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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/lumpy-sv">Debian Med / lumpy-sv</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/lumpy-sv/-/commit/8c3bee8abe76155dbbed1ededd0cc945bdaa44bf">8c3bee8a</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-09-18T19:02:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.3.1+dfsg</pre>
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<h4>5 changed files:</h4>
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<a href="#b0053d00d366a7a3c8ad6c0eeb248600d3a88cd7">
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−
data/pe.pos_sorted.bam
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<a href="#9c96e881a2ac3c7486ee97d687168a454098b653">
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−
data/sr.pos_sorted.bam
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<li class="file-stats">
<a href="#084853be9f0fe263435529d2d13c02427128e50c">
src/filter/filter.c
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<li class="file-stats">
<a href="#33430d3fc42f8abdbd2755ab0890ebdcb2527daa">
src/lumpy/SV_Pair.cpp
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<li class="file-stats">
<a href="#23b693086b64e38af877f1bfe39755c3b9896d13">
src/lumpy/SV_Pair.h
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<h4>Changes:</h4>
<li id="b0053d00d366a7a3c8ad6c0eeb248600d3a88cd7">
<a href="https://salsa.debian.org/med-team/lumpy-sv/-/commit/8c3bee8abe76155dbbed1ededd0cc945bdaa44bf#b0053d00d366a7a3c8ad6c0eeb248600d3a88cd7"><strong>data/pe.pos_sorted.bam</strong>
deleted
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No preview for this file type
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<li id="9c96e881a2ac3c7486ee97d687168a454098b653">
<a href="https://salsa.debian.org/med-team/lumpy-sv/-/commit/8c3bee8abe76155dbbed1ededd0cc945bdaa44bf#9c96e881a2ac3c7486ee97d687168a454098b653"><strong>data/sr.pos_sorted.bam</strong>
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No preview for this file type
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</li>
<li id="084853be9f0fe263435529d2d13c02427128e50c">
<a href="https://salsa.debian.org/med-team/lumpy-sv/-/commit/8c3bee8abe76155dbbed1ededd0cc945bdaa44bf#084853be9f0fe263435529d2d13c02427128e50c"><strong>src/filter/filter.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="375" 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="375" 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">@@ -375,4 +375,5 @@ int main(int argc, char **argv)</td>
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375
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375
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;"><</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="376" 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">
376
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="c"> <span class="n" style="color: #333;">errx</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"lumpy_filter: error reading bam: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">bam_file_name</span><span class="p">);</span></span>
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377
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377
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="378" 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">
378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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378
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="c"><span class="p">}</span></span></pre>
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<li id="33430d3fc42f8abdbd2755ab0890ebdcb2527daa">
<a href="https://salsa.debian.org/med-team/lumpy-sv/-/commit/8c3bee8abe76155dbbed1ededd0cc945bdaa44bf#33430d3fc42f8abdbd2755ab0890ebdcb2527daa"><strong>src/lumpy/SV_Pair.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="52" 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">@@ -52,6 +52,8 @@ SV_Pair(const BamAlignment &bam_a,</td>
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52
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num old_line" data-linenumber="53" 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">
53
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<td class="diff-line-num new_line" data-linenumber="53" 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">
53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"> <span class="n" style="color: #333;">min_mapping_quality</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_b</span><span class="p">.</span><span class="n" style="color: #333;">MapQuality</span><span class="p">;</span></span>
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54
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"> <span class="n" style="color: #333;">read_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_a</span><span class="p">.</span><span class="n" style="color: #333;">Name</span><span class="p">;</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"></span>
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55
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">interval</span> <span class="n" style="color: #333;">tmp_a</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_b</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_a</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_a</span><span class="p">.</span><span class="n" style="color: #333;">Position</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_a</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_a</span><span class="p">.</span><span class="n" style="color: #333;">GetEndPosition</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="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 new_line" data-linenumber="343" 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">@@ -341,6 +343,7 @@ void</td>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp"><span class="n" style="color: #333;">SV_Pair</span><span class="o" style="font-weight: 600;">::</span></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp"><span class="n" style="color: #333;">print_evidence</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">read_id</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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344
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp"> <span class="n" style="color: #333;">print_bedpe</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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345
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348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp"><span class="p">}</span></span>
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346
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<td class="diff-line-num new_line" data-linenumber="349" 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">
349
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//}}}</span></span>
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<li id="23b693086b64e38af877f1bfe39755c3b9896d13">
<a href="https://salsa.debian.org/med-team/lumpy-sv/-/commit/8c3bee8abe76155dbbed1ededd0cc945bdaa44bf#23b693086b64e38af877f1bfe39755c3b9896d13"><strong>src/lumpy/SV_Pair.h</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="61" 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">@@ -61,6 +61,7 @@ class SV_Pair: public SV_Evidence</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">interval</span> <span class="n" style="color: #333;">read_r</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">read_l_is_split</span><span class="p">,</span> <span class="n" style="color: #333;">read_r_is_split</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">SV_PairReader</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">reader</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC64" 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;">read_id</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">SV_Pair</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BamAlignment</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bam_a</span><span class="p">,</span></span>
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