span class="n" style="color: #333;">expctd_hdr</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq_id</span><span class="p">;</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">compare</span><span class="p">(</span><span class="n" style="color: #333;">expctd_hdr</span><span class="p">);</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"><span class="p">}</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">num_success</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="LC29" 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;">string</span> <span class="n" style="color: #333;">c_</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"CTGCTGGGTCATGGGCCCATCATGATGGTCTTGGCGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCATCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAGAAAGAT------------------------------AGGAAGGAGAAGAAGAGACGWGGCGCAGATACTAGTGTCGGAATTGTTGGMCTCCTGCTGACCACAGCTATGGMAGCGGAGGTCACKAGACGTGGGAGTGCATACTATATGTACTTGGACWGAAACGATGCKGGGGAGGCCATATCTTTTCCAACCACATTGGGGTTGAATAAGTG"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"> <span class="n" style="color: #333;">num_success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">call_cns_check_outfile</span><span class="p">(</span><span class="s" style="color: #d14;">"TESTID"</span><span class="p">,</span> <span class="s" style="color: #d14;">"../data/test.gap"</span><span class="p">,</span> <span class="sc" style="color: #d14;">'-'</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="LC31" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">num_success</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="LC32" class="line" lang="cpp"> <span class="n" style="color: #333;">num_success</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">call_cns_check_outfile</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"../data/test.gap"</span><span class="p">,</span> <span class="sc" style="color: #d14;">'N'</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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33
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<pre style="margin: 0;">+<span id="LC33" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">num_success</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="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">num_success</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">call_cns_check_outfile</span><span class="p">(</span><span class="s" style="color: #d14;">"TESTID2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"../data/test.gap"</span><span class="p">,</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</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="LC35" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">num_success</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="LC36" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">num_success</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="LC37" 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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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ivar/-/commit/701a9ea32e3c15bf4d0fb7adeacea2451c117c82#e0b2f123a81564bf31738653c669118954480d42"><strong>tests/test_getmasked.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">@@ -10,7 +10,7 @@ int main()</td>
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<pre style="margin: 0;"> <span id="LC10" 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;">ifstream</span> <span class="n" style="color: #333;">masked_indices_file</span><span class="p">(</span><span class="s" style="color: #d14;">"../data/test.masked_primer_indices.txt"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC11" 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;">string</span> <span class="n" style="color: #333;">indices</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"> <span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">masked_indices_file</span><span class="p">,</span> <span class="n" style="color: #333;">indices</span><span class="p">);</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">indices</span><span class="p">.</span><span class="n" style="color: #333;">compare</span><span class="p">(</span><span class="s" style="color: #d14;">"WNV_400_2_LEFT</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">WNV_400_2_<span class="idiff left">LEFT_alt</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff right">WNV_400_1_LEF</span>T</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">WNV_400_1_LEFT_alt</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">WNV_400_3_LEFT"</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="LC13" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">indices</span><span class="p">.</span><span class="n" style="color: #333;">compare</span><span class="p">(</span><span class="s" style="color: #d14;">"WNV_400_2_LEFT</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">WNV_400_2_<span class="idiff left">RIGHT</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">WNV_400_2_LEFT_alt</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">WNV_400_1_LEFT</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff right">WNV_400_1_RIGH</span>T</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">WNV_400_1_LEFT_alt</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">WNV_400_3_LEFT"</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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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"> <span class="n" style="color: #333;">success</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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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">num_tests</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">success</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="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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16
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<li id="5e14845d439307e7a73e85d110f0b545b6265fa9">
<a href="https://salsa.debian.org/med-team/ivar/-/commit/701a9ea32e3c15bf4d0fb7adeacea2451c117c82#5e14845d439307e7a73e85d110f0b545b6265fa9"><strong>tests/test_primer_trim.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="105" 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="105" 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">@@ -105,7 +105,7 @@ int main(){</td>
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105
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="p">}</span></span>
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106
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Condense cigar</span></span>
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107
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107
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<pre style="margin: 0;"> <span id="LC107" 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;">cout</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="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Condensing cigar ... "</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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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">t</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">condense_cigar</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">cigar</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">nlength</span></span><span class="p">);</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">condense_cigar</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">t</span></span><span class="p">);</span></span>
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109
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">replace_cigar</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">nlength</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span><span class="p">);</span></span>
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110
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">cigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_get_cigar</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">);</span></span>
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111
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"> <span class="n" style="color: #333;">print_cigar</span><span class="p">(</span><span class="n" style="color: #333;">cigar</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">nlength</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="120" 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">@@ -120,11 +120,19 @@ int main(){</td>
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120
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="p">}</span></span>
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121
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"> <span class="p">}</span></span>
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">primer_ctr</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">free_cigar</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">);</span></span>
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123
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">ctr</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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125
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<pre style="margin: 0;"> <span id="LC126" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" ---- "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">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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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"> <span class="p">}</span></span>
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127
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check if primers found at all</span></span>
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128
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">primer_ctr</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;">success</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="n" style="color: #333;">bam_destroy1</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">);</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="n" style="color: #333;">bam_itr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">iter</span><span class="p">);</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="n" style="color: #333;">sam_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">);</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="n" style="color: #333;">hts_idx_destroy</span><span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">);</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">hts_close</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">);</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"></span>
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129
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">success</span><span class="p">;</span></span>
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130
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<li id="bc53edf1aafd372a6a2ab1583c4dce2eb60702a7">
<a href="https://salsa.debian.org/med-team/ivar/-/commit/701a9ea32e3c15bf4d0fb7adeacea2451c117c82#bc53edf1aafd372a6a2ab1583c4dce2eb60702a7"><strong>tests/test_primer_trim_edge_cases.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">@@ -66,7 +66,7 @@ int main(){</td>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">print_cigar</span><span class="p">(</span><span class="n" style="color: #333;">cigar</span><span class="p">,</span> <span class="n" style="color: #333;">aln</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">n_cigar</span><span class="p">);</span></span>
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67
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Condense cigar</span></span>
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68
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68
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<pre style="margin: 0;"> <span id="LC68" 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;">cout</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="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Condensing cigar ... "</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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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">t</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">condense_cigar</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">cigar</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">nlength</span></span><span class="p">);</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">condense_cigar</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">t</span></span><span class="p">);</span></span>
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70
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">replace_cigar</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">nlength</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span><span class="p">);</span></span>
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71
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">cigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_get_cigar</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">);</span></span>
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72
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">print_cigar</span><span class="p">(</span><span class="n" style="color: #333;">cigar</span><span class="p">,</span> <span class="n" style="color: #333;">aln</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">n_cigar</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">@@ -82,8 +82,16 @@ int main(){</td>
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"> <span class="n" style="color: #333;">primer_ctr</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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83
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"> <span class="n" style="color: #333;">ctr</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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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="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" ---- "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">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="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">free_cigar</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">);</span></span>
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85
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="p">}</span></span>
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86
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check if primers found at all</span></span>
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87
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">primer_ctr</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;">success</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">bam_destroy1</span><span class="p">(</span><span class="n" style="color: #333;">aln</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;">bam_itr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">iter</span><span class="p">);</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="n" style="color: #333;">sam_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">);</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="n" style="color: #333;">hts_idx_destroy</span><span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">);</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="n" style="color: #333;">hts_close</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">success</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ivar/-/commit/701a9ea32e3c15bf4d0fb7adeacea2451c117c82#72cf1548681e3cd27df54db6d2a928d482a578e9"><strong>tests/test_trim.cpp</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include<iostream></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "../src/trim_primer_quality.h"</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "../src/primer_bed.h"</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "htslib/sam.h"</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC7" 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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">n_cigar</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"> <span class="n" style="color: #333;">hts_pos_t</span> <span class="n" style="color: #333;">isize</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"><span class="p">}</span> <span class="n" style="color: #333;">result_t</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">test_trim</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">sliding_window</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">no_write_flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">mark_qcfail_flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_length</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">testname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nexpected</span><span class="p">,</span> <span class="n" style="color: #333;">result_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">expected</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">success</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="LC15" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">res</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"> <span class="n" style="color: #333;">bam1_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aln</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_init1</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC19" 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;">string</span> <span class="n" style="color: #333;">bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"../data/test.unmapped.sorted.bam"</span><span class="p">;</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" 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;">string</span> <span class="n" style="color: #333;">bed</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"../data/test.bed"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC21" 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;">string</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"/tmp/trim"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC22" 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;">string</span> <span class="n" style="color: #333;">bam_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"/tmp/trim.bam"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" 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;">string</span> <span class="n" style="color: #333;">region_</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" 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;">string</span> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"@PG</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ID:ivar-trim</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">PN:ivar</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">VN:1.0.0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">CL:ivar trim</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Test with default paramaters</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trim_bam_qual_primer</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">bed</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">region_</span><span class="p">,</span> <span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="n" style="color: #333;">sliding_window</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">no_write_flag</span><span class="p">,</span> <span class="n" style="color: #333;">mark_qcfail_flag</span><span class="p">,</span> <span class="n" style="color: #333;">min_length</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC29" 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="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" 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;">"default paramater test failed: trim_bam_qual_primer() returned "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">res</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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32
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<pre style="margin: 0;">+<span id="LC32" 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="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">samFile</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hts_open</span><span class="p">(</span><span class="n" style="color: #333;">bam_out</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">in</span><span class="p">)</span> <span class="p">{</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC36" 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;">"default paramater test failed: Can't open "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">bam_out</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="LC37" 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="LC38" class="line" lang="cpp"> <span class="n" style="color: #333;">sam_hdr_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hdr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_hdr_read</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC39" 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;">hdr</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC41" 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;">"default paramater test failed: Can't read header from "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">bam_out</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="LC42" 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="LC43" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</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="LC44" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">sam_read1</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">aln</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="LC45" 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="n" style="color: #333;">aln</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">n_cigar</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">aln</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">l_qseq</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">aln</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">mtid</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">aln</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">mpos</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">aln</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">isize</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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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">isize</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">expected</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">isize</span><span class="p">)</span> <span class="p">{</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" 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="n" style="color: #333;">testname</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" test failed: found isize "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">aln</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">isize</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" at record "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">": expected "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">expected</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">isize</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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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="p">}</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"> <span class="p">}</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">nexpected</span><span class="p">)</span> <span class="p">{</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" 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="n" style="color: #333;">testname</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" test failed: found "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" records: expected "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">nexpected</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="LC55" class="line" lang="cpp"> <span class="p">}</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"> <span class="n" style="color: #333;">sam_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">hdr</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="cpp"> <span class="p">}</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">sam_close</span><span class="p">(</span><span class="n" style="color: #333;">in</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="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">success</span><span class="p">;</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"><span class="p">}</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">success</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="LC66" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Default paramaters</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;">result_t</span> <span class="n" style="color: #333;">expected</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="p">{</span> <span class="mi" style="color: #099;">163</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">364</span> <span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">163</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">382</span> <span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">83</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">356</span><span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">83</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">382</span><span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">67</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">398</span><span class="p">}</span> <span class="p">};</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">test_trim</span><span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="mi" style="color: #099;">30</span><span class="p">,</span> <span class="s" style="color: #d14;">"default paramaters"</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">))</span> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="p">}</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// -e (write missing primers)</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">result_t</span> <span class="n" style="color: #333;">expected</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="p">{</span><span class="mi" style="color: #099;">131</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="mi" style="color: #099;">403</span><span class="p">},</span> <span class="p">{</span> <span class="mi" style="color: #099;">163</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">364</span> <span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">163</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">382</span> <span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">163</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">242</span><span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">83</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">242</span><span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">147</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">150</span><span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">83</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">356</span><span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">83</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">382</span><span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">67</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">398</span><span class="p">}</span> <span class="p">};</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">test_trim</span><span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="mi" style="color: #099;">30</span><span class="p">,</span> <span class="s" style="color: #d14;">"write missing primers"</span><span class="p">,</span> <span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">))</span> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// -f (mark quality trimmed as failed)</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">result_t</span> <span class="n" style="color: #333;">expected</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="p">{</span> <span class="mi" style="color: #099;">163</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">364</span> <span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">163</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">382</span> <span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">611</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">150</span><span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">83</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">356</span><span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">83</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">382</span><span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">67</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">398</span><span class="p">}</span> <span class="p">};</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">test_trim</span><span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="mi" style="color: #099;">30</span><span class="p">,</span> <span class="s" style="color: #d14;">"default paramaters"</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">))</span> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// -e -f (write everything)</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="p">{</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">result_t</span> <span class="n" style="color: #333;">expected</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="p">{</span><span class="mi" style="color: #099;">643</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="mi" style="color: #099;">403</span><span class="p">},</span> <span class="p">{</span> <span class="mi" style="color: #099;">163</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">364</span> <span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">163</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">382</span> <span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">675</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">242</span><span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">595</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">242</span><span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">611</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">150</span><span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">659</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">150</span><span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">83</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">356</span><span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">83</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">382</span><span class="p">},</span> <span class="p">{</span><span class="mi" style="color: #099;">67</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">398</span><span class="p">}</span> <span class="p">};</span></span>
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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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">test_trim</span><span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="mi" style="color: #099;">30</span><span class="p">,</span> <span class="s" style="color: #d14;">"write everything"</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">))</span> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<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>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">success</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"></span></pre>
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<a href="https://salsa.debian.org/med-team/ivar/-/commit/701a9ea32e3c15bf4d0fb7adeacea2451c117c82#3493333b4fffcb1202514aaf222d6f12b362eeea"><strong>tests/test_unpaired_trim.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">@@ -30,6 +30,7 @@ int main(){</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"> <span class="n" style="color: #333;">bam1_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aln</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_init1</span><span class="p">();</span></span>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"> <span class="n" style="color: #333;">cigar_</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</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="cpp"> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span></span>
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36
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<pre style="margin: 0;"> <span id="LC36" 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">@@ -99,6 +100,7 @@ int main(){</td>
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99
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">get_overlapping_primers</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">,</span> <span class="n" style="color: #333;">primers</span><span class="p">,</span> <span class="n" style="color: #333;">overlapping_primers</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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100
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">overlapping_primers</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>
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101
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"> <span class="n" style="color: #333;">cand_primer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_min_start</span><span class="p">(</span><span class="n" style="color: #333;">overlapping_primers</span><span class="p">);</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="n" style="color: #333;">free_cigar</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">);</span></span>
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102
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">primer_trim</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">,</span> <span class="n" style="color: #333;">cand_primer</span><span class="p">.</span><span class="n" style="color: #333;">get_start</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="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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103
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">replace_cigar</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">nlength</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span><span class="p">);</span></span>
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104
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">overlapping_primers</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;">rev_overlapping_primer_sizes</span><span class="p">[</span><span class="n" style="color: #333;">primer_ctr</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">@@ -128,7 +130,7 @@ int main(){</td>
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128
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"> <span class="p">}</span></span>
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129
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Condense cigar</span></span>
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<pre style="margin: 0;"> <span id="LC132" 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;">cout</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="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Condensing cigar ... "</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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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">t</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">condense_cigar</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">cigar</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">nlength</span></span><span class="p">);</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">condense_cigar</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">t</span></span><span class="p">);</span></span>
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132
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"> <span class="n" style="color: #333;">replace_cigar</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">nlength</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span><span class="p">);</span></span>
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133
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">cigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_get_cigar</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">);</span></span>
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134
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">nlength</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -142,8 +144,16 @@ int main(){</td>
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142
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="143" 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">
143
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="144" 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">
144
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">primer_ctr</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">free_cigar</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">);</span></span>
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145
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"> <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="c1" style="color: #998; font-style: italic;">// Check if primers found at all</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;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">primer_ctr</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;">success</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333;">bam_destroy1</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">);</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="n" style="color: #333;">bam_itr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">iter</span><span class="p">);</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"> <span class="n" style="color: #333;">sam_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"> <span class="n" style="color: #333;">hts_idx_destroy</span><span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">);</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">hts_close</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">);</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"></span>
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148
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">success</span><span class="p">;</span></span>
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149
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp"><span class="p">}</span></span></pre>
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