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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/stacks">Debian Med / stacks</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/stacks/-/commit/c366057c830457612a98fd9c07cbc1fb62de6e32">c366057c</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-06-12T02:36:29+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.58+dfsg</pre>
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<h4>8 changed files:</h4>
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<li class="file-stats">
<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
ChangeLog
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<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
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<li class="file-stats">
<a href="#2ac910f25c5abf10789b3fb7b3ce38cf161fab70">
src/DNANSeq.cc
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<li class="file-stats">
<a href="#f5c35b248509352c0cdf71dc8a43ba4b11929ad2">
src/DNANSeq.h
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<li class="file-stats">
<a href="#3434beadf1ef3f7fcfd269ed1422e2f222167418">
src/aln_utils.cc
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<li class="file-stats">
<a href="#1ccd43bdcf61a0b2daa44610b0aea29189bdeae0">
src/kmers.cc
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<li class="file-stats">
<a href="#5d057fdf8543f341f83844acdc94851f57407d44">
src/populations.cc
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<a href="#115f7027957c0ea3ba55c87ad3b1eaea3b5ebe8d">
src/ustacks.cc
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<h4>Changes:</h4>
<li id="00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
<a href="https://salsa.debian.org/med-team/stacks/-/commit/c366057c830457612a98fd9c07cbc1fb62de6e32#00fe7828d56d7a3ee4030d6cea057cf13f50e70c"><strong>ChangeLog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">Stacks</span> <span class="m" style="color: #099;">2.58</span> <span class="p">-</span> <span class="n" style="color: #333;">June</span><span class="p">,</span> <span class="m" style="color: #099;">08</span><span class="p">,</span> <span class="m" style="color: #099;">2021</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="mosel"><span class="p">----------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"> <span class="n" style="color: #333;">Bugfix</span><span class="p">:</span> <span class="n" style="color: #333;">Fixed</span> <span class="n" style="color: #333;">several</span> <span class="n" style="color: #333;">memory</span> <span class="n" style="color: #333;">errors</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ustacks</span> <span class="n" style="color: #333;">related</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">processing</span> <span class="n" style="color: #333;">trimmed</span> <span class="n" style="color: #333;">reads</span><span class="p">.</span> </span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">Stacks</span> <span class="m" style="color: #099;">2.57</span> <span class="p">-</span> <span class="n" style="color: #333;">May</span><span class="p">,</span> <span class="m" style="color: #099;">10</span><span class="p">,</span> <span class="m" style="color: #099;">2021</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="mosel"><span class="p">---------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="mosel"> <span class="n" style="color: #333;">Feature</span><span class="p">:</span> <span class="n" style="color: #333;">updated</span> <span class="n" style="color: #333;">process_radtags</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">that</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">specify</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">sample</span> <span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">barcodes</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">multiple</span></span>
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<li id="87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
<a href="https://salsa.debian.org/med-team/stacks/-/commit/c366057c830457612a98fd9c07cbc1fb62de6e32#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</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">@@ -2,7 +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(2.59)</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">AC_INIT([Stacks], [2.5<span class="idiff left right">7</span>])</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">AC_INIT([Stacks], [2.5<span class="idiff left right">8</span>])</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">AC_CONFIG_AUX_DIR([config])</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">AM_INIT_AUTOMAKE([-Wall -Werror foreign parallel-tests subdir-objects])</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">AC_CONFIG_SRCDIR([src/ustacks.cc])</span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/c366057c830457612a98fd9c07cbc1fb62de6e32#2ac910f25c5abf10789b3fb7b3ce38cf161fab70"><strong>src/DNANSeq.cc</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">@@ -134,15 +134,15 @@ char DNANSeq::operator[](uint pos) const {</td>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">DNANSeq</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">seq</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;">buf</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC137" 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;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC137" 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="k" style="font-weight: 600;"><span class="idiff left">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">buf</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="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">)[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="cpp"> <span class="n" style="color: #333;">buf</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="sc" style="color: #d14;">'\0'</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;">buf</span><span class="p">[</span><span class="k" style="font-weight: 600;"><span class="idiff left">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">size</span><span class="p">()]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">DNANSeq</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">seq</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">str</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="cpp"> <span class="n" style="color: #333;">str</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC145" 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;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"> <span class="n" style="color: #333;">str</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC145" 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="k" style="font-weight: 600;"><span class="idiff left">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">str</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="k" style="font-weight: 600;">this</span><span class="p">)[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">str</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"><span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/c366057c830457612a98fd9c07cbc1fb62de6e32#f5c35b248509352c0cdf71dc8a43ba4b11929ad2"><strong>src/DNANSeq.h</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-</span></span>
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<pre style="margin: 0;"> <span id="LC2" 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="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 20<span class="idiff left">1</span>1, Julian Catchen <jcatchen@<span class="idiff right">uoregon</span>.edu></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 20<span class="idiff left">2</span>1, Julian Catchen <jcatchen@<span class="idiff right">illinois</span>.edu></span></span>
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<pre style="margin: 0;"> <span id="LC4" 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="LC5" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// This file is part of Stacks.</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/c366057c830457612a98fd9c07cbc1fb62de6e32#3434beadf1ef3f7fcfd269ed1422e2f222167418"><strong>src/aln_utils.cc</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">@@ -232,15 +232,14 @@ apply_cigar_to_seq(const char *seq, const Cigar &cigar)</td>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">edited_seq</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC234" 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="LC235" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Calculate the <span class="idiff left right">overall </span>sequence length.</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Calculate the sequence length<span class="idiff left right"> and the length prescribed by the CIGAR</span>.</span></span>
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<pre style="margin: 0;"> <span id="LC236" 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="LC237" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">seqlen</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="LC238" 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;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="cpp"> <span class="n" style="color: #333;">seqlen</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 class="n" style="color: #333;">second</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">cigar_seqlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cigar_length_padded</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="LC239" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"> <span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="cpp"> <span class="n" style="color: #333;">edited_seq</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">seqlen</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp"> <span class="n" style="color: #333;">edited_seq</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">cigar_</span>seqlen</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC244" 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;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp"> <span class="n" style="color: #333;">op</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 class="n" style="color: #333;">first</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">@@ -264,10 +263,14 @@ apply_cigar_to_seq(const char *seq, const Cigar &cigar)</td>
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264
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263
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<pre style="margin: 0;"> <span id="LC263" 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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265
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'M'</span><span class="p">:</span></span>
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266
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp"> <span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">dist</span><span class="p">;</span></span>
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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="p">)</span> <span class="p">{</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="idiff left"> </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">bp</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 right">seqlen</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"> <span class="n" style="color: #333;">edited_seq</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">bp</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp"> <span class="n" style="color: #333;">bp</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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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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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"> <span class="n" style="color: #333;">edited_seq</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="sc" style="color: #d14;">'N'</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;">bp</span><span class="o" style="font-weight: 600;">++</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="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp"> <span class="nl">default:</span></span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</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">@@ -286,15 +289,14 @@ apply_cigar_to_model_seq(const char *seq, const Cigar &cigar)</td>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">edited_seq</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC291" 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="LC289" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Calculate the <span class="idiff left right">overall </span>sequence length.</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Calculate the sequence length<span class="idiff left right"> and the length prescribed by the CIGAR</span>.</span></span>
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<pre style="margin: 0;"> <span id="LC293" 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="LC291" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">seqlen</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="LC292" 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;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="cpp"> <span class="n" style="color: #333;">seqlen</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 class="n" style="color: #333;">second</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">cigar_seqlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cigar_length_padded</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="LC296" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp"> <span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="cpp"> <span class="n" style="color: #333;">edited_seq</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">seqlen</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"> <span class="n" style="color: #333;">edited_seq</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">cigar_</span>seqlen</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="cpp"></span>
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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="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;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cpp"> <span class="n" style="color: #333;">op</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 class="n" style="color: #333;">first</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -318,10 +320,14 @@ apply_cigar_to_model_seq(const char *seq, const Cigar &cigar)</td>
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<pre style="margin: 0;"> <span id="LC320" 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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<pre style="margin: 0;"> <span id="LC321" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'M'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp"> <span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">dist</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="idiff left"> </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">bp</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 right">seqlen</span></span><span class="p">)</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;">edited_seq</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">bp</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="cpp"> <span class="n" style="color: #333;">bp</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp"> <span class="n" style="color: #333;">edited_seq</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="sc" style="color: #d14;">'U'</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp"> <span class="n" style="color: #333;">bp</span><span class="o" style="font-weight: 600;">++</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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<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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<pre style="margin: 0;"> <span id="LC332" class="line" lang="cpp"> <span class="nl">default:</span></span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/c366057c830457612a98fd9c07cbc1fb62de6e32#1ccd43bdcf61a0b2daa44610b0aea29189bdeae0"><strong>src/kmers.cc</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-</span></span>
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<pre style="margin: 0;"> <span id="LC2" 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="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2010-201<span class="idiff left right">5</span>, Julian Catchen <jcatchen@illinois.edu></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2010-20<span class="idiff left right">2</span>1, Julian Catchen <jcatchen@illinois.edu></span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// This file is part of Stacks.</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="196" 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="196" 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">@@ -196,19 +196,20 @@ populate_kmer_hash(map<int, MergedStack *> &merged, KmerHashMap &kmer_map, vecto</td>
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196
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cpp"> <span class="n" style="color: #333;">MergedStack</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tag</span><span class="p">;</span></span>
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197
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">kmers</span><span class="p">;</span></span>
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198
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">exists</span><span class="p">;</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">num_kmers</span><span class="p">;</span></span>
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199
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp"></span>
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201
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<pre style="margin: 0;"> <span id="LC201" 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="LC202" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Break each stack down into k-mers and create a hash map of those k-mers</span></span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// recording in which sequences they occur.</span></span>
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<pre style="margin: 0;"> <span id="LC204" 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="LC204" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">num_kmers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">merged</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">con</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmer_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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<pre style="margin: 0;">-<span id="LC205" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</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;">merged</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;">merged</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="cpp"> <span class="n" style="color: #333;">tag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Don't compute distances for masked tags</span></span>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">masked</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">num_kmers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmer_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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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp"> <span class="n" style="color: #333;">generate_kmers</span><span class="p">(</span><span class="n" style="color: #333;">tag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">con</span><span class="p">,</span> <span class="n" style="color: #333;">kmer_len</span><span class="p">,</span> <span class="n" style="color: #333;">num_kmers</span><span class="p">,</span> <span class="n" style="color: #333;">kmers</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Hash the kmers</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">@@ -248,7 +249,7 @@ populate_kmer_hash(map<int, Locus *> &catalog, CatKmerHashMap &kmer_map, vector<</td>
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248
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</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;">catalog</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;">catalog</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="cpp"> <span class="n" style="color: #333;">tag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="cpp"> <span class="n" style="color: #333;">num_kmers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">strlen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">tag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff">con</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmer_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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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp"> <span class="n" style="color: #333;">num_kmers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left right">len</span></span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmer_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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<pre style="margin: 0;"> <span id="LC253" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC254" 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="LC255" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Iterate through the possible Catalog alleles</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">@@ -3415,7 +3415,7 @@ int load_marker_list(string path, set<int> &list) {</td>
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<pre style="margin: 0;"> <span id="LC3415" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span></span>
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<pre style="margin: 0;"> <span id="LC3416" class="line" lang="cpp"><span class="n" style="color: #333;">LocusFilter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">load_whitelist</span><span class="p">(</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="LC3417" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC3418" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">id</span>_len</span><span class="p">];</span></span>
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3418
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<pre style="margin: 0;">+<span id="LC3418" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">max</span>_len</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC3419" class="line" lang="cpp"> <span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">fh</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">ifstream</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">in</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC3420" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC3421" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">fail</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3428" 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">@@ -3428,7 +3428,7 @@ LocusFilter::load_whitelist(string path)</td>
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<pre style="margin: 0;"> <span id="LC3428" 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;">e</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC3429" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC3430" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">line_num</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="LC3431" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">id</span>_len</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC3431" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">max</span>_len</span><span class="p">))</span> <span class="p">{</span></span>
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3432
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<pre style="margin: 0;"> <span id="LC3432" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">line_num</span><span class="p">;</span></span>
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3433
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<pre style="margin: 0;"> <span id="LC3433" class="line" lang="cpp"></span>
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3434
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3434
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<pre style="margin: 0;"> <span id="LC3434" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3482,7 +3482,7 @@ LocusFilter::load_whitelist(string path)</td>
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<pre style="margin: 0;"> <span id="LC3482" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC3483" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC3484" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">load_marker_column_list</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">list</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC3485" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">id</span>_len</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC3485" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">max</span>_len</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC3486" class="line" lang="cpp"> <span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">fh</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">ifstream</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">in</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC3487" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC3488" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">fail</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3495,7 +3495,7 @@ int load_marker_column_list(string path, map<int, set<int> > &list) {</td>
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<pre style="margin: 0;"> <span id="LC3495" 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;">e</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC3496" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC3497" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">line_num</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="LC3498" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">id</span>_len</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC3498" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">max</span>_len</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC3499" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC3500" 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="LC3501" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Skip blank & commented lines ; correct windows-style line ends.</span></span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-</span></span>
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<pre style="margin: 0;"> <span id="LC2" 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="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2010-202<span class="idiff left right">0</span>, Julian Catchen <jcatchen@illinois.edu></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright 2010-202<span class="idiff left right">1</span>, Julian Catchen <jcatchen@illinois.edu></span></span>
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<pre style="margin: 0;"> <span id="LC4" 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="LC5" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// This file is part of Stacks.</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="198" 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">@@ -198,6 +198,7 @@ try{</td>
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198
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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199
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Merging secondary stacks (max. dist. N="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">max_rem_dist</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" from consensus)...</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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200
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">utilized</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">merge_remainders</span><span class="p">(</span><span class="n" style="color: #333;">merged</span><span class="p">,</span> <span class="n" style="color: #333;">unique</span><span class="p">,</span> <span class="n" style="color: #333;">remainders</span><span class="p">);</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp"> <span class="n" style="color: #333;">call_consensus</span><span class="p">(</span><span class="n" style="color: #333;">merged</span><span class="p">,</span> <span class="n" style="color: #333;">unique</span><span class="p">,</span> <span class="n" style="color: #333;">remainders</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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201
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">util_gapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">merge_gapped_remainders</span><span class="p">(</span><span class="n" style="color: #333;">merged</span><span class="p">,</span> <span class="n" style="color: #333;">unique</span><span class="p">,</span> <span class="n" style="color: #333;">remainders</span><span class="p">);</span></span>
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202
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cpp"> <span class="n" style="color: #333;">call_consensus</span><span class="p">(</span><span class="n" style="color: #333;">merged</span><span class="p">,</span> <span class="n" style="color: #333;">unique</span><span class="p">,</span> <span class="n" style="color: #333;">remainders</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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203
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Merged "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">utilized</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">util_gapped</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" out of "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">n_r_reads</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" secondary reads ("</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="258" 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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -258,6 +259,16 @@ try{</td>
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258
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="cpp"> <span class="n" style="color: #333;">write_results</span><span class="p">(</span><span class="n" style="color: #333;">merged</span><span class="p">,</span> <span class="n" style="color: #333;">unique</span><span class="p">,</span> <span class="n" style="color: #333;">remainders</span><span class="p">);</span></span>
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259
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"done.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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260
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cpp"></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Free remaining memory.</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unique</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;">unique</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">remainders</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;">remainders</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">merged</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;">merged</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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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;">delete</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"> </span>
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261
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"ustacks is done.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="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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273
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<pre style="margin: 0;"> <span id="LC273" 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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263
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp"><span class="p">}</span> <span class="k" style="font-weight: 600;">catch</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;">exception</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</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="305" 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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -305,14 +316,13 @@ merge_gapped_alns(map<int, Stack *> &unique, map<int, Rem *> &rem, map<int, Merg</td>
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305
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tag_2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alns</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;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">tag_2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alns</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">pct_id</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">tag_2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alns</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">pct_id</span><span class="p">)</span></span>
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306
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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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307
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="cpp"></span>
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308
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tag_1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">!=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">tag_2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alns</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">id</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="319" 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">
319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tag_1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">!=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="idiff left right"> </span><span class="n" style="color: #333;">tag_2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alns</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">id</span><span class="p">)</span></span>
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309
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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310
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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="cpp"></span>
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311
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322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp"> <span class="n" style="color: #333;">cigar_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">invert_cigar</span><span class="p">(</span><span class="n" style="color: #333;">tag_1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alns</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">cigar</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="323" 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">
323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="cpp"> <span class="n" style="color: #333;">cigar_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tag_2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alns</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">cigar</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="313" 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">
313
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<td class="new_line diff-line-num" data-linenumber="324" 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">
324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp"></span>
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314
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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="n" style="color: #333;">cigar_1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cigar_2</span><span class="p">)</span> <span class="p">{</span></span>
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315
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"CIGAR: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cigar_1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"> <span class="n" style="color: #333;">parse_cigar</span><span class="p">(</span><span class="n" style="color: #333;">tag_1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alns</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">cigar</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">cigar</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>
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328
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -400,9 +410,10 @@ edit_gapped_seqs(map<int, Stack *> &unique, map<int, Rem *> &rem, MergedStack *t</td>
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400
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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;">int</span> <span class="n" style="color: #333;">stack_id</span><span class="p">;</span></span>
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401
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411
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="cpp"> <span class="n" style="color: #333;">Stack</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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402
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412
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="cpp"> <span class="n" style="color: #333;">Rem</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC403" 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;">buf</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;">cigar_length_padded</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="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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414
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC415" 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;">buf</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;">cigar_length_padded</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="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="cpp"> </span>
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406
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<pre style="margin: 0;"> <span id="LC417" 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;">tag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">utags</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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407
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="cpp"> <span class="n" style="color: #333;">stack_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">utags</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unique</span><span class="p">[</span><span class="n" style="color: #333;">stack_id</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">@@ -417,7 +428,7 @@ edit_gapped_seqs(map<int, Stack *> &unique, map<int, Rem *> &rem, MergedStack *t</td>
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<pre style="margin: 0;"> <span id="LC428" 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;">tag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">remtags</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="cpp"> <span class="n" style="color: #333;">stack_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">remtags</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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430
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rem</span><span class="p">[</span><span class="n" style="color: #333;">stack_id</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">(</span><span class="n" style="color: #333;">buf</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;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">apply_cigar_to_seq</span><span class="p">(</span><span class="n" style="color: #333;">buf</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>
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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">@@ -1025,25 +1036,7 @@ merge_gapped_remainders(map<int, MergedStack *> &merged, map<int, Stack *> &uniq</td>
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1025
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<pre style="margin: 0;"> <span id="LC1036" 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;">tag_1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rem_queue</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1026
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1037
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<pre style="margin: 0;"> <span id="LC1037" class="line" lang="cpp"> <span class="n" style="color: #333;">Rem</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;">rem</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">tag_1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rem_queue</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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1027
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1038
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<pre style="margin: 0;"> <span id="LC1038" class="line" lang="cpp"></span>
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1028
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<pre style="margin: 0;">-<span id="LC1028" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// //</span></span>
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1029
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<pre style="margin: 0;">-<span id="LC1029" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// // We want to align the last max_rem_dist * 2 nucleotides. If sequences are already the wrong length,</span></span>
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1030
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<pre style="margin: 0;">-<span id="LC1030" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// // adjust so the 3' ends are lined up properly in the alignment matrix.</span></span>
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1031
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<pre style="margin: 0;">-<span id="LC1031" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// //</span></span>
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1032
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<pre style="margin: 0;">-<span id="LC1032" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// diff = tag_1->len - r->seq->size();</span></span>
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1033
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<pre style="margin: 0;">-<span id="LC1033" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// q_start = r->seq->size() - (max_rem_dist * 2) - 1;</span></span>
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1034
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<pre style="margin: 0;">-<span id="LC1034" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// q_end = r->seq->size() - 1;</span></span>
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1035
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<pre style="margin: 0;">-<span id="LC1035" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// s_start = tag_1->len - (max_rem_dist * 2) - 1;</span></span>
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1036
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<pre style="margin: 0;">-<span id="LC1036" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// s_end = tag_1->len - 1;</span></span>
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1037
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<pre style="margin: 0;">-<span id="LC1037" class="line" lang="cpp"></span>
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1038
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<pre style="margin: 0;">-<span id="LC1038" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// q_start = diff > 0 ? q_start + diff : q_start;</span></span>
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1039
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<pre style="margin: 0;">-<span id="LC1039" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// s_start = diff < 0 ? s_start + abs(diff) : s_start;</span></span>
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<pre style="margin: 0;">-<span id="LC1040" class="line" lang="cpp"></span>
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1041
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<pre style="margin: 0;">-<span id="LC1041" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// cerr << "Consensus size: " << tag_1->len << "; remainder size: " << r->seq->size() << "\n"</span></span>
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1042
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<pre style="margin: 0;">-<span id="LC1042" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// << "Con seq: " << tag_1->con << " (" << strlen(tag_1->con) << ")\n"</span></span>
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1043
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<pre style="margin: 0;">-<span id="LC1043" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// << "Rem seq: " << r->seq->seq() << "\n"</span></span>
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1044
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<pre style="margin: 0;">-<span id="LC1044" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// << "q_start: " << q_start << "; q_end: " << q_end << "; s_start: " << s_start << "; s_end: " << s_end << "\n";</span></span>
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1045
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<pre style="margin: 0;">-<span id="LC1045" class="line" lang="cpp"></span>
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1046
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<pre style="margin: 0;">-<span id="LC1046" 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;">init</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;">seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">tag_1</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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1039
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<pre style="margin: 0;">+<span id="LC1039" 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;">init</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;">seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">tag_1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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1047
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1040
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<pre style="margin: 0;"> <span id="LC1040" class="line" lang="cpp"></span>
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1048
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1041
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<pre style="margin: 0;"> <span id="LC1041" 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;">align</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;">seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">tag_1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">con</span><span class="p">))</span> <span class="p">{</span></span>
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1049
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1042
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<pre style="margin: 0;"> <span id="LC1042" class="line" lang="cpp"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aln</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">result</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1092" 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="1085" 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">@@ -1092,20 +1085,27 @@ merge_gapped_remainders(map<int, MergedStack *> &merged, map<int, Stack *> &uniq</td>
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1092
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1085
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<pre style="margin: 0;"> <span id="LC1085" class="line" lang="cpp"> <span class="p">}</span></span>
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1093
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1086
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<pre style="margin: 0;"> <span id="LC1086" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cigar</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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1094
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1087
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<pre style="margin: 0;"> <span id="LC1087" class="line" lang="cpp"> <span class="p">}</span></span>
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1088
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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1089
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<pre style="margin: 0;">+<span id="LC1089" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 1. Push newly created alignment gaps into existing constituent primary and remainder sequences.</span></span>
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1090
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<pre style="margin: 0;">+<span id="LC1090" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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1095
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1091
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<pre style="margin: 0;"> <span id="LC1091" class="line" lang="cpp"> <span class="n" style="color: #333;">edit_gapped_seqs</span><span class="p">(</span><span class="n" style="color: #333;">unique</span><span class="p">,</span> <span class="n" style="color: #333;">rem</span><span class="p">,</span> <span class="n" style="color: #333;">tag_1</span><span class="p">,</span> <span class="n" style="color: #333;">cigar</span><span class="p">);</span></span>
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1096
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<pre style="margin: 0;">-<span id="LC1096" class="line" lang="cpp"></span>
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1097
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1092
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<pre style="margin: 0;"> <span id="LC1092" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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1098
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<pre style="margin: 0;">-<span id="LC1098" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Add this aligned remainder tag to the locus after adjusting the other reads but before adjusting the consensus.</span></span>
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1093
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">2. </span>Add this aligned remainder tag to the locus after adjusting the other reads but before adjusting the consensus.</span></span>
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1099
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1094
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<pre style="margin: 0;"> <span id="LC1094" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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1100
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1095
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<pre style="margin: 0;"> <span id="LC1095" class="line" lang="cpp"> <span class="n" style="color: #333;">tag_1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">remtags</span><span class="p">.</span><span class="n" style="color: #333;">push_back</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;">id</span><span class="p">);</span></span>
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1096
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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1097
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<pre style="margin: 0;">+<span id="LC1097" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 3. Adjust the consensus.</span></span>
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1098
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<pre style="margin: 0;">+<span id="LC1098" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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1101
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1099
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<pre style="margin: 0;"> <span id="LC1099" class="line" lang="cpp"> <span class="n" style="color: #333;">update_consensus</span><span class="p">(</span><span class="n" style="color: #333;">tag_1</span><span class="p">,</span> <span class="n" style="color: #333;">unique</span><span class="p">,</span> <span class="n" style="color: #333;">rem</span><span class="p">);</span></span>
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1102
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1100
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<pre style="margin: 0;"> <span id="LC1100" class="line" lang="cpp"> <span class="p">}</span></span>
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1101
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<pre style="margin: 0;"> <span id="LC1101" class="line" lang="cpp"> <span class="p">}</span></span>
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1104
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1102
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<pre style="margin: 0;"> <span id="LC1102" class="line" lang="cpp"></span>
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1105
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1103
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<pre style="margin: 0;"> <span id="LC1103" class="line" lang="cpp"> <span class="n" style="color: #333;">tag_1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rem_queue</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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1106
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1104
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<pre style="margin: 0;"> <span id="LC1104" class="line" lang="cpp"> <span class="p">}</span></span>
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1107
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<pre style="margin: 0;">-<span id="LC1107" class="line" lang="cpp"> <span class="p">}</span></span>
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1108
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1105
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<pre style="margin: 0;"> <span id="LC1105" class="line" lang="cpp"></span>
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1106
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<pre style="margin: 0;">+<span id="LC1106" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">aln</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1107" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1108" class="line" lang="cpp"> </span>
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1109
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<pre style="margin: 0;"> <span id="LC1109" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">utilized</span><span class="p">;</span></span>
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1110
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1110
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<pre style="margin: 0;"> <span id="LC1110" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1111" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1117,24 +1117,27 @@ call_alleles(MergedStack *mtag, vector<DNANSeq *> &reads, vector<read_type> &rea</td>
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1117
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1117
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<pre style="margin: 0;"> <span id="LC1117" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">allele</span><span class="p">;</span></span>
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1118
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1118
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<pre style="margin: 0;"> <span id="LC1118" class="line" lang="cpp"> <span class="n" style="color: #333;">DNANSeq</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">d</span><span class="p">;</span></span>
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1119
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1119
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<pre style="margin: 0;"> <span id="LC1119" 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="p">;</span></span>
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1120
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<pre style="margin: 0;">+<span id="LC1120" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">snp_cnt</span><span class="p">;</span></span>
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1120
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1121
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<pre style="margin: 0;"> <span id="LC1121" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SNP</span> <span class="o" style="font-weight: 600;">*>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">snp</span><span class="p">;</span></span>
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1121
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1122
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<pre style="margin: 0;"> <span id="LC1122" class="line" lang="cpp"></span>
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1123
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<pre style="margin: 0;"> <span id="LC1123" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">row</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;">row</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">height</span><span class="p">;</span> <span class="n" style="color: #333;">row</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1123
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<pre style="margin: 0;">-<span id="LC1123" class="line" lang="cpp"> <span class="n" style="color: #333;">allele</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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1124
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<pre style="margin: 0;">-<span id="LC1124" class="line" lang="cpp"></span>
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1125
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<pre style="margin: 0;">-<span id="LC1125" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">snp_cnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1126
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<pre style="margin: 0;">-<span id="LC1126" class="line" lang="cpp"></span>
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1127
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1124
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<pre style="margin: 0;"> <span id="LC1124" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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1128
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1125
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<pre style="margin: 0;"> <span id="LC1125" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Only call a haplotype from primary reads.</span></span>
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1129
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1126
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<pre style="margin: 0;"> <span id="LC1126" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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1130
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1127
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<pre style="margin: 0;"> <span id="LC1127" 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;">call_sec_hapl</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">read_types</span><span class="p">[</span><span class="n" style="color: #333;">row</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">secondary</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1131
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1128
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<pre style="margin: 0;"> <span id="LC1128" class="line" lang="cpp"></span>
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1129
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<pre style="margin: 0;">+<span id="LC1129" class="line" lang="cpp"> <span class="n" style="color: #333;">allele</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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1130
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<pre style="margin: 0;">+<span id="LC1130" class="line" lang="cpp"> <span class="n" style="color: #333;">snp_cnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1131
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<pre style="margin: 0;">+<span id="LC1131" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reads</span><span class="p">[</span><span class="n" style="color: #333;">row</span><span class="p">];</span></span>
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1132
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<pre style="margin: 0;">+<span id="LC1132" class="line" lang="cpp"></span>
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1132
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1133
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<pre style="margin: 0;"> <span id="LC1133" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">snp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mtag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">snps</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">snp</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">mtag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">snps</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">snp</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1133
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1134
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<pre style="margin: 0;"> <span id="LC1134" 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;">snp</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">snp_type_het</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1134
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1135
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<pre style="margin: 0;"> <span id="LC1135" class="line" lang="cpp"></span>
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1135
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1136
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<pre style="margin: 0;"> <span id="LC1136" class="line" lang="cpp"> <span class="n" style="color: #333;">snp_cnt</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1136
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1137
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<pre style="margin: 0;"> <span id="LC1137" class="line" lang="cpp"></span>
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1137
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<pre style="margin: 0;">-<span id="LC1137" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reads</span><span class="p">[</span><span class="n" style="color: #333;">row</span><span class="p">];</span></span>
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1138
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<pre style="margin: 0;">+<span id="LC1138" 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;">snp</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC1139" 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="LC1140" class="line" lang="cpp"></span>
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1141
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<pre style="margin: 0;"> <span id="LC1141" class="line" lang="cpp"> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">d</span><span class="p">)[(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">snp</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">col</span><span class="p">];</span></span>
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1142
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<pre style="margin: 0;"> <span id="LC1142" class="line" lang="cpp"></span>
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1143
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<pre style="margin: 0;"> <span id="LC1143" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1183" 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">@@ -1183,30 +1186,34 @@ call_consensus(map<int, MergedStack *> &merged, map<int, Stack *> &unique, map<i</td>
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1186
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<pre style="margin: 0;"> <span id="LC1186" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// that tag into our array as many times as it originally occurred.</span></span>
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1184
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1187
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<pre style="margin: 0;"> <span id="LC1187" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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1185
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1188
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<pre style="margin: 0;"> <span id="LC1188" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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1186
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<pre style="margin: 0;">-<span id="LC1186" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">DNANSeq</span> <span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">reads</span><span class="p">;</span></span>
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1187
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<pre style="margin: 0;">-<span id="LC1187" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">read_type</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">read_types</span><span class="p">;</span></span>
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1188
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<pre style="margin: 0;">-<span id="LC1188" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">uint</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">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="n" style="color: #333;"><span class="idiff">unique</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">mtag</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">utags</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">front</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">seq</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff right">()</span>;</span></span>
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<pre style="margin: 0;">-<span id="LC1189" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC1189" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">DNANSeq</span> <span class="o" style="font-weight: 600;">*></span> <span class="idiff left right"> </span><span class="n" style="color: #333;">reads</span><span class="p">;</span></span>
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1190
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<pre style="margin: 0;">+<span id="LC1190" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">read_type</span><span class="o" style="font-weight: 600;">></span> <span class="idiff left right"> </span><span class="n" style="color: #333;">read_types</span><span class="p">;</span></span>
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1191
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<pre style="margin: 0;">+<span id="LC1191" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">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 right">0</span></span><span class="p">;</span></span>
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1192
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<pre style="margin: 0;">+<span id="LC1192" class="line" lang="cpp"> </span>
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1190
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1193
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<pre style="margin: 0;"> <span id="LC1193" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</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;">mtag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">utags</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">mtag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">utags</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1191
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1194
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<pre style="margin: 0;"> <span id="LC1194" class="line" lang="cpp"> <span class="n" style="color: #333;">utag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unique</span><span class="p">[</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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1192
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1195
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<pre style="margin: 0;"> <span id="LC1195" class="line" lang="cpp"></span>
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1196
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<pre style="margin: 0;">+<span id="LC1196" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check for maximum length.</span></span>
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1197
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<pre style="margin: 0;">+<span id="LC1197" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">utag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">utag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">length</span><span class="p">;</span></span>
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1198
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<pre style="margin: 0;">+<span id="LC1198" class="line" lang="cpp"></span>
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1193
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1199
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<pre style="margin: 0;"> <span id="LC1199" 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;">k</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;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">utag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">count</span><span class="p">();</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1194
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1200
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<pre style="margin: 0;"> <span id="LC1200" class="line" lang="cpp"> <span class="n" style="color: #333;">reads</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">utag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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1195
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1201
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<pre style="margin: 0;"> <span id="LC1201" class="line" lang="cpp"> <span class="n" style="color: #333;">read_types</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">primary</span><span class="p">);</span></span>
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1196
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<pre style="margin: 0;">-<span id="LC1196" class="line" lang="cpp"></span>
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1197
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<pre style="margin: 0;">-<span id="LC1197" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">utag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">length</span><span class="p">);</span></span>
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1198
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1202
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<pre style="margin: 0;"> <span id="LC1202" class="line" lang="cpp"> <span class="p">}</span></span>
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1199
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1203
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<pre style="margin: 0;"> <span id="LC1203" class="line" lang="cpp"> <span class="p">}</span></span>
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1200
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1204
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<pre style="margin: 0;"> <span id="LC1204" class="line" lang="cpp"></span>
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1205
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<pre style="margin: 0;">+<span id="LC1205" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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1201
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1206
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<pre style="margin: 0;"> <span id="LC1206" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// For each remainder tag that has been merged into this Stack, add the sequence.</span></span>
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1207
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<pre style="margin: 0;">+<span id="LC1207" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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1202
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1208
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<pre style="margin: 0;"> <span id="LC1208" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</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;">mtag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">remtags</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">mtag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">remtags</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1203
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1209
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<pre style="margin: 0;"> <span id="LC1209" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rem</span><span class="p">[</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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1204
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1210
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<pre style="margin: 0;"> <span id="LC1210" class="line" lang="cpp"></span>
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1211
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<pre style="margin: 0;">+<span id="LC1211" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check for maximum length.</span></span>
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1212
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<pre style="margin: 0;">+<span id="LC1212" class="line" lang="cpp"> <span class="n" style="color: #333;">length</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;">seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">length</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;">seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">length</span><span class="p">;</span></span>
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1213
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<pre style="margin: 0;">+<span id="LC1213" class="line" lang="cpp"></span>
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1205
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1214
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<pre style="margin: 0;"> <span id="LC1214" 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;">k</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;">k</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;">count</span><span class="p">();</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1206
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<td class="new_line diff-line-num" data-linenumber="1215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1215
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<pre style="margin: 0;"> <span id="LC1215" class="line" lang="cpp"> <span class="n" style="color: #333;">reads</span><span class="p">.</span><span class="n" style="color: #333;">push_back</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;">seq</span><span class="p">);</span></span>
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1207
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<td class="new_line diff-line-num" data-linenumber="1216" 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">
1216
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<pre style="margin: 0;"> <span id="LC1216" class="line" lang="cpp"> <span class="n" style="color: #333;">read_types</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">secondary</span><span class="p">);</span></span>
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1208
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<pre style="margin: 0;">-<span id="LC1208" class="line" lang="cpp"></span>
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1209
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<td class="new_line diff-line-num old" data-linenumber="1217" 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="LC1209" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</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;">seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">length</span><span class="p">);</span></span>
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1210
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<td class="new_line diff-line-num" data-linenumber="1217" 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">
1217
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<pre style="margin: 0;"> <span id="LC1217" class="line" lang="cpp"> <span class="p">}</span></span>
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1211
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<td class="new_line diff-line-num" data-linenumber="1218" 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">
1218
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<pre style="margin: 0;"> <span id="LC1218" class="line" lang="cpp"> <span class="p">}</span></span>
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1212
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1219
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<pre style="margin: 0;"> <span id="LC1219" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1230,7 +1237,7 @@ call_consensus(map<int, MergedStack *> &merged, map<int, Stack *> &unique, map<i</td>
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1230
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<td class="new_line diff-line-num" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1237
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<pre style="margin: 0;"> <span id="LC1237" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="1231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1231
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<td class="new_line diff-line-num" data-linenumber="1238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1238
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<pre style="margin: 0;"> <span id="LC1238" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">row</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;">row</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">height</span><span class="p">;</span> <span class="n" style="color: #333;">row</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1232" 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">
1232
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<td class="new_line diff-line-num" data-linenumber="1239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1239
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<pre style="margin: 0;"> <span id="LC1239" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reads</span><span class="p">[</span><span class="n" style="color: #333;">row</span><span class="p">];</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1233
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<td class="new_line diff-line-num old" data-linenumber="1240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1233" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nuc</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">d</span><span class="p">)[</span><span class="n" style="color: #333;">col</span><span class="p">]))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1234" 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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1240
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<pre style="margin: 0;">+<span id="LC1240" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">col</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">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">nuc</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">d</span><span class="p">)[</span><span class="n" style="color: #333;">col</span><span class="p">]))</span></span>
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1234
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1241
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<pre style="margin: 0;"> <span id="LC1241" class="line" lang="cpp"> <span class="n" style="color: #333;">nuc</span><span class="p">[(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">d</span><span class="p">)[</span><span class="n" style="color: #333;">col</span><span class="p">]]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1235
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1242
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<pre style="margin: 0;"> <span id="LC1242" class="line" lang="cpp"> <span class="p">}</span></span>
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1236
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<td class="new_line diff-line-num" data-linenumber="1243" 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">
1243
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<pre style="margin: 0;"> <span id="LC1243" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1267" 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="1274" 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">@@ -1267,13 +1274,13 @@ call_consensus(map<int, MergedStack *> &merged, map<int, Stack *> &unique, map<i</td>
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1267
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1274
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<pre style="margin: 0;"> <span id="LC1274" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1268" 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">
1268
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<td class="new_line diff-line-num" data-linenumber="1275" 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">
1275
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<pre style="margin: 0;"> <span id="LC1275" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="1269" 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">
1269
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<td class="new_line diff-line-num" data-linenumber="1276" 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">
1276
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<pre style="margin: 0;"> <span id="LC1276" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span><span class="n" style="color: #333;">model_type</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1270" 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">
1270
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<td class="new_line diff-line-num old" data-linenumber="1277" 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="LC1270" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">snp</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1271" 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="new_line diff-line-num new" data-linenumber="1277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1277
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<pre style="margin: 0;">+<span id="LC1277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;"><span class="idiff left">modelt</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></span><span class="n" style="color: #333;">snp</span><span class="p">:</span></span>
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1271
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1278
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<pre style="margin: 0;"> <span id="LC1278" class="line" lang="cpp"> <span class="n" style="color: #333;">call_multinomial_snp</span><span class="p">(</span><span class="n" style="color: #333;">mtag</span><span class="p">,</span> <span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">nuc</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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1272
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1279
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<pre style="margin: 0;"> <span id="LC1279" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1273
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<td class="new_line diff-line-num old" data-linenumber="1280" 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="LC1273" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">bounded</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1280" 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">
1280
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<pre style="margin: 0;">+<span id="LC1280" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;"><span class="idiff left">modelt</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></span><span class="n" style="color: #333;">bounded</span><span class="p">:</span></span>
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1274
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<td class="new_line diff-line-num" data-linenumber="1281" 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">
1281
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<pre style="margin: 0;"> <span id="LC1281" class="line" lang="cpp"> <span class="n" style="color: #333;">call_bounded_multinomial_snp</span><span class="p">(</span><span class="n" style="color: #333;">mtag</span><span class="p">,</span> <span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">nuc</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1275" 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">
1275
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<td class="new_line diff-line-num" data-linenumber="1282" 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">
1282
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<pre style="margin: 0;"> <span id="LC1282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1276
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<td class="new_line diff-line-num old" data-linenumber="1283" 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="LC1276" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fixed</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1283
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<pre style="margin: 0;">+<span id="LC1283" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;"><span class="idiff left right">modelt</span></span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fixed</span><span class="p">:</span></span>
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1277
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<td class="new_line diff-line-num" data-linenumber="1284" 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">
1284
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<pre style="margin: 0;"> <span id="LC1284" class="line" lang="cpp"> <span class="n" style="color: #333;">call_multinomial_fixed</span><span class="p">(</span><span class="n" style="color: #333;">mtag</span><span class="p">,</span> <span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">nuc</span><span class="p">);</span></span>
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1278
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1285
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<pre style="margin: 0;"> <span id="LC1285" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1279
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1286
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<pre style="margin: 0;"> <span id="LC1286" class="line" lang="cpp"> <span class="nl">default:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1290" 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="1297" 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">@@ -1290,7 +1297,7 @@ call_consensus(map<int, MergedStack *> &merged, map<int, Stack *> &unique, map<i</td>
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1290
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1297
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<pre style="margin: 0;"> <span id="LC1297" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="1291" 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">
1291
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<td class="new_line diff-line-num" data-linenumber="1298" 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">
1298
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<pre style="margin: 0;"> <span id="LC1298" class="line" lang="cpp"> <span class="n" style="color: #333;">call_alleles</span><span class="p">(</span><span class="n" style="color: #333;">mtag</span><span class="p">,</span> <span class="n" style="color: #333;">reads</span><span class="p">,</span> <span class="n" style="color: #333;">read_types</span><span class="p">);</span></span>
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1292
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1299
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<pre style="margin: 0;"> <span id="LC1299" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="1293" 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">
1293
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<td class="new_line diff-line-num old" data-linenumber="1300" 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="LC1293" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">model_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fixed</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1294" 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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1300
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<pre style="margin: 0;">+<span id="LC1300" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">model_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">modelt</span></span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fixed</span><span class="p">)</span> <span class="p">{</span></span>
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1294
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1301
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<pre style="margin: 0;"> <span id="LC1301" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="old_line diff-line-num" data-linenumber="1295" 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">
1295
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<td class="new_line diff-line-num" data-linenumber="1302" 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">
1302
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<pre style="margin: 0;"> <span id="LC1302" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Mask nucleotides that are not fixed.</span></span>
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1296
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<td class="new_line diff-line-num" data-linenumber="1303" 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">
1303
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<pre style="margin: 0;"> <span id="LC1303" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1314" 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="1321" 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">@@ -1314,6 +1321,8 @@ update_consensus(MergedStack *mtag, map<int, Stack *> &unique, map<int, Rem *> &</td>
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<td class="old_line diff-line-num" data-linenumber="1314" 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">
1314
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<td class="new_line diff-line-num" data-linenumber="1321" 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">
1321
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<pre style="margin: 0;"> <span id="LC1321" class="line" lang="cpp"><span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1315" 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">
1315
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<td class="new_line diff-line-num" data-linenumber="1322" 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">
1322
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<pre style="margin: 0;"> <span id="LC1322" class="line" lang="cpp"> <span class="n" style="color: #333;">Stack</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">utag</span><span class="p">;</span></span>
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1316
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1323
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<pre style="margin: 0;"> <span id="LC1323" class="line" lang="cpp"> <span class="n" style="color: #333;">Rem</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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1324
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<pre style="margin: 0;">+<span id="LC1324" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">length</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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1325
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<pre style="margin: 0;">+<span id="LC1325" class="line" lang="cpp"> </span>
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1317
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1326
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<pre style="margin: 0;"> <span id="LC1326" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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1318
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1327
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<pre style="margin: 0;"> <span id="LC1327" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Create a two-dimensional array, each row containing one read. For</span></span>
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1319
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1328
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<pre style="margin: 0;"> <span id="LC1328" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// each unique tag that has been merged together, add the sequence for</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1333" 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">@@ -1324,6 +1333,9 @@ update_consensus(MergedStack *mtag, map<int, Stack *> &unique, map<int, Rem *> &</td>
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1324
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1333
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<pre style="margin: 0;"> <span id="LC1333" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mtag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">utags</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">mtag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">utags</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1325
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1334
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<pre style="margin: 0;"> <span id="LC1334" class="line" lang="cpp"> <span class="n" style="color: #333;">utag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unique</span><span class="p">[</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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1326
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1335
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<pre style="margin: 0;"> <span id="LC1335" class="line" lang="cpp"></span>
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1336
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<pre style="margin: 0;">+<span id="LC1336" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check for maximum length.</span></span>
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1337
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<pre style="margin: 0;">+<span id="LC1337" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">utag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">utag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">length</span><span class="p">;</span></span>
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1338
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<pre style="margin: 0;">+<span id="LC1338" class="line" lang="cpp"></span>
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1327
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1339
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<pre style="margin: 0;"> <span id="LC1339" 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;">k</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;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">utag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">count</span><span class="p">();</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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1328
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1340
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<pre style="margin: 0;"> <span id="LC1340" class="line" lang="cpp"> <span class="n" style="color: #333;">reads</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">utag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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1329
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1341
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<pre style="margin: 0;"> <span id="LC1341" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1344" 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">@@ -1332,6 +1344,9 @@ update_consensus(MergedStack *mtag, map<int, Stack *> &unique, map<int, Rem *> &</td>
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1332
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1344
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<pre style="margin: 0;"> <span id="LC1344" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mtag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">remtags</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">mtag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">remtags</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1333
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1345
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<pre style="margin: 0;"> <span id="LC1345" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rem</span><span class="p">[</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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1334
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1346
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<pre style="margin: 0;"> <span id="LC1346" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC1347" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check for maximum length.</span></span>
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1348
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<pre style="margin: 0;">+<span id="LC1348" class="line" lang="cpp"> <span class="n" style="color: #333;">length</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;">seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">length</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;">seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">length</span><span class="p">;</span></span>
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1349
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<pre style="margin: 0;">+<span id="LC1349" class="line" lang="cpp"></span>
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1335
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1350
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<pre style="margin: 0;"> <span id="LC1350" 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;">k</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;">k</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;">count</span><span class="p">();</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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1336
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1351
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<pre style="margin: 0;"> <span id="LC1351" class="line" lang="cpp"> <span class="n" style="color: #333;">reads</span><span class="p">.</span><span class="n" style="color: #333;">push_back</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;">seq</span><span class="p">);</span></span>
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1337
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1352
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<pre style="margin: 0;"> <span id="LC1352" 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="1341" 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="1356" 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">@@ -1341,7 +1356,6 @@ update_consensus(MergedStack *mtag, map<int, Stack *> &unique, map<int, Rem *> &</td>
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1341
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1356
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<pre style="margin: 0;"> <span id="LC1356" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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1342
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1357
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<pre style="margin: 0;"> <span id="LC1357" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">con</span><span class="p">;</span></span>
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1343
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1358
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<pre style="margin: 0;"> <span id="LC1358" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">row</span><span class="p">,</span> <span class="n" style="color: #333;">col</span><span class="p">;</span></span>
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1344
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<pre style="margin: 0;">-<span id="LC1344" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reads</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;">size</span><span class="p">();</span></span>
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1345
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1359
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<pre style="margin: 0;"> <span id="LC1359" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">height</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reads</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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1346
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1360
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<pre style="margin: 0;"> <span id="LC1360" class="line" lang="cpp"> <span class="n" style="color: #333;">DNANSeq</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">d</span><span class="p">;</span></span>
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1347
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1361
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<pre style="margin: 0;"> <span id="LC1361" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1358" 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="1372" 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">@@ -1358,6 +1372,10 @@ update_consensus(MergedStack *mtag, map<int, Stack *> &unique, map<int, Rem *> &</td>
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1358
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1372
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<pre style="margin: 0;"> <span id="LC1372" class="line" lang="cpp"></span>
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1359
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1373
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<pre style="margin: 0;"> <span id="LC1373" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">row</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;">row</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">height</span><span class="p">;</span> <span class="n" style="color: #333;">row</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1360
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1374
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<pre style="margin: 0;"> <span id="LC1374" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reads</span><span class="p">[</span><span class="n" style="color: #333;">row</span><span class="p">];</span></span>
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1375
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<pre style="margin: 0;">+<span id="LC1375" class="line" lang="cpp"></span>
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1376
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<pre style="margin: 0;">+<span id="LC1376" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">())</span></span>
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1377
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<pre style="margin: 0;">+<span id="LC1377" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1378
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<pre style="margin: 0;">+<span id="LC1378" class="line" lang="cpp"> </span>
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1361
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1379
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<pre style="margin: 0;"> <span id="LC1379" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">d</span><span class="p">)[</span><span class="n" style="color: #333;">col</span><span class="p">])</span> <span class="p">{</span></span>
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1362
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1380
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<pre style="margin: 0;"> <span id="LC1380" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'A'</span><span class="p">:</span></span>
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1363
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1381
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<pre style="margin: 0;"> <span id="LC1381" class="line" lang="cpp"> <span class="n" style="color: #333;">nucs</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="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1672" 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="1690" 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">@@ -1672,7 +1690,9 @@ merge_tags(MergedStack *tag_1, MergedStack *tag_2, int id)</td>
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1672
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1690
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<pre style="margin: 0;"> <span id="LC1690" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">new_tag</span><span class="p">;</span></span>
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1673
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1691
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<pre style="margin: 0;"> <span id="LC1691" class="line" lang="cpp"><span class="p">}</span></span>
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1674
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1692
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<pre style="margin: 0;"> <span id="LC1692" class="line" lang="cpp"></span>
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1675
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<pre style="margin: 0;">-<span id="LC1675" class="line" lang="cpp"><span class="n" style="color: #333;">MergedStack</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">merge_tags</span><span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">MergedStack</span> <span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">merged</span><span class="p">,</span> <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">merge_list</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">id</span><span class="p">)</span> <span class="p">{</span></span>
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1693
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<pre style="margin: 0;">+<span id="LC1693" class="line" lang="cpp"><span class="n" style="color: #333;">MergedStack</span> <span class="o" style="font-weight: 600;">*</span></span>
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1694
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<pre style="margin: 0;">+<span id="LC1694" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">merge_tags</span><span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">MergedStack</span> <span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">merged</span><span class="p">,</span> <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">merge_list</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">id</span><span class="p">)</span></span>
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1695
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<pre style="margin: 0;">+<span id="LC1695" class="line" lang="cpp"><span class="p">{</span></span>
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1676
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1696
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<pre style="margin: 0;"> <span id="LC1696" class="line" lang="cpp"> <span class="n" style="color: #333;">MergedStack</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tag_1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tag_2</span><span class="p">;</span></span>
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1677
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1697
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<pre style="margin: 0;"> <span id="LC1697" class="line" lang="cpp"></span>
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1678
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1698
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<pre style="margin: 0;"> <span id="LC1698" class="line" lang="cpp"> <span class="n" style="color: #333;">tag_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MergedStack</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1701" 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="1721" 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">@@ -1701,7 +1721,9 @@ MergedStack *merge_tags(map<int, MergedStack *> &merged, set<int> &merge_list, i</td>
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1701
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1721
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<pre style="margin: 0;"> <span id="LC1721" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tag_1</span><span class="p">;</span></span>
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1702
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1722
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<pre style="margin: 0;"> <span id="LC1722" class="line" lang="cpp"><span class="p">}</span></span>
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1703
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1723
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<pre style="margin: 0;"> <span id="LC1723" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1704" class="line" lang="cpp"><span class="n" style="color: #333;">MergedStack</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">merge_tags</span><span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">MergedStack</span> <span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">merged</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">merge_list</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">merge_list_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">id</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1724" class="line" lang="cpp"><span class="n" style="color: #333;">MergedStack</span> <span class="o" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">+<span id="LC1725" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">merge_tags</span><span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">MergedStack</span> <span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">merged</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">merge_list</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">merge_list_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">id</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1726" class="line" lang="cpp"><span class="p">{</span></span>
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1727
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<pre style="margin: 0;"> <span id="LC1727" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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1728
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<pre style="margin: 0;"> <span id="LC1728" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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1729
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<pre style="margin: 0;"> <span id="LC1729" class="line" lang="cpp"> <span class="n" style="color: #333;">MergedStack</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tag_1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tag_2</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2703" 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="2725" 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">@@ -2703,7 +2725,7 @@ void load_radtags(string in_file, DNASeqHashMap &radtags, size_t& n_reads) {</td>
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2703
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2725
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<pre style="margin: 0;"> <span id="LC2725" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Error: different sequence lengths detected, this will interfere with Stacks "</span></span>
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2704
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2726
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<pre style="margin: 0;"> <span id="LC2726" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"algorithms, trim reads to uniform length (override this check with --force-diff-len).</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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2705
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2727
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<pre style="margin: 0;"> <span id="LC2727" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC2706" 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;">force_diff_len</span><span class="p">)</span> <span class="p">{</span></span>
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2728
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<pre style="margin: 0;">+<span id="LC2728" 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;"><span class="idiff left">len_mismatch</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;">force_diff_len</span><span class="p">)</span> <span class="p">{</span></span>
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2729
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<pre style="margin: 0;"> <span id="LC2729" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: different sequence lengths detected, this could interfere with Stacks algorithms.</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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2708
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2730
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<pre style="margin: 0;"> <span id="LC2730" class="line" lang="cpp"> <span class="p">}</span></span>
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2709
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2731
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<pre style="margin: 0;"> <span id="LC2731" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">corrected</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="3026" 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="3048" 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">@@ -3026,11 +3048,12 @@ void help() {</td>
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3026
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3048
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<pre style="margin: 0;"> <span id="LC3048" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" H: disable calling haplotypes from secondary reads.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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3027
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3049
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<pre style="margin: 0;"> <span id="LC3049" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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3028
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3050
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<pre style="margin: 0;"> <span id="LC3050" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Stack assembly options:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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3029
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<pre style="margin: 0;">-<span id="LC3029" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <span class="idiff left right">d,--deleverage: enable the Deleveraging algorithm, used for resolving over merged tags</span>.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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3051
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<pre style="margin: 0;">+<span id="LC3051" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <span class="idiff left right">--force-diff-len: allow raw input reads of different lengths, e.g. after trimming (default: ustacks perfers raw input reads of uniform length)</span>.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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3030
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3052
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<pre style="margin: 0;"> <span id="LC3052" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --keep-high-cov: disable the algorithm that removes highly-repetitive stacks and nearby errors.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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3031
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<pre style="margin: 0;"> <span id="LC3053" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --high-cov-thres: highly-repetitive stacks threshold, in standard deviation units (default: 3.0).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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3032
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3054
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<pre style="margin: 0;"> <span id="LC3054" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --max-locus-stacks <num>: maximum number of stacks at a single de novo locus (default 3).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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3033
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<pre style="margin: 0;">-<span id="LC3033" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --k-len <len>: specify k-mer size for matching between alleles and loci (automatically calculated by default).</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC3055" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --k-len <len>: specify k-mer size for matching between alleles and loci (automatically calculated by default).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC3056" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --deleverage: enable the Deleveraging algorithm, used for resolving over merged tags.</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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3034
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3057
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<pre style="margin: 0;"> <span id="LC3057" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Gapped assembly options:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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3035
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<pre style="margin: 0;"> <span id="LC3058" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --max-gaps: number of gaps allowed between stacks before merging (default: 2).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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3036
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3059
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<pre style="margin: 0;"> <span id="LC3059" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80).</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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