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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/cutesv">Debian Med / cutesv</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/cutesv/-/commit/58057786f4b4dd1c2102b3a611dbb41bdec71b51">58057786</a></strong>
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<span>by Andreas Tille</span>
<i>at 2021-11-17T07:31:24+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.0.12</pre>
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<h4>8 changed files:</h4>
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<li class="file-stats">
<a href="#cb30988f5740390a8481d0862a77255382f1d282">
src/cuteSV/cuteSV
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<li class="file-stats">
<a href="#0bfe092743cea5d3af11da6c04f08751874e443f">
src/cuteSV/cuteSV_Description.py
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<li class="file-stats">
<a href="#3e70135aa8ed111ed0bb0f64d67a620219fa0100">
src/cuteSV/cuteSV_forcecalling.py
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<li class="file-stats">
<a href="#574314691821c0c231aebc23a73fca28c1520c68">
src/cuteSV/cuteSV_genotype.py
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<li class="file-stats">
<a href="#21e41c4b12487369c1b0785837e5645eef3dd2fd">
src/cuteSV/cuteSV_resolveDUP.py
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<li class="file-stats">
<a href="#5036d93aa7e220983c82369e2f61f864da66b9a8">
src/cuteSV/cuteSV_resolveINV.py
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<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/cutesv/-/commit/58057786f4b4dd1c2102b3a611dbb41bdec71b51#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="91" 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="91" 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">@@ -91,7 +91,7 @@ A new wiki page about diploid-assembly-based SV detection using cuteSV has been</td>
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<td class="old_line diff-line-num" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="markdown">|--merge_ins_threshold|Maximum distance of insertion signals to be merged.|100|</span>
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<td class="old_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="markdown">|--min_support|Minimum number of reads that support a SV to be reported.|10|</span>
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<td class="old_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="markdown">|--min_size|Minimum length of SV to be reported.|30|</span>
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<td class="old_line diff-line-num old" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="markdown">|--max_size|M<span class="idiff left">in</span>imum <span class="idiff right">length</span> of SV to be reported.|100000|</span>
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<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="markdown">|--max_size|M<span class="idiff left">ax</span>imum <span class="idiff">size</span> of SV to be reported.<span class="idiff right"> Full length SVs are reported when using -1.</span>|100000|</span>
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<td class="old_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="markdown">|--genotype|Enable to generate genotypes.|False|</span>
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<td class="old_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="markdown">|--gt_round|Maximum round of iteration for alignments searching if perform genotyping.|500|</span>
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<td class="old_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="markdown">|-Ivcf|Optional given vcf file. Enable to perform force calling.|NULL|</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="116" 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="116" 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">@@ -116,7 +116,12 @@ Please cite the manuscript of cuteSV before using these callsets.</td>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="markdown"><span class="p">---</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Changelog</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="markdown"><span class="sb" style="color: #d14;"> cutesv (v1.0.11):</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="markdown"><span class="sb" style="color: #d14;"> cuteSV (v1.0.12):</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 1. Add Allele frequency (AF) info in the outputs.</span></span>
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<td class="old_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 2. Fix an index error when force calling BND variants.</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 3. Modify the parameter of --max_size and enable to report full length of SVs.</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="markdown"><span class="sb" style="color: #d14;"> cuteSV (v1.0.11):</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 1. Add a script for post-processing typically cuteSV callsets from assembly-based alignments to generate the diploid-assembly-based SV calls.</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 2. Give a wiki page for helping uses to achieve assembly-based SV calling.</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 3. Improve acquirement of inserted sequence in a read whose primary alignment contains hardclips.</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">@@ -126,13 +131,13 @@ Please cite the manuscript of cuteSV before using these callsets.</td>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 7. Update the sort commands used in cuteSV. </span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 8. Update the parameter of --max_split_parts.</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="markdown"><span class="sb" style="color: #d14;"> cute<span class="idiff left right">sv</span> (v1.0.10):</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="markdown"><span class="sb" style="color: #d14;"> cute<span class="idiff left right">SV</span> (v1.0.10):</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 1. Fix a bug leading to calculate wrong TRA positions.</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 2. Add a file format conversion script that enable to transfer the vcf file to bedpe file. </span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 3. Involve several clustering-and-refinement strategies in force calling function.</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 4. Assessed the performance of force calling with Giab HG002 sample datasets (including CLR, CCS, and ONT platforms).</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="markdown"><span class="sb" style="color: #d14;"> cute<span class="idiff left right">sv</span> (v1.0.9):</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="markdown"><span class="sb" style="color: #d14;"> cute<span class="idiff left right">SV</span> (v1.0.9):</span></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 1. Change 0-based pos into 1-based pos in DUP in order to support bcftools conversion.</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 2. Correct REF and ALT fields. Adjust END value of INS to make it equal to the value of POS.</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 3. Improve the description of errors.</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -142,7 +147,7 @@ Please cite the manuscript of cuteSV before using these callsets.</td>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 7. Add force calling function and enable cuteSV to perform population-based SV calling.</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 8. Fix several minor bugs.</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="markdown"><span class="sb" style="color: #d14;"> cute<span class="idiff left right">sv</span> (v1.0.8):</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="markdown"><span class="sb" style="color: #d14;"> cute<span class="idiff left right">SV</span> (v1.0.8):</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 1. Rewirte the function of ins/del signatures clustering.</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 2. Update the recommandation parameters for different sequencing datasets.</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 3. Replace <DEL>/<INS> with its variant allele sequence, which needs the reference genome sequence as input.</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">@@ -165,7 +170,6 @@ Please cite the manuscript of cuteSV before using these callsets.</td>
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 3.Fix bugs in inversion and translocation calling.</span></span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 4.Add new option for specificly setting the maximum size of SV to be discovered. The default value is 100,000 bp. </span></span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="markdown"><span class="sb" style="color: #d14;"> cuteSV (v1.0.4):</span></span>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 1.Add a new option for specificly setting the threshold of SV signals merging in the same read. The default parameter is 500 bp. You can reduce it for high-quality sequencing datasets like PacBio HiFi (CCS).</span></span>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 2.Make the genotyping function optional.</span></span>
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<a href="https://salsa.debian.org/med-team/cutesv/-/commit/58057786f4b4dd1c2102b3a611dbb41bdec71b51#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</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 @@ with open('README.md') as f:</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"cuteSV"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.0.1<span class="idiff left right">1</span>"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.0.1<span class="idiff left right">2</span>"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Long-read-based human genomic structural variation detection with cuteSV"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">author</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Jiang Tao"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">author_email</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"tjiang@hit.edu.cn"</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/cutesv/-/commit/58057786f4b4dd1c2102b3a611dbb41bdec71b51#cb30988f5740390a8481d0862a77255382f1d282"><strong>src/cuteSV/cuteSV</strong></a>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;"> * All rights Reserved, Designed By HIT-Bioinformatics </span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;"> * @Title: cuteSV </span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;"> * @author: tjiang</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;"> * @dat<span class="idiff left">a</span>: <span class="idiff">May 16</span>th 202<span class="idiff right">0</span></span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="s" style="color: #d14;"> * @version V1.0.1<span class="idiff left right">1</span></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;"> * @dat<span class="idiff left">e</span>: <span class="idiff">Oct 4</span>th 202<span class="idiff right">1</span></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="s" style="color: #d14;"> * @version V1.0.1<span class="idiff left right">2</span></span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">'''</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pysam</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">@@ -202,7 +202,7 @@ def analysis_split_read(split_read, SV_size, RLength, read_name, candidate, MaxS</td>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">candidate</span><span class="p">[</span><span class="s" style="color: #d14;">"INS"</span><span class="p">]:</span></span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">candidate</span><span class="p">[</span><span class="s" style="color: #d14;">"INS"</span><span class="p">][</span><span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ele_1</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">100</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ele_1</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ele_1</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">MaxSize</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ele_1</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">100</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ele_1</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ele_1</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">MaxSize</span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MaxSize</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">candidate</span><span class="p">[</span><span class="s" style="color: #d14;">"INS"</span><span class="p">][</span><span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]].</span><span class="n" style="color: #333;">append</span><span class="p">([(</span><span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ele_1</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> </span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ele_1</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ele_1</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="LC208" class="line" lang="python"> <span class="n" style="color: #333;">read_name</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -211,7 +211,7 @@ def analysis_split_read(split_read, SV_size, RLength, read_name, candidate, MaxS</td>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">candidate</span><span class="p">[</span><span class="s" style="color: #d14;">"DEL"</span><span class="p">]:</span></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">candidate</span><span class="p">[</span><span class="s" style="color: #d14;">"DEL"</span><span class="p">][</span><span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ele_1</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">100</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ele_1</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ele_1</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">MaxSize</span><span class="p">:</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ele_1</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">100</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ele_1</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ele_1</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">MaxSize</span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MaxSize</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">candidate</span><span class="p">[</span><span class="s" style="color: #d14;">"DEL"</span><span class="p">][</span><span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]].</span><span class="n" style="color: #333;">append</span><span class="p">([</span><span class="n" style="color: #333;">ele_1</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> </span>
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ele_1</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ele_1</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> </span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">read_name</span><span class="p">])</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -329,7 +329,7 @@ def analysis_split_read(split_read, SV_size, RLength, read_name, candidate, MaxS</td>
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329
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># print(ele_2)</span></span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="python"> <span class="n" style="color: #333;">dis_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ele_1</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span></span>
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331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="python"> <span class="n" style="color: #333;">dis_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ele_2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ele_1</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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332
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">dis_ref</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">100</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">dis_read</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">dis_ref</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">SV_size</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">dis_read</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">dis_ref</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">MaxSize</span><span class="p">:</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">dis_ref</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">100</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">dis_read</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">dis_ref</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">SV_size</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">dis_read</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">dis_ref</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">MaxSize</span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MaxSize</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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333
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># print(min(ele_2[2], ele_1[3]), dis_read - dis_ref, read_name)</span></span>
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334
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334
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ele_1</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">candidate</span><span class="p">[</span><span class="s" style="color: #d14;">'INS'</span><span class="p">]:</span></span>
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335
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335
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="python"> <span class="n" style="color: #333;">candidate</span><span class="p">[</span><span class="s" style="color: #d14;">'INS'</span><span class="p">][</span><span class="n" style="color: #333;">ele_1</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>
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<a href="https://salsa.debian.org/med-team/cutesv/-/commit/58057786f4b4dd1c2102b3a611dbb41bdec71b51#0bfe092743cea5d3af11da6c04f08751874e443f"><strong>src/cuteSV/cuteSV_Description.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,12 +2,12 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;"> * All rights Reserved, Designed By HIT-Bioinformatics </span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;"> * @Title: cuteSV_Description.py</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;"> * @author: tjiang</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;"> * @date: <span class="idiff left right">May 16</span>th 2021</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;"> * @version V1.0.1<span class="idiff left right">1</span></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;"> * @date: <span class="idiff left right">Oct 4</span>th 2021</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;"> * @version V1.0.1<span class="idiff left right">2</span></span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">'''</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"><span class="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1.0.1<span class="idiff left right">1</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1.0.1<span class="idiff left right">2</span>'</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">cuteSVdp</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"> <span class="s" style="color: #d14;">'''</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">@@ -63,7 +63,7 @@ def parseArgs(argv):</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"input"</span><span class="p">,</span> </span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"[BAM]"</span><span class="p">,</span> </span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> </span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Sorted .bam file f<span class="idiff left right">o</span>rm NGMLR or Minimap2."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Sorted .bam file fr<span class="idiff left right">o</span>m NGMLR or Minimap2."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"reference"</span><span class="p">,</span> </span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> </span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"The reference genome in fasta format."</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">@@ -134,7 +134,7 @@ def parseArgs(argv):</td>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">default</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">30</span><span class="p">,</span> </span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>
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136
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">GroupSVCluster</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-L'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--max_size'</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="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Maximum size of SV to be reported.[%(default)s]"</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="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Maximum size of SV to be reported.<span class="idiff left right"> All SVs are reported when using -1. </span>[%(default)s]"</span><span class="p">,</span> </span>
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138
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">default</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100000</span><span class="p">,</span> </span>
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139
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">GroupSVCluster</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-sl'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--min_siglength'</span><span class="p">,</span> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="271" 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="271" 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">@@ -271,6 +271,7 @@ def Generation_VCF_header(file, contiginfo, sample, argv):</td>
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271
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"##INFO=<ID=RE,Number=1,Type=Integer,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Number of read support this record</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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272
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"##INFO=<ID=STRAND,Number=A,Type=String,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"##INFO=<ID=RNAMES,Number=.,Type=String,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Supporting read names of SVs (comma separated)</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"##INFO=<ID=AF,Number=A,Type=Float,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Allele Frequency.</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"##FILTER=<ID=q5,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Quality below 5</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># FORMAT</span></span>
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276
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># file.write("\n")</span></span>
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<a href="https://salsa.debian.org/med-team/cutesv/-/commit/58057786f4b4dd1c2102b3a611dbb41bdec71b51#3e70135aa8ed111ed0bb0f64d67a620219fa0100"><strong>src/cuteSV/cuteSV_forcecalling.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="76" 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="76" 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">@@ -76,30 +76,40 @@ def parse_record(record):</td>
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76
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">sv_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_svtype</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">'SVTYPE'</span><span class="p">])</span></span>
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77
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">chrom1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">chrom</span></span>
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78
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_to_int</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">chrom2</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sv_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'INS'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">sv_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'DEL'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'SVLEN'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;">###</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">parse_to_int</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">'SVLEN'</span><span class="p">]))</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_to_int</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sv_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'TRA'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">tra_alt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">alts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tra_alt</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="s" style="color: #d14;">'N'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tra_alt</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'['</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">tra_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'A'</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'CHR2'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">chrom2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">'CHR2'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'END'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_to_int</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">'END'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">tra_alt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">alts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tra_alt</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="s" style="color: #d14;">'N'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tra_alt</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'['</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">tra_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'A'</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">tra_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'B'</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">tra_alt</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="s" style="color: #d14;">'['</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">tra_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'C'</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">tra_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'B'</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">tra_alt</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="s" style="color: #d14;">'['</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">tra_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'C'</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">tra_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'D'</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tra_alt</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="s" style="color: #d14;">'N'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">tra_alt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tra_alt</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">tra_alt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tra_alt</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">chrom2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tra_alt</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">':'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">tra_alt</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">':'</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="LC103" class="line" lang="python"> <span class="n" style="color: #333;">tra_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'D'</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tra_alt</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="s" style="color: #d14;">'N'</span><span class="p">:</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">tra_alt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tra_alt</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</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="python"> <span class="n" style="color: #333;">tra_alt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tra_alt</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</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="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">':'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tra_alt</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="python"> <span class="n" style="color: #333;">chrom2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tra_alt</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">':'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</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="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">tra_alt</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">':'</span><span class="p">)[</span><span class="mi" style="color: #099;">1</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="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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103
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.'</span></span>
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104
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sv_type</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'TRA'</span><span class="p">:</span></span>
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105
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">chrom2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">chrom</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="382" 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">@@ -372,6 +382,8 @@ def call(call_gt_args, idx, row_count, para, strands, seq, var_type):</td>
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372
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">var_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'TRA'</span><span class="p">:</span></span>
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373
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python"> <span class="n" style="color: #333;">gt_re</span><span class="p">,</span> <span class="n" style="color: #333;">DR</span><span class="p">,</span> <span class="n" style="color: #333;">genotype</span><span class="p">,</span> <span class="n" style="color: #333;">GL</span><span class="p">,</span> <span class="n" style="color: #333;">GQ</span><span class="p">,</span> <span class="n" style="color: #333;">QUAL</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">call_gt_tra</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">call_gt_args</span><span class="p">)</span></span>
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374
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="python"> <span class="n" style="color: #333;">rname_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">call_gt_args</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">para</span><span class="p">.</span><span class="n" style="color: #333;">alts</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'<TRA>'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">para</span><span class="p">.</span><span class="n" style="color: #333;">alts</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'<BND>'</span><span class="p">:</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">call_gt_args</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">':'</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">call_gt_args</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span> <span class="c1" style="color: #998; font-style: italic;"># chr2:end</span></span>
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375
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="python"> <span class="n" style="color: #333;">rname</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">','</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">rname_list</span><span class="p">)</span></span>
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376
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">rname</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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377
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="python"> <span class="n" style="color: #333;">rname</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'NULL'</span></span>
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<a href="https://salsa.debian.org/med-team/cutesv/-/commit/58057786f4b4dd1c2102b3a611dbb41bdec71b51#574314691821c0c231aebc23a73fca28c1520c68"><strong>src/cuteSV/cuteSV_genotype.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -101,11 +101,13 @@ def generate_output(args, semi_result, contigINFO, argv, ref_g):</td>
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101
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">svid</span><span class="p">[</span><span class="s" style="color: #d14;">"INV"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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102
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"></span>
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103
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">genotype</span></span>
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104
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">Generation_VCF_header</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">,</span> <span class="n" style="color: #333;">contigINFO</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">)</span></span>
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105
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#CHROM</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">POS</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ID</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">REF</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ALT</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">QUAL</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">FILTER</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">INFO</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">FORMAT</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</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="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sample</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"></span>
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107
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">semi_result</span><span class="p">:</span></span>
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108
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"DEL"</span><span class="p">,</span> <span class="s" style="color: #d14;">"INS"</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="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])))</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_size</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_size</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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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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109
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INS"</span><span class="p">:</span></span>
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110
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">cal_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -119,6 +121,11 @@ def generate_output(args, semi_result, contigINFO, argv, ref_g):</td>
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119
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">CILEN</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">6</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="python"> <span class="n" style="color: #333;">RE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">],</span></span>
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121
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">RNAMES</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">12</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">report_readid</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"NULL"</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="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">action</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="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="126" 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">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";AF="</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">])),</span> <span class="mi" style="color: #099;">4</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="python"> <span class="k" style="font-weight: 600;">except</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="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";AF=."</span></span>
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122
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"DEL"</span><span class="p">:</span></span>
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123
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";STRAND=+-"</span></span>
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124
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"."</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="142" 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="149" 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">@@ -142,6 +149,8 @@ def generate_output(args, semi_result, contigINFO, argv, ref_g):</td>
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142
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">PASS</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_lable</span><span class="p">))</span></span>
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143
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">svid</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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144
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"DUP"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="152" 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">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])))</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_size</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_size</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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<td class="new_line diff-line-num new" data-linenumber="153" 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">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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145
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">cal_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])))</span></span>
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146
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{PRECISION};SVTYPE={SVTYPE};SVLEN={SVLEN};END={END};RE={RE};STRAND=-+;RNAMES={RNAMES}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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147
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">PRECISION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"IMPRECISE"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"0/0"</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"PRECISE"</span><span class="p">,</span> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="159" 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">@@ -150,6 +159,11 @@ def generate_output(args, semi_result, contigINFO, argv, ref_g):</td>
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150
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">END</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cal_end</span><span class="p">),</span> </span>
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151
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">RE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">],</span></span>
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152
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">RNAMES</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">report_readid</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"NULL"</span><span class="p">)</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">action</span><span class="p">:</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="164" 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">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";AF="</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">])),</span> <span class="mi" style="color: #099;">4</span><span class="p">))</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";AF=."</span></span>
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153
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"."</span><span class="p">:</span></span>
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154
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">filter_lable</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"PASS"</span></span>
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155
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="171" 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="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -171,6 +185,8 @@ def generate_output(args, semi_result, contigINFO, argv, ref_g):</td>
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171
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">PASS</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_lable</span><span class="p">))</span></span>
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172
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">svid</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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173
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INV"</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="188" 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">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])))</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_size</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_size</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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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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174
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">cal_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])))</span></span>
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175
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{PRECISION};SVTYPE={SVTYPE};SVLEN={SVLEN};END={END};RE={RE};STRAND={STRAND};RNAMES={RNAMES}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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176
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">PRECISION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"IMPRECISE"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"0/0"</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"PRECISE"</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">@@ -180,6 +196,11 @@ def generate_output(args, semi_result, contigINFO, argv, ref_g):</td>
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180
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">RE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">],</span></span>
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181
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">STRAND</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">],</span></span>
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182
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">RNAMES</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">report_readid</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"NULL"</span><span class="p">)</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">action</span><span class="p">:</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";AF="</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">])),</span> <span class="mi" style="color: #099;">4</span><span class="p">))</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";AF=."</span></span>
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183
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"."</span><span class="p">:</span></span>
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184
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">filter_lable</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"PASS"</span></span>
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -210,6 +231,11 @@ def generate_output(args, semi_result, contigINFO, argv, ref_g):</td>
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210
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># END = str(int(i[4]) + 1), </span></span>
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232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">RE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">],</span></span>
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233
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python"> <span class="n" style="color: #333;">RNAMES</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">report_readid</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"NULL"</span><span class="p">)</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">action</span><span class="p">:</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";AF="</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">])</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">])),</span> <span class="mi" style="color: #099;">4</span><span class="p">))</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</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="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";AF=."</span></span>
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213
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239
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"."</span><span class="p">:</span></span>
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214
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240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">filter_lable</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"PASS"</span></span>
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215
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241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="244" 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">@@ -244,7 +270,7 @@ def generate_pvcf(args, result, contigINFO, argv, ref_g):</td>
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244
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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245
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<td class="new_line diff-line-num" data-linenumber="271" 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">
271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python"> <span class="n" style="color: #333;">filter_lable</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"PASS"</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">13</span><span class="p">])</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mf" style="color: #099;">5.0</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"q5"</span></span>
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246
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<td class="new_line diff-line-num" data-linenumber="272" 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">
272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'INS'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="247" 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">
247
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<td class="new_line diff-line-num old" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_size</span><span class="p">:</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_size</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">max_size</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">:</span></span>
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248
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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249
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">12</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'<INS>'</span><span class="p">:</span></span>
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250
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">ref_g</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]].</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)])</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="287" 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">@@ -261,6 +287,10 @@ def generate_pvcf(args, result, contigINFO, argv, ref_g):</td>
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261
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">CILEN</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">],</span> </span>
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262
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python"> <span class="n" style="color: #333;">RE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span></span>
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263
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="python"> <span class="n" style="color: #333;">RNAMES</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">report_readid</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"NULL"</span><span class="p">)</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";AF="</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="mi" style="color: #099;">4</span><span class="p">))</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";AF=."</span></span>
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"{CHR}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{POS}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{ID}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{REF}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{ALT}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{QUAL}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{PASS}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{INFO}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{FORMAT}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{GT}:{DR}:{RE}:{PL}:{GQ}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="python"> <span class="n" style="color: #333;">CHR</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> </span>
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266
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">POS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</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="278" 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="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -278,7 +308,7 @@ def generate_pvcf(args, result, contigINFO, argv, ref_g):</td>
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278
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="python"> <span class="n" style="color: #333;">GQ</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span></span>
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279
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309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="python"> <span class="p">))</span></span>
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280
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310
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'DEL'</span><span class="p">:</span></span>
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281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_size</span><span class="p">:</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_size</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">max_size</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">:</span></span>
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282
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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283
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313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">12</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'<DEL>'</span><span class="p">:</span></span>
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284
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314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">ref_g</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]].</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">):</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])])</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="325" 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">@@ -295,6 +325,10 @@ def generate_pvcf(args, result, contigINFO, argv, ref_g):</td>
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295
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325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python"> <span class="n" style="color: #333;">CILEN</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">],</span> </span>
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296
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326
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python"> <span class="n" style="color: #333;">RE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span></span>
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297
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327
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="python"> <span class="n" style="color: #333;">RNAMES</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">report_readid</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"NULL"</span><span class="p">)</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";AF="</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="mi" style="color: #099;">4</span><span class="p">))</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";AF=."</span></span>
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332
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"{CHR}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{POS}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{ID}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{REF}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{ALT}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{QUAL}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{PASS}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{INFO}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{FORMAT}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{GT}:{DR}:{RE}:{PL}:{GQ}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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333
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="python"> <span class="n" style="color: #333;">CHR</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> </span>
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300
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334
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python"> <span class="n" style="color: #333;">POS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</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="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -312,6 +346,8 @@ def generate_pvcf(args, result, contigINFO, argv, ref_g):</td>
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312
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346
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python"> <span class="n" style="color: #333;">GQ</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span></span>
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313
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python"> <span class="p">))</span></span>
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314
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348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'DUP'</span><span class="p">:</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_size</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_size</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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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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351
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{PRECISION};SVTYPE={SVTYPE};SVLEN={SVLEN};END={END};RE={RE};RNAMES={RNAMES};STRAND=-+"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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316
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352
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="python"> <span class="n" style="color: #333;">PRECISION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"IMPRECISE"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"0/0"</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"PRECISE"</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="python"> <span class="n" style="color: #333;">SVTYPE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="355" 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">@@ -319,6 +355,10 @@ def generate_pvcf(args, result, contigINFO, argv, ref_g):</td>
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319
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355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="python"> <span class="n" style="color: #333;">END</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">],</span> </span>
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320
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356
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="python"> <span class="n" style="color: #333;">RE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span></span>
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321
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357
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="python"> <span class="n" style="color: #333;">RNAMES</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">report_readid</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"NULL"</span><span class="p">)</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";AF="</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="mi" style="color: #099;">4</span><span class="p">))</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";AF=."</span></span>
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322
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362
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"{CHR}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{POS}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{ID}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{REF}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{ALT}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{QUAL}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{PASS}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{INFO}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{FORMAT}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{GT}:{DR}:{RE}:{PL}:{GQ}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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323
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363
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="python"> <span class="n" style="color: #333;">CHR</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> </span>
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324
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364
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="python"> <span class="n" style="color: #333;">POS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</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="336" 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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -336,6 +376,8 @@ def generate_pvcf(args, result, contigINFO, argv, ref_g):</td>
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336
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="python"> <span class="n" style="color: #333;">GQ</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span></span>
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337
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377
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="python"> <span class="p">))</span></span>
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338
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378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'INV'</span><span class="p">:</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_size</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_size</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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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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339
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{PRECISION};SVTYPE={SVTYPE};SVLEN={SVLEN};END={END};RE={RE};RNAMES={RNAMES};STRAND={STRAND}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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340
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">PRECISION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"IMPRECISE"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"0/0"</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"PRECISE"</span><span class="p">,</span> </span>
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341
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python"> <span class="n" style="color: #333;">SVTYPE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="386" 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">@@ -344,6 +386,10 @@ def generate_pvcf(args, result, contigINFO, argv, ref_g):</td>
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344
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="python"> <span class="n" style="color: #333;">RE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</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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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="python"> <span class="n" style="color: #333;">RNAMES</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">report_readid</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"NULL"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="python"> <span class="n" style="color: #333;">STRAND</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">14</span><span class="p">])</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";AF="</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="mi" style="color: #099;">4</span><span class="p">))</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";AF=."</span></span>
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347
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"{CHR}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{POS}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{ID}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{REF}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{ALT}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{QUAL}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{PASS}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{INFO}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{FORMAT}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{GT}:{DR}:{RE}:{PL}:{GQ}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="python"> <span class="n" style="color: #333;">CHR</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> </span>
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349
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python"> <span class="n" style="color: #333;">POS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</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="367" 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">@@ -367,6 +413,14 @@ def generate_pvcf(args, result, contigINFO, argv, ref_g):</td>
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413
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="python"> <span class="n" style="color: #333;">SVTYPE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> </span>
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414
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="python"> <span class="n" style="color: #333;">RE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span></span>
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369
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="python"> <span class="n" style="color: #333;">RNAMES</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">report_readid</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"NULL"</span><span class="p">)</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";AF="</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="mi" style="color: #099;">4</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";AF=."</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">':'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">15</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="python"> <span class="n" style="color: #333;">info_list</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";CHR2={CHR2};END={END}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="python"> <span class="n" style="color: #333;">CHR2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">15</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">':'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="python"> <span class="n" style="color: #333;">END</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">15</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">':'</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="LC424" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"{CHR}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{POS}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{ID}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{REF}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{ALT}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{QUAL}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{PASS}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{INFO}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{FORMAT}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{GT}:{DR}:{RE}:{PL}:{GQ}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="python"> <span class="n" style="color: #333;">CHR</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> </span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="python"> <span class="n" style="color: #333;">POS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</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/cutesv/-/commit/58057786f4b4dd1c2102b3a611dbb41bdec71b51#21e41c4b12487369c1b0785837e5645eef3dd2fd"><strong>src/cuteSV/cuteSV_resolveDUP.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="87" 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">@@ -87,7 +87,7 @@ def generate_dup_cluster(semi_dup_cluster, chr, read_count, max_cluster_bias,</td>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">breakpoint_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">breakpoint_2</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">semi_dup_cluster</span><span class="p">[</span><span class="n" style="color: #333;">low_b</span><span class="p">:</span><span class="n" style="color: #333;">up_b</span><span class="p">]))</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sv_size</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">breakpoint_2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">breakpoint_1</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">MaxSize</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sv_size</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">breakpoint_2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">breakpoint_1</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">MaxSize</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sv_size</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">breakpoint_2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">breakpoint_1</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MaxSize</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">action</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># time_start = time.time()</span></span>
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<a href="https://salsa.debian.org/med-team/cutesv/-/commit/58057786f4b4dd1c2102b3a611dbb41bdec71b51#5036d93aa7e220983c82369e2f61f864da66b9a8"><strong>src/cuteSV/cuteSV_resolveINV.py</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">@@ -121,7 +121,7 @@ def generate_semi_inv_cluster(semi_inv_cluster, chr, svtype, read_count, sv_size</td>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">inv_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">breakpoint_2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">breakpoint_1</span></span>
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">inv_len</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">sv_size</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">max_count_id</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">read_count</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># candidate_single_SV.append('%s\t%s\t%d\t%d\t%d\n'%(chr, svtype, breakpoint_1, breakpoint_2, max_count_id))</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">inv_len</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">MaxSize</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">inv_len</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">MaxSize</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MaxSize</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">action</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># time_start = time.time()</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="172" 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">@@ -172,7 +172,7 @@ def generate_semi_inv_cluster(semi_inv_cluster, chr, svtype, read_count, sv_size</td>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">inv_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">breakpoint_2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">breakpoint_1</span></span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">inv_len</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">sv_size</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">max_count_id</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">read_count</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># candidate_single_SV.append('%s\t%s\t%d\t%d\t%d\n'%(chr, svtype, breakpoint_1, breakpoint_2, max_count_id))</span></span>
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">inv_len</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">MaxSize</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">inv_len</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">MaxSize</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MaxSize</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">action</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</span></span>
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># time_start = time.time()</span></span>
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