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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/dnarrange">Debian Med / dnarrange</a>
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Commits:
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<strong><a href="https://salsa.debian.org/med-team/dnarrange/-/commit/09fd911da715779e655b168237444f4fb46daac0">09fd911d</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2022-05-30T22:00:25+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.5.2</pre>
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<h4>4 changed files:</h4>
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<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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dnarrange
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setup.py
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<h4>Changes:</h4>
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<a href="https://salsa.debian.org/med-team/dnarrange/-/commit/09fd911da715779e655b168237444f4fb46daac0#24139dae656713ba861751fb2c2ac38839349a7a"><strong>.gitattributes</strong>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">setup.py export-subst</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">tests/ export-ignore</span></pre></td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># dnarrange</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown">This is a method to find rearrangements in "long" DNA reads relative</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown">to a genome sequence.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown">to a genome sequence. It can characterize changes such as chromosome</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown">shattering, gene conversion, and processed pseudogene insertion. For</span>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown">more details, please see: <span class="p">[</span><span class="nv" style="color: #008080;">A pipeline for complete characterization of</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="nv" style="color: #008080;">complex germline rearrangements from long DNA reads</span><span class="p">][</span><span class="ss" style="color: #990073;">paper</span><span class="p">]</span>.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown">You can install dnarrange (together with all other software that it</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown">uses) from <span class="p">[</span><span class="nv" style="color: #008080;">Bioconda</span><span class="p">][]</span> or <span class="p">[</span><span class="nv" style="color: #008080;">Debian Med</span><span class="p">][]</span>.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Step 1: Align the reads to the genome</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="74" 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="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -74,8 +80,7 @@ it requires the latter to be</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC80" class="line" lang="markdown">This in turn requires the <span class="p">[</span><span class="nv" style="color: #008080;">Python Imaging</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC81" class="line" lang="markdown"><span class="nv" style="color: #008080;">Library</span><span class="p">](</span><span class="sx" style="color: #d14;">https://pillow.readthedocs.io/</span><span class="p">)</span> to be installed.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC82" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num old" data-linenumber="83" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC77" class="line" lang="markdown"><span class="p">*</span> A useful option is <span class="sb" style="color: #d14;">`--rmsk1`</span>, to show repeats, which often cause</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC78" class="line" lang="markdown"> rearrangements.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC83" class="line" lang="markdown"><span class="p">*</span> A useful option is <span class="sb" style="color: #d14;">`-a`</span>, to display files of genes, repeats, etc.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC85" class="line" lang="markdown">Tips for viewing the pictures on a Mac: open the folder in Finder, and</span>
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<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -91,6 +96,8 @@ of 2) reads per group:</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC96" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC97" class="line" lang="markdown"><span class="sb" style="color: #d14;"> dnarrange -s3 groups.maf > strict.maf</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC98" class="line" lang="markdown"></span>
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99
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**If the results are clear enough, you can stop here!**</span></span>
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100
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC100" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Step 4: Merge each group into a consensus sequence</span></span>
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102
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC102" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC103" class="line" lang="markdown"><span class="sb" style="color: #d14;"> dnarrange-merge reads.fq myseq.par groups.maf > merged.fa</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">@@ -265,13 +272,9 @@ genome more slowly-and-carefully (e.g. without repeat-masking).</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC272" class="line" lang="markdown">you can see them with <span class="sb" style="color: #d14;">`dnarrange-merge --help`</span>, and they're described</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC273" class="line" lang="markdown">at the [lamassemble] site.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC274" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC268" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Paper</span></span>
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269
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC269" class="line" lang="markdown"></span>
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270
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC270" class="line" lang="markdown">For more details, please see: <span class="p">[</span><span class="nv" style="color: #008080;">A pipeline for complete</span></span>
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271
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC271" class="line" lang="markdown"><span class="nv" style="color: #008080;">characterization of complex germline rearrangements from long DNA</span></span>
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272
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<td class="new_line diff-line-num old" data-linenumber="275" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC272" class="line" lang="markdown"><span class="nv" style="color: #008080;">reads</span><span class="p">][</span><span class="ss" style="color: #990073;">paper</span><span class="p">]</span> by S Mitsuhashi, S Ohori, et al.</span>
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273
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<td class="new_line diff-line-num old" data-linenumber="275" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC273" class="line" lang="markdown"></span>
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274
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC275" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">BED</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://genome.ucsc.edu/FAQ/FAQformat.html#format1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="276" 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">
276
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC276" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">Bioconda</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://bioconda.github.io/</span></span>
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<td class="new_line diff-line-num new" data-linenumber="277" 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">
277
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC277" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">Debian Med</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://www.debian.org/devel/debian-med/</span></span>
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275
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC278" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">MAFFT</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://mafft.cbrc.jp/alignment/software/</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC279" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">lamassemble</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://gitlab.com/mcfrith/lamassemble</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC280" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">paper</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://doi.org/10.1186/s13073-020-00762-1</span></span></pre></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">@@ -401,22 +401,17 @@ def sharedRearrangement(opts, types, alignmentsA, alignmentsB,</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC401" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC402" class="line" lang="python"> <span class="n" style="color: #333;">isRevAX</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnAX</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC403" class="line" lang="python"> <span class="n" style="color: #333;">isRevAY</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnAY</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC404" class="line" lang="python"> <span class="n" style="color: #333;">isUpstreamInQueryA</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">alnNumAX</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">alnNumAY</span><span class="p">)</span></span>
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405
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC404" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">alnNumBY</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alnNumsBY</span><span class="p">:</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC405" class="line" lang="python"> <span class="n" style="color: #333;">alnBY</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignmentsB</span><span class="p">[</span><span class="n" style="color: #333;">alnNumBY</span><span class="p">]</span></span>
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406
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC406" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">alnNumBX</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alnNumsBX</span><span class="p">:</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC407" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">alnNumBX</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">alnNumBY</span><span class="p">:</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC408" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC407" class="line" lang="python"> <span class="n" style="color: #333;">alnBX</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignmentsB</span><span class="p">[</span><span class="n" style="color: #333;">alnNumBX</span><span class="p">]</span></span>
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<td class="new_line diff-line-num old" data-linenumber="408" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC410" class="line" lang="python"> <span class="n" style="color: #333;">alnBY</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignmentsB</span><span class="p">[</span><span class="n" style="color: #333;">alnNumBY</span><span class="p">]</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC408" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">isRevAY</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">alnBY</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]:</span></span>
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<td class="new_line diff-line-num old" data-linenumber="409" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC412" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isRevAX</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">alnBX</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span></span>
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413
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC413" class="line" lang="python"> <span class="n" style="color: #333;">isUpstreamInQueryA</span> <span class="ow" style="font-weight: 600;">is</span> <span class="p">(</span><span class="n" style="color: #333;">alnNumBX</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">alnNumBY</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC409" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alnNumBX</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">alnNumBY</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">isRevAX</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">alnBX</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC410" class="line" lang="python"> <span class="n" style="color: #333;">isSharedRearrangement</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC411" class="line" lang="python"> <span class="n" style="color: #333;">alnAX</span><span class="p">,</span> <span class="n" style="color: #333;">alnAY</span><span class="p">,</span> <span class="n" style="color: #333;">alnBX</span><span class="p">,</span> <span class="n" style="color: #333;">alnBY</span><span class="p">)):</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC412" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"+"</span></span>
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413
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC413" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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418
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<td class="new_line diff-line-num old" data-linenumber="414" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC418" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isRevAX</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">alnBX</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span></span>
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419
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<td class="new_line diff-line-num old" data-linenumber="414" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC419" class="line" lang="python"> <span class="n" style="color: #333;">isUpstreamInQueryA</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333;">alnNumBX</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">alnNumBY</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span></span>
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<td class="new_line diff-line-num new" data-linenumber="414" 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">
414
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC414" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alnNumBX</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">alnNumBY</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">isRevAX</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">alnBX</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span></span>
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420
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415
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC415" class="line" lang="python"> <span class="n" style="color: #333;">isSharedRearrangement</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span></span>
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421
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416
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC416" class="line" lang="python"> <span class="n" style="color: #333;">alnAX</span><span class="p">,</span> <span class="n" style="color: #333;">alnAY</span><span class="p">,</span> <span class="n" style="color: #333;">alnBX</span><span class="p">,</span> <span class="n" style="color: #333;">alnBY</span><span class="p">)):</span></span>
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422
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417
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC417" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"-"</span></span>
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<a href="https://salsa.debian.org/med-team/dnarrange/-/commit/09fd911da715779e655b168237444f4fb46daac0#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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1
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">setuptools</span></span>
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2
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2
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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3
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">commitInfo</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (HEAD -> master, tag: 1.5.<span class="idiff left right deletion">1</span>)"</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">(</span><span class="s" style="color: #d14;">"( )"</span><span class="p">).</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">commitInfo</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (HEAD -> master, tag: 1.5.<span class="idiff left right addition">2</span>)"</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">(</span><span class="s" style="color: #d14;">"( )"</span><span class="p">).</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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4
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4
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">commitInfo</span><span class="p">[</span><span class="n" style="color: #333;">commitInfo</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="s" style="color: #d14;">"tag:"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span></span>
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5
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5
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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6
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6
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">setuptools</span><span class="p">.</span><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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