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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/tiddit">Debian Med / tiddit</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/tiddit/-/commit/5573c4550fe1b5ff049305fdc12a9d08c59d4f52">5573c455</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-16T22:08:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.12.0+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tiddit/-/commit/896a7e4a15cd3fbfee2aeb1fe6484d08e998dbf0">896a7e4a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-16T22:08:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tiddit/-/commit/046921cc9230c85db9670671f0bfc8d574b07acf">046921cc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-16T22:08:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.12.0+dfsg'
Update to upstream version '2.12.0+dfsg'
with Debian dir 7233100093e735edf5ac12edfbf1a0a5dcdcb67e</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tiddit/-/commit/0ceaa361906cd8c7615990e541b8efb954b285f4">0ceaa361</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-16T22:08:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tiddit/-/commit/1dcbe52e4fd1d95379e96cfd06d18cd7ac7b0271">1dcbe52e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-16T22:08:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Rules-Requires-Root: no
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tiddit/-/commit/9882d404b687b95e8ffa29949dff7b43f277c6d1">9882d404</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-16T22:08:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tiddit/-/commit/8418e3259546b3928f4153b9849ac62a3b5518c1">8418e325</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-16T22:10:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#2ff2722d014ed036cd63fac102a8a8d03276bc4e">
TIDDIT.py
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
<li class="file-stats">
<a href="#b6c83ca2a4ea6b793cb00a89dd01be5a17651ec0">
src/TIDDIT.cpp
</a>
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<li class="file-stats">
<a href="#0eb83d3bb09da0f0f44274fc9c6d44af4c341470">
src/TIDDIT_calling.py
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<li class="file-stats">
<a href="#a7f6feec36e34dfb90c2cb7e6839db13d5541a78">
src/TIDDIT_coverage.py
</a>
</li>
<li class="file-stats">
<a href="#0ba5da9960f61279893d66005ef6974b3bacfe82">
<span class="new-file">
+
versioned_singularity/TIDDIT.2.12.0
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</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="2ff2722d014ed036cd63fac102a8a8d03276bc4e">
<a href="https://salsa.debian.org/med-team/tiddit/-/compare/5c956ccf3bc42619eba486b8db871781570e0601...8418e3259546b3928f4153b9849ac62a3b5518c1#2ff2722d014ed036cd63fac102a8a8d03276bc4e"><strong>TIDDIT.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" 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">@@ -8,7 +8,7 @@ wd=os.path.dirname(os.path.realpath(__file__))</td>
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<td class="diff-line-num old_line" data-linenumber="8" 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">
8
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<td class="diff-line-num new_line" data-linenumber="8" 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">
8
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">'{}/src/'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">wd</span><span class="p">))</span></span>
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<td class="diff-line-num old_line" data-linenumber="9" 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">
9
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<td class="diff-line-num new_line" data-linenumber="9" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">TIDDIT_calling</span></span>
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<td class="diff-line-num old_line" data-linenumber="10" 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">
10
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<td class="diff-line-num new_line" data-linenumber="10" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="11" 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">
11
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<td class="diff-line-num new_line old" data-linenumber="11" 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="LC11" 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;">"2.1<span class="idiff left right">1</span>.0"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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">
11
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<pre style="margin: 0;">+<span id="LC11" 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;">"2.1<span class="idiff left right">2</span>.0"</span></span>
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<td class="diff-line-num old_line" data-linenumber="12" 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">
12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="s" style="color: #d14;">"""TIDDIT-{}"""</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="p">),</span><span class="n" style="color: #333;">add_help</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="13" 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">
13
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13
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<pre style="margin: 0;"> <span id="LC13" 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;">'--sv'</span> <span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"call structural variation"</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="14" 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="LC14" 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;">'--cov'</span> <span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"generate a coverage bed file"</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/tiddit/-/compare/5c956ccf3bc42619eba486b8db871781570e0601...8418e3259546b3928f4153b9849ac62a3b5518c1#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">tiddit (2.12.0+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Repository-Browse.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 16 Jun 2020 22:08:57 +0200</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext">tiddit (2.11.0+dfsg-1) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="12" 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="LC12" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> * Initial release (Closes: #961659)</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/tiddit/-/compare/5c956ccf3bc42619eba486b8db871781570e0601...8418e3259546b3928f4153b9849ac62a3b5518c1#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" 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">@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> cmake,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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<td class="diff-line-num new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> cython3,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" 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">@@ -14,6 +14,7 @@ Standards-Version: 4.5.0</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/tiddit</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/tiddit.git</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Homepage: https://github.com/SciLifeLab/TIDDIT</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Package: tiddit</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Architecture: any</span>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/tiddit/-/compare/5c956ccf3bc42619eba486b8db871781570e0601...8418e3259546b3928f4153b9849ac62a3b5518c1#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Bug-Database: https://github.com/SciLifeLab/TIDDIT/issues</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Bug-Submit: https://github.com/SciLifeLab/TIDDIT/issues/new</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Registry:</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Entry: tiddit</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Repository: https://github.com/SciLifeLab/TIDDIT.git</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Repository-Browse: https://github.com/SciLifeLab/TIDDIT</span></pre>
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<li id="b6c83ca2a4ea6b793cb00a89dd01be5a17651ec0">
<a href="https://salsa.debian.org/med-team/tiddit/-/compare/5c956ccf3bc42619eba486b8db871781570e0601...8418e3259546b3928f4153b9849ac62a3b5518c1#b6c83ca2a4ea6b793cb00a89dd01be5a17651ec0"><strong>src/TIDDIT.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,7 +46,7 @@ int main(int argc, char **argv) {</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_variant_size</span><span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100000000</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">outputFileHeader</span> <span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"output"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.1<span class="idiff left right">1</span>.0"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.1<span class="idiff left right">2</span>.0"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//collect all options as a vector</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">arguments</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">argc</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/tiddit/-/compare/5c956ccf3bc42619eba486b8db871781570e0601...8418e3259546b3928f4153b9849ac62a3b5518c1#0eb83d3bb09da0f0f44274fc9c6d44af4c341470"><strong>src/TIDDIT_calling.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">@@ -234,9 +234,21 @@ def cluster(args):</td>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">chrA</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">chromosomes</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">calls</span><span class="p">[</span><span class="n" style="color: #333;">chrA</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span><span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="p">(</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 class="n" style="color: #333;">chrA</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">signals_chrA</span><span class="o" style="font-weight: 600;">=</span><span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">signals</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span> <span class="p">[</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">],</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">],</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">],</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">],</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">hit</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span><span class="s" style="color: #d14;">'SELECT chrB,posA,posB,forwardA,qualA,forwardB,qualB,resolution,name FROM TIDDITcall WHERE chrA == </span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\'</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 class="n" style="color: #333;">chrA</span><span class="p">)).</span><span class="n" style="color: #333;">fetchall</span><span class="p">()]</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">chrB</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">chromosomes</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">signal_data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span> <span class="p">[</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">],</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">],</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">],</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">hit</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span><span class="s" style="color: #d14;">'SELECT posA,posB,forwardA,qualA,forwardB,qualB,resolution,name FROM TIDDITcall WHERE chrA == </span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;"> AND chrB == </span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\'</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 class="n" style="color: #333;">chrA</span><span class="p">,</span><span class="n" style="color: #333;">chrB</span><span class="p">)).</span><span class="n" style="color: #333;">fetchall</span><span class="p">()])</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">chrB</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">signals_chrA</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">signals_chrA</span><span class="p">[</span><span class="n" style="color: #333;">chrB</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">signal</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">signals</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="n" style="color: #333;">signals_chrA</span><span class="p">[</span><span class="n" style="color: #333;">signal</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]].</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">signal</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="LC246" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">chrB</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">signals_chrA</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">signals_chrA</span><span class="p">[</span><span class="n" style="color: #333;">chrB</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">signals_chrA</span><span class="p">[</span><span class="n" style="color: #333;">chrB</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">chrB</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">chromosomes</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">signal_data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">signals_chrA</span><span class="p">[</span><span class="n" style="color: #333;">chrB</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">signal_data</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="python"></span>
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<li id="a7f6feec36e34dfb90c2cb7e6839db13d5541a78">
<a href="https://salsa.debian.org/med-team/tiddit/-/compare/5c956ccf3bc42619eba486b8db871781570e0601...8418e3259546b3928f4153b9849ac62a3b5518c1#a7f6feec36e34dfb90c2cb7e6839db13d5541a78"><strong>src/TIDDIT_coverage.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">@@ -88,7 +88,7 @@ def determine_ploidy(args,chromosomes,coverage_data,Ncontent,library_stats):</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="p">(</span><span class="s" style="color: #d14;">"make sure that the contigs of the bam file and the reference match"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">quit</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"></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="nb" style="color: #0086b3;"><span class="idiff left">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">cov</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;"><span class="idiff left">cov</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">size</span></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;">coverage_norm</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">median</span><span class="p">(</span><span class="n" style="color: #333;">cov</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;">else</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;">coverage_norm</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="107" 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">@@ -107,7 +107,11 @@ def determine_ploidy(args,chromosomes,coverage_data,Ncontent,library_stats):</td>
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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;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">cov</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">coverage_data</span><span class="p">[</span><span class="n" style="color: #333;">chromosome</span><span class="p">][</span><span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">where</span><span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">coverage_data</span><span class="p">[</span><span class="n" style="color: #333;">chromosome</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">Q</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">coverage_data</span><span class="p">[</span><span class="n" style="color: #333;">chromosome</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;">0</span><span class="p">)</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="LC109" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">chromosomal_average</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">median</span><span class="p">(</span><span class="n" style="color: #333;">cov</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cov</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">chromosomal_average</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">median</span><span class="p">(</span><span class="n" style="color: #333;">cov</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC112" 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="LC113" class="line" lang="python"> <span class="n" style="color: #333;">chromosomal_average</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="LC114" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">force_ploidy</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC116" 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="LC117" class="line" lang="python"> <span class="n" style="color: #333;">ploidies</span><span class="p">[</span><span class="n" style="color: #333;">chromosome</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="nb" style="color: #0086b3;">round</span><span class="p">((</span><span class="n" style="color: #333;">chromosomal_average</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">coverage_norm</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;">n</span><span class="p">))</span></span>
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<li id="0ba5da9960f61279893d66005ef6974b3bacfe82">
<a href="https://salsa.debian.org/med-team/tiddit/-/compare/5c956ccf3bc42619eba486b8db871781570e0601...8418e3259546b3928f4153b9849ac62a3b5518c1#0ba5da9960f61279893d66005ef6974b3bacfe82"><strong>versioned_singularity/TIDDIT.2.12.0</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">BootStrap: debootstrap</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">OSVersion: trusty</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">MirrorURL: http://us.archive.ubuntu.com/ubuntu/</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">%runscript</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> echo "This is what happens when you run the container..."</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">%post</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> echo "Hello from inside the container"</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> sed -i 's/$/ universe/' /etc/apt/sources.list</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> apt-get update</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> apt-get -y --force-yes install build-essential cmake make zlib1g-dev python python-dev python-setuptools git wget libbz2-dev unzip</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> easy_install pip</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> pip install numpy cython</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> wget https://github.com/SciLifeLab/TIDDIT/archive/TIDDIT-2.12.0.zip</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> unzip TIDDIT-2.12.0.zip</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> mv TIDDIT-TIDDIT-2.12.0/* /bin/</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> cd /bin/ && ./INSTALL.sh</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> chmod +x /bin/TIDDIT.py</span></pre>
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