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<h3>
Étienne Mollier pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/ivar">Debian Med / ivar</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ivar/-/commit/b02028a7de0247141fb9648bcd2e4e048363a38c">b02028a7</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-27T20:18:36+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.1+dfsg</pre>
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<h4>13 changed files:</h4>
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<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
</a>
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<li class="file-stats">
<a href="#393887da53235ee427bfdfb35cd6b4e07e880da4">
src/interval_tree.cpp
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<li class="file-stats">
<a href="#a81369f32a4ff6b6f704aa029f6c65bd099a6dd9">
src/interval_tree.h
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<li class="file-stats">
<a href="#1ed56bc299f4a6bb415bcf995da6bf4ba876e7a4">
src/ivar.cpp
</a>
</li>
<li class="file-stats">
<a href="#866d85bf13e1fa8b98ce1b6c3d29af2e31287c2c">
src/primer_bed.cpp
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</li>
<li class="file-stats">
<a href="#8a641f0ef8d03c9561553ccae691be19019c32d3">
src/primer_bed.h
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<li class="file-stats">
<a href="#00b6081be5179b8efd2e37aec59ecf773a10c3ed">
src/trim_primer_quality.cpp
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<li class="file-stats">
<a href="#fdbb3539733405317eca774fe99c6ab1d8306beb">
src/trim_primer_quality.h
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<li class="file-stats">
<a href="#0c55f5b6f21374c58c1ef1f9fd933d0d419350a2">
tests/test_amplicon_search.cpp
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<li class="file-stats">
<a href="#5b33689eb2b190a723341547830d23181ca6d242">
tests/test_interval_tree.cpp
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<li class="file-stats">
<a href="#461dd163e8fdef342b3dcb28bba477068047700f">
tests/test_isize_trim.cpp
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<li class="file-stats">
<a href="#bc53edf1aafd372a6a2ab1583c4dce2eb60702a7">
tests/test_primer_trim_edge_cases.cpp
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<li class="file-stats">
<a href="#72cf1548681e3cd27df54db6d2a928d482a578e9">
tests/test_trim.cpp
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</ul>
<h4>Changes:</h4>
<li id="87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
<a href="https://salsa.debian.org/med-team/ivar/-/commit/b02028a7de0247141fb9648bcd2e4e048363a38c#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"># Process this file with autoconf to produce a configure script.</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">AC_PREREQ([2.63])</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">AC_INIT([ivar], [1.3], [gkarthik@scripps.edu])</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">AC_INIT([ivar], [1.3<span class="idiff left right">.1</span>], [gkarthik@scripps.edu])</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">AM_INIT_AUTOMAKE([foreign subdir-objects])</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">AC_CONFIG_HEADERS([config.h])</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<li id="393887da53235ee427bfdfb35cd6b4e07e880da4">
<a href="https://salsa.debian.org/med-team/ivar/-/commit/b02028a7de0247141fb9648bcd2e4e048363a38c#393887da53235ee427bfdfb35cd6b4e07e880da4"><strong>src/interval_tree.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="38" 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">@@ -38,13 +38,13 @@ void IntervalTree::insert(ITNode *root, Interval data){</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// update max value of ancestor node</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">low</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cpp"> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">low</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">high</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">high</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// A utility function to check if <span class="idiff left right">given two intervals overlap</span></span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">do<span class="idiff left right">Overla</span>p</span><span class="p">(</span><span class="n" style="color: #333;">Interval</span> <span class="n" style="color: #333;">i1</span><span class="p">,</span> <span class="n" style="color: #333;">Interval</span> <span class="n" style="color: #333;">i2</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// A utility function to check if <span class="idiff left right">the 1st interval envelops the second</span></span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">do<span class="idiff left right">Envelo</span>p</span><span class="p">(</span><span class="n" style="color: #333;">Interval</span> <span class="n" style="color: #333;">i1</span><span class="p">,</span> <span class="n" style="color: #333;">Interval</span> <span class="n" style="color: #333;">i2</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">i1</span><span class="p">.</span><span class="n" style="color: #333;">low</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">i2</span><span class="p">.</span><span class="n" style="color: #333;">low</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">i1</span><span class="p">.</span><span class="n" style="color: #333;">high</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">i2</span><span class="p">.</span><span class="n" style="color: #333;">high</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -53,23 +53,23 @@ bool doOverlap(Interval i1, Interval i2){</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// The main function that searches an interval i in a given</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Interval Tree.</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;"><span class="idiff left right">overla</span>pSearch</span><span class="p">(</span><span class="n" style="color: #333;">ITNode</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">Interval</span> <span class="n" style="color: #333;">i</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;"><span class="idiff left right">envelo</span>pSearch</span><span class="p">(</span><span class="n" style="color: #333;">ITNode</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">Interval</span> <span class="n" style="color: #333;">i</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Base Case, tree is empty</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cout << root->data->low << ":" << root->data->high << std::endl;</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">root</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If given interval overlaps with root</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">do<span class="idiff left right">Overla</span>p</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">),</span> <span class="n" style="color: #333;">i</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">do<span class="idiff left right">Envelo</span>p</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">),</span> <span class="n" style="color: #333;">i</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If left child of root is present and max of left child is</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// greater than or equal to given interval, then i may</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">overlap with an interval</span> in left subtree</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">left</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">low</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">overla</span>pSearch</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">left</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="LC67" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">be enveloped by an amplicon</span> in left subtree</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">left</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">high</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">envelo</span>pSearch</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">left</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="LC70" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Else interval can only <span class="idiff left right">overlap with</span> right subtree</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">overla</span>pSearch</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">right</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="LC71" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Else interval can only <span class="idiff left right">be enveloped by amplicon in</span> right subtree</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">envelo</span>pSearch</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">right</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="LC73" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// A helper function for inorder traversal of the tree</span></span>
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<a href="https://salsa.debian.org/med-team/ivar/-/commit/b02028a7de0247141fb9648bcd2e4e048363a38c#a81369f32a4ff6b6f704aa029f6c65bd099a6dd9"><strong>src/interval_tree.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,7 +25,7 @@ class ITNode{</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> void setRight(ITNode *node);</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="nl">public:</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"> <span class="n" style="color: #333;">ITNode</span><span class="p">(</span><span class="n" style="color: #333;">Interval</span> <span class="n" style="color: #333;">value</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">data</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Interval</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)),</span> <span class="n" style="color: #333;">left</span><span class="p">(</span><span class="nb" style="color: #0086b3;">nullptr</span><span class="p">),</span> <span class="n" style="color: #333;">right</span><span class="p">(</span><span class="nb" style="color: #0086b3;">nullptr</span><span class="p">),</span> <span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">low</span></span><span class="p">)</span> <span class="p">{}</span> <span class="c1" style="color: #998; font-style: italic;">// constructor</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"> <span class="n" style="color: #333;">ITNode</span><span class="p">(</span><span class="n" style="color: #333;">Interval</span> <span class="n" style="color: #333;">value</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">data</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Interval</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)),</span> <span class="n" style="color: #333;">left</span><span class="p">(</span><span class="nb" style="color: #0086b3;">nullptr</span><span class="p">),</span> <span class="n" style="color: #333;">right</span><span class="p">(</span><span class="nb" style="color: #0086b3;">nullptr</span><span class="p">),</span> <span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">high</span></span><span class="p">)</span> <span class="p">{}</span> <span class="c1" style="color: #998; font-style: italic;">// constructor</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"> <span class="n" style="color: #333;">Interval</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">data</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// pointer to node's interval data object</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"> <span class="n" style="color: #333;">ITNode</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">right</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// pointer to node's left & right child node objects</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max</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">@@ -38,13 +38,13 @@ class IntervalTree{</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"><span class="nl">private:</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">ITNode</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_root</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">ITNode</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">Interval</span> <span class="n" style="color: #333;">data</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;"><span class="idiff left right">overla</span>pSearch</span><span class="p">(</span><span class="n" style="color: #333;">ITNode</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">Interval</span> <span class="n" style="color: #333;">data</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;"><span class="idiff left right">envelo</span>pSearch</span><span class="p">(</span><span class="n" style="color: #333;">ITNode</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">Interval</span> <span class="n" style="color: #333;">data</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">inOrder</span><span class="p">(</span><span class="n" style="color: #333;">ITNode</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">root</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"><span class="nl">public:</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">IntervalTree</span><span class="p">();</span> <span class="c1" style="color: #998; font-style: italic;">// constructor</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">Interval</span> <span class="n" style="color: #333;">data</span><span class="p">){</span> <span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">_root</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">);}</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;"><span class="idiff left">overla</span>pSearch</span><span class="p">(</span><span class="n" style="color: #333;">Interval</span> <span class="n" style="color: #333;">data</span><span class="p">){</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff right">overla</span>pSearch</span><span class="p">(</span><span class="n" style="color: #333;">_root</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">);}</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;"><span class="idiff left">envelo</span>pSearch</span><span class="p">(</span><span class="n" style="color: #333;">Interval</span> <span class="n" style="color: #333;">data</span><span class="p">){</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff right">envelo</span>pSearch</span><span class="p">(</span><span class="n" style="color: #333;">_root</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">);}</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">inOrder</span><span class="p">()</span> <span class="p">{</span><span class="n" style="color: #333;">inOrder</span><span class="p">(</span><span class="n" style="color: #333;">_root</span><span class="p">);}</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/ivar/-/commit/b02028a7de0247141fb9648bcd2e4e048363a38c#1ed56bc299f4a6bb415bcf995da6bf4ba876e7a4"><strong>src/ivar.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,7 +16,7 @@</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "suffix_tree.h"</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "get_common_variants.h"</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.3"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.3<span class="idiff left right">.1</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">args_t</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -i</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,6 +37,7 @@ struct args_t {</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">gap</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -n</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">keep_min_coverage</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -k</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">primer_pair_file</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -f</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">primer_offset</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -x</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">file_list</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -f</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">write_no_primers_flag</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -e</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">gff</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -g</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -65,8 +66,9 @@ void print_trim_usage(){</td>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Input Options Description</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -i (Required) Sorted bam file, with aligned reads, to trim primers and quality</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="LC68" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -b BED file with primer sequences and positions. If no BED file is specified, only quality trimming will be done.</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="LC68" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -f Primer pair information file containing left and right primer names for the same amplicon separated by a tab</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="LC69" class="line" lang="cpp"> <span class="s" style="color: #d14;">" If provided, reads will be filtered based on their overlap with amplicons prior to trimming</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="LC69" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -f [EXPERIMENTAL] Primer pair information file containing left and right primer names for the same amplicon separated by a tab</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="s" style="color: #d14;">" If provided, reads that do not fall within atleat one amplicon will be ignored prior to primer trimming.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -x Primer position offset (Default: 0). Reads that occur at the specified offset positions relative to primer positions will also be trimmed.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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70
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -m Minimum length of read to retain after trimming (Default: 30)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -q Minimum quality threshold for sliding window to pass (Default: 20)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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72
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -s Width of sliding window (Default: 4)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="165" 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">@@ -165,7 +167,7 @@ void print_version_info(){</td>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Please raise issues and bug reports at https://github.com/andersen-lab/ivar/</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trim_opt_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"i:b:f:p:m:q:s:ekh?"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trim_opt_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"i:b:f:<span class="idiff left right">x:</span>p:m:q:s:ekh?"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">variants_opt_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"p:t:q:m:r:g:h?"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">consensus_opt_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"i:p:q:t:m:n:kh?"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">removereads_opt_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"i:p:t:b:h?"</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -221,6 +223,7 @@ int main(int argc, char* argv[]){</td>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">keep_for_reanalysis</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">bed</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">primer_pair_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">primer_offset</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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224
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt</span><span class="p">(</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="n" style="color: #333;">trim_opt_str</span><span class="p">);</span></span>
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225
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228
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span> <span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="p">{</span></span>
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226
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229
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span> <span class="n" style="color: #333;">opt</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -232,6 +235,9 @@ int main(int argc, char* argv[]){</td>
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232
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235
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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233
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236
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'f'</span><span class="p">:</span></span>
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234
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">primer_pair_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'x'</span><span class="p">:</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">primer_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>
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235
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241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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236
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242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'p'</span><span class="p">:</span></span>
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243
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp"> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="264" 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="270" 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">@@ -264,7 +270,7 @@ int main(int argc, char* argv[]){</td>
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264
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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;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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265
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="cpp"> <span class="p">}</span></span>
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266
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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;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_filename_without_extension</span><span class="p">(</span><span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span><span class="s" style="color: #d14;">".bam"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="267" 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">
267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trim_bam_qual_primer</span><span class="p">(</span><span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">bed</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">region</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">sliding_window</span><span class="p">,</span> <span class="n" style="color: #333;">cl_cmd</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">(),</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">write_no_primers_flag</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">keep_for_reanalysis</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_length</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">primer_pair_file</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trim_bam_qual_primer</span><span class="p">(</span><span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">bed</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">region</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">sliding_window</span><span class="p">,</span> <span class="n" style="color: #333;">cl_cmd</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">(),</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">write_no_primers_flag</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">keep_for_reanalysis</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">min_length</span><span class="p">,</span> <span class="n" style="color: #333;">g_args</span><span class="p">.</span><span class="n" style="color: #333;">primer_pair_file</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g_args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">primer_offset</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp"> <span class="p">}</span></span>
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269
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// ivar variants</span></span>
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270
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">compare</span><span class="p">(</span><span class="s" style="color: #d14;">"variants"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<a href="https://salsa.debian.org/med-team/ivar/-/commit/b02028a7de0247141fb9648bcd2e4e048363a38c#866d85bf13e1fa8b98ce1b6c3d29af2e31287c2c"><strong>src/primer_bed.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -85,6 +85,75 @@ void print_bed_format(){</td>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"It requires the following columns delimited by a tab: chrom, chromStart, chromEnd, name, score, strand"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"><span class="p">}</span></span>
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">populate_from_file</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">offset</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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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">data</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>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">line</span><span class="p">;</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">primers</span><span class="p">;</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int16_t</span> <span class="n" style="color: #333;">indice</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span><span class="n" style="color: #333;">line</span><span class="p">)){</span> <span class="c1" style="color: #998; font-style: italic;">// Remove extra lineStream</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">lineStream</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">cell</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ctr</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">primer</span> <span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">set_strand</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Set strand to NULL</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">lineStream</span><span class="p">,</span><span class="n" style="color: #333;">cell</span><span class="p">,</span><span class="sc" style="color: #d14;">'\t'</span><span class="p">)){</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span><span class="n" style="color: #333;">ctr</span><span class="p">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">set_region</span><span class="p">(</span><span class="n" style="color: #333;">cell</span><span class="p">);</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">all_of</span><span class="p">(</span><span class="n" style="color: #333;">cell</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">cell</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">isdigit</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="106" 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">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">set_start</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;">stoul</span><span class="p">(</span><span class="n" style="color: #333;">cell</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">offset</span><span class="p">);</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">print_bed_format</span><span class="p">();</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">primers</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">primers</span><span class="p">;</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="p">}</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="113" 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">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="114" 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">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">all_of</span><span class="p">(</span><span class="n" style="color: #333;">cell</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">cell</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">isdigit</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="115" 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">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">set_end</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stoul</span><span class="p">(</span><span class="n" style="color: #333;">cell</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;">offset</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Bed format - End is not 0 based</span></span>
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<td class="new_line diff-line-num new" data-linenumber="116" 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">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="117" 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">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="n" style="color: #333;">print_bed_format</span><span class="p">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="118" 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">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="n" style="color: #333;">primers</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="119" 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">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">primers</span><span class="p">;</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="p">}</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">set_name</span><span class="p">(</span><span class="n" style="color: #333;">cell</span><span class="p">);</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">4</span><span class="p">:</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">all_of</span><span class="p">(</span><span class="n" style="color: #333;">cell</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">cell</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">isdigit</span><span class="p">))</span> <span class="p">{</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">set_score</span><span class="p">(</span><span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">cell</span><span class="p">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="128" 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">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="n" style="color: #333;">print_bed_format</span><span class="p">();</span> <span class="c1" style="color: #998; font-style: italic;">// score is missing, send warning but continue populating</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">WARNING: The BED file provided did not have the expected score column, but iVar will continue trimming</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">set_score</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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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="p">}</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">5</span><span class="p">:</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cell</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'+'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cell</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">)</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">set_strand</span><span class="p">(</span><span class="n" style="color: #333;">cell</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">print_bed_format</span><span class="p">();</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="n" style="color: #333;">primers</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">primers</span><span class="p">;</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="p">}</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"> <span class="p">}</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp"> <span class="n" style="color: #333;">ctr</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"> <span class="p">}</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">indice</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ctr</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">6</span><span class="p">)</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Strand not found in primer BED file so strand will not be considered for trimming"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">set_indice</span><span class="p">(</span><span class="n" style="color: #333;">indice</span><span class="p">);</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">set_pair_indice</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">set_read_count</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="n" style="color: #333;">primers</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="n" style="color: #333;">indice</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="p">}</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Found "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">primers</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" primers in BED file"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">primers</span><span class="p">;</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"><span class="p">}</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"></span>
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88
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">populate_from_file</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">path</span><span class="p">){</span></span>
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89
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">data</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>
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90
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">line</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="181" 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">@@ -112,7 +181,7 @@ std::vector<primer> populate_from_file(std::string path){</td>
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112
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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113
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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114
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">all_of</span><span class="p">(</span><span class="n" style="color: #333;">cell</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">cell</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">isdigit</span><span class="p">))</span> <span class="p">{</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">set_end</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stoul</span><span class="p">(</span><span class="n" style="color: #333;">cell</span><span class="p">)</span><span class="o" style="font-weight: 600;"><span class="idiff left right">-</span></span><span class="mi" style="color: #099;">1</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Bed format - End is not 0 based</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">set_end</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stoul</span><span class="p">(</span><span class="n" style="color: #333;">cell</span><span class="p">)</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">1</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Bed format - End is not 0 based</span></span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cpp"> <span class="n" style="color: #333;">print_bed_format</span><span class="p">();</span></span>
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118
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="cpp"> <span class="n" style="color: #333;">primers</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<a href="https://salsa.debian.org/med-team/ivar/-/commit/b02028a7de0247141fb9648bcd2e4e048363a38c#8a641f0ef8d03c9561553ccae691be19019c32d3"><strong>src/primer_bed.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,6 +46,7 @@ class primer {</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">populate_from_file</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">offset</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">populate_from_file</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">path</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">get_primers</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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51
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">get_primer_indice</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/ivar/-/commit/b02028a7de0247141fb9648bcd2e4e048363a38c#00b6081be5179b8efd2e37aec59ecf773a10c3ed"><strong>src/trim_primer_quality.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -331,7 +331,7 @@ int get_bigger_primer(std::vector<primer> primers){</td>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">max_primer_len</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// check if read <span class="idiff left right">overlaps with</span> any of the amplicons</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// check if read <span class="idiff left right">is enveloped by</span> any of the amplicons</span></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">amplicon_filter</span><span class="p">(</span><span class="n" style="color: #333;">IntervalTree</span> <span class="n" style="color: #333;">amplicons</span><span class="p">,</span> <span class="n" style="color: #333;">bam1_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">r</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="cpp"> <span class="n" style="color: #333;">Interval</span> <span class="n" style="color: #333;">fragment_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Interval</span><span class="p">(</span><span class="mi" style="color: #099;">0</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="LC337" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">isize</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -342,16 +342,16 @@ bool amplicon_filter(IntervalTree amplicons, bam1_t* r){</td>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="cpp"> <span class="n" style="color: #333;">fragment_coords</span><span class="p">.</span><span class="n" style="color: #333;">high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_endpos</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// debugging</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">amplicon_flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">amplicons</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">overla</span>pSearch</span><span class="p">(</span><span class="n" style="color: #333;">fragment_coords</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">amplicon_flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">amplicons</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">envelo</span>pSearch</span><span class="p">(</span><span class="n" style="color: #333;">fragment_coords</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">amplicon_flag</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">trim_bam_qual_primer</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bed</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam_out</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">region_</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">sliding_window</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">write_no_primer_reads</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">keep_for_reanalysis</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">30</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">pair_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">trim_bam_qual_primer</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bed</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam_out</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">region_</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">sliding_window</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">write_no_primer_reads</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">keep_for_reanalysis</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">30</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">pair_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">primer_offset</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 class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">retval</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="LC351" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">primers</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_primer_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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353
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">bed</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()){</span></span>
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354
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="cpp"> <span class="n" style="color: #333;">primers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">populate_from_file</span><span class="p">(</span><span class="n" style="color: #333;">bed</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp"> <span class="n" style="color: #333;">primers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">populate_from_file</span><span class="p">(</span><span class="n" style="color: #333;">bed</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">primer_offset</span></span><span class="p">);</span></span>
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355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">primers</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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356
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Exiting."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="363" 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">@@ -363,6 +363,8 @@ int trim_bam_qual_primer(std::string bam, std::string bed, std::string bam_out,</td>
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363
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363
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<pre style="margin: 0;"> <span id="LC363" 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;">pair_info</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()){</span></span>
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364
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="cpp"> <span class="n" style="color: #333;">amplicons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">populate_amplicons</span><span class="p">(</span><span class="n" style="color: #333;">pair_info</span><span class="p">,</span> <span class="n" style="color: #333;">primers</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="cpp"> <span class="p">}</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Amplicons detected: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp"> <span class="n" style="color: #333;">amplicons</span><span class="p">.</span><span class="n" style="color: #333;">inOrder</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()){</span></span>
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Bam file is empty."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="605" 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="607" 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">@@ -605,7 +607,10 @@ int trim_bam_qual_primer(std::string bam, std::string bed, std::string bam_out,</td>
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605
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607
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">unmapped_counter</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" unmapped reads were not written to file."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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606
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608
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<pre style="margin: 0;"> <span id="LC608" class="line" lang="cpp"> <span class="p">}</span></span>
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607
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609
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">amplicon_flag_ctr</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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608
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<pre style="margin: 0;">-<span id="LC608" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">amplicon_flag_ctr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" reads were ignored because they did not fall within an amplicon"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">round_int</span><span class="p">(</span><span class="n" style="color: #333;">amplicon_flag_ctr</span><span class="p">,</span> <span class="n" style="color: #333;">mapped</span><span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"% ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">amplicon_flag_ctr</span> </span>
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">") reads were ignored because they did not fall within an amplicon"</span> </span>
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC615" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">failed_frag_size</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC616" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">round_int</span><span class="p">(</span><span class="n" style="color: #333;">failed_frag_size</span><span class="p">,</span> <span class="n" style="color: #333;">mapped</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/ivar/-/commit/b02028a7de0247141fb9648bcd2e4e048363a38c#fdbb3539733405317eca774fe99c6ab1d8306beb"><strong>src/trim_primer_quality.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,7 +31,7 @@ inline void free_cigar(cigar_ t) { if (t.free_cig) free(t.cigar); }</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">add_pg_line_to_header</span><span class="p">(</span><span class="n" style="color: #333;">bam_hdr_t</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cmd</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">trim_bam_qual_primer</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bed</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam_out</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">region_</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">sliding_window</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">write_no_primer_reads</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">mark_qcfail_flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_length</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">pair_info</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">trim_bam_qual_primer</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bed</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam_out</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">region_</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">sliding_window</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">write_no_primer_reads</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">mark_qcfail_flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_length</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">pair_info</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">primer_offset</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">free_cigar</span><span class="p">(</span><span class="n" style="color: #333;">cigar_</span> <span class="n" style="color: #333;">t</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="nf" style="color: #900; font-weight: 600;">get_pos_on_query</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cigar</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">ncigar</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">ref_start</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="nf" style="color: #900; font-weight: 600;">get_pos_on_reference</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cigar</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">ncigar</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">ref_start</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,11 +5,11 @@</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "../src/primer_bed.h"</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "../src/interval_tree.h"</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">test_amplicon_search</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam_file</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bed_file</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">pair_info_file</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">expected</span><span class="p">[])</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">test_amplicon_search</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam_file</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bed_file</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">pair_info_file</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">primer_offset</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">expected</span><span class="p">[])</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">primers</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"> <span class="n" style="color: #333;">IntervalTree</span> <span class="n" style="color: #333;">amplicons</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="cpp"> <span class="n" style="color: #333;">primers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">populate_from_file</span><span class="p">(</span><span class="n" style="color: #333;">bed_file</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"> <span class="n" style="color: #333;">primers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">populate_from_file</span><span class="p">(</span><span class="n" style="color: #333;">bed_file</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">primer_offset</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Total Number of primers: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">primers</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"> <span class="n" style="color: #333;">amplicons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">populate_amplicons</span><span class="p">(</span><span class="n" style="color: #333;">pair_info_file</span><span class="p">,</span> <span class="n" style="color: #333;">primers</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"> <span class="n" style="color: #333;">samFile</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hts_open</span><span class="p">(</span><span class="n" style="color: #333;">bam_file</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,13 +35,14 @@ int main(){</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">success</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"../data/test_amplicon.sorted.bam"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">pair_indice</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"../data/pair_info_2.tsv"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">primer_offset</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="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bed</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"../data/test_isize.bed"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"/tmp/data/trim_amplicon"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"/tmp/trim_amplicon.bam"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">IntervalTree</span> <span class="n" style="color: #333;">amplicons</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">expected</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">test_amplicon_search</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">bed</span><span class="p">,</span> <span class="n" style="color: #333;">pair_indice</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">test_amplicon_search</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">bed</span><span class="p">,</span> <span class="n" style="color: #333;">pair_indice</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">primer_offset</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">expected</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"> <span class="n" style="color: #333;">amplicons</span><span class="p">.</span><span class="n" style="color: #333;">inOrder</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">success</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ivar/-/commit/b02028a7de0247141fb9648bcd2e4e048363a38c#5b33689eb2b190a723341547830d23181ca6d242"><strong>tests/test_interval_tree.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,7 @@ int test_itree_overlap(IntervalTree tree, Interval queries[], int num_tests, boo</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">result</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="LC8" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</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;">num_tests</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="LC9" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">overla</span>pSearch</span><span class="p">(</span><span class="n" style="color: #333;">queries</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="LC10" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">envelo</span>pSearch</span><span class="p">(</span><span class="n" style="color: #333;">queries</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="LC11" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">expected</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Interval Tree overlap behavior incorrect for interval "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">queries</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">low</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">queries</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">high</span> </span>
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<a href="https://salsa.debian.org/med-team/ivar/-/commit/b02028a7de0247141fb9648bcd2e4e048363a38c#461dd163e8fdef342b3dcb28bba477068047700f"><strong>tests/test_isize_trim.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,6 +21,7 @@ int test_isize_trim(uint8_t min_qual, uint8_t sliding_window, bool no_write_flag</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"../data/test_isize.sorted.bam"</span><span class="p">;</span></span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bed</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"../data/test_isize.bed"</span><span class="p">;</span></span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">pair_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">primer_offset</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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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"../data/trim_isize"</span><span class="p">;</span></span>
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"../data/trim_isize.bam"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="30" 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">@@ -29,7 +30,7 @@ int test_isize_trim(uint8_t min_qual, uint8_t sliding_window, bool no_write_flag</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"@PG</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ID:ivar-trim</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">PN:ivar</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">VN:1.0.0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">CL:ivar trim</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Test and check result</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trim_bam_qual_primer</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">bed</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">region_</span><span class="p">,</span> <span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="n" style="color: #333;">sliding_window</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">no_write_flag</span><span class="p">,</span> <span class="n" style="color: #333;">keep_for_reanalysis</span><span class="p">,</span> <span class="n" style="color: #333;">min_length</span><span class="p">,</span> <span class="n" style="color: #333;">pair_info</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trim_bam_qual_primer</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">bed</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">region_</span><span class="p">,</span> <span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="n" style="color: #333;">sliding_window</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">no_write_flag</span><span class="p">,</span> <span class="n" style="color: #333;">keep_for_reanalysis</span><span class="p">,</span> <span class="n" style="color: #333;">min_length</span><span class="p">,</span> <span class="n" style="color: #333;">pair_info</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">primer_offset</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">res</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/ivar/-/commit/b02028a7de0247141fb9648bcd2e4e048363a38c#bc53edf1aafd372a6a2ab1583c4dce2eb60702a7"><strong>tests/test_primer_trim_edge_cases.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,8 @@</td>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(){</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"../data/primer_only/primer_edge_cases.bam"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">primers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">populate_from_file</span><span class="p">(</span><span class="s" style="color: #d14;">"../data/test.bed"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">primer_offset</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="LC8" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">primers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">populate_from_file</span><span class="p">(</span><span class="s" style="color: #d14;">"../data/test.bed"</span><span class="p">,</span> <span class="n" style="color: #333;">primer_offset</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_primer_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"> <span class="n" style="color: #333;">max_primer_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_bigger_primer</span><span class="p">(</span><span class="n" style="color: #333;">primers</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">region_</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/ivar/-/commit/b02028a7de0247141fb9648bcd2e4e048363a38c#72cf1548681e3cd27df54db6d2a928d482a578e9"><strong>tests/test_trim.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,6 +21,7 @@ int test_trim(uint8_t min_qual, uint8_t sliding_window, bool no_write_flag, bool</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"../data/test.unmapped.sorted.bam"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bed</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"../data/test.bed"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">pair_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">primer_offset</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="LC25" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"/tmp/trim"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bam_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"/tmp/trim.bam"</span><span class="p">;</span></span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="29" 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">@@ -28,7 +29,7 @@ int test_trim(uint8_t min_qual, uint8_t sliding_window, bool no_write_flag, bool</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"@PG</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ID:ivar-trim</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">PN:ivar</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">VN:1.0.0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">CL:ivar trim</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Test and check result</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trim_bam_qual_primer</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">bed</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">region_</span><span class="p">,</span> <span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="n" style="color: #333;">sliding_window</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">no_write_flag</span><span class="p">,</span> <span class="n" style="color: #333;">keep_for_reanalysis</span><span class="p">,</span> <span class="n" style="color: #333;">min_length</span><span class="p">,</span> <span class="n" style="color: #333;">pair_info</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trim_bam_qual_primer</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">bed</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">region_</span><span class="p">,</span> <span class="n" style="color: #333;">min_qual</span><span class="p">,</span> <span class="n" style="color: #333;">sliding_window</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">no_write_flag</span><span class="p">,</span> <span class="n" style="color: #333;">keep_for_reanalysis</span><span class="p">,</span> <span class="n" style="color: #333;">min_length</span><span class="p">,</span> <span class="n" style="color: #333;">pair_info</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">primer_offset</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">res</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">testname</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" failed: trim_bam_qual_primer() returned "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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