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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/seqmagick">Debian Med / seqmagick</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqmagick/-/commit/d34b51cc1e956d78bc1de7d0d4d2d439cf482618">d34b51cc</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-16T20:27:44+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Encode for adding support to utf-8
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqmagick/-/commit/795200d3ac6a9aa7408d23d35a6d7a7ad534308f">795200d3</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-16T20:30:36+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Replcae Bio.trie with pygtrie
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqmagick/-/commit/22654021b817cddf8870337bd018ab1a04da3c48">22654021</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-16T20:30:50+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update Depends
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqmagick/-/commit/1cb6f30d06c405f02619e07e82b10246c88480ce">1cb6f30d</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-16T20:32:50+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqmagick/-/commit/ebad370334640b4fb3fee27c605a95fb6ec0d561">ebad3703</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-16T20:43:53+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix manpage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqmagick/-/commit/430238731025a5cedd970e3e33d214777c753f2a">43023873</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-16T20:44:29+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqmagick/-/commit/79c713cb5f58b18e1b590f649e45443ef391351d">79c713cb</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-16T20:45:06+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqmagick/-/commit/006fc2ddef5edfa9ae9d45d6444fa49a38c5c71b">006fc2dd</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-16T20:45:06+05:30</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/seqmagick/-/commit/39ce5de0e67f18cec4b483fb785e061c05af56c1">39ce5de0</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-16T20:45:30+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqmagick/-/commit/3dc2f74e2a541c0ab64a8ea77f885ae08aff4cdf">3dc2f74e</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-16T20:45:31+05:30</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/seqmagick/-/commit/e1d5a7e31df79d7d068bac7ec502ca4ef5ceb49d">e1d5a7e3</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-16T20:45:49+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
Changes-By: lintian-brush
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>
</ul>
<h4>10 changed files:</h4>
<ul>
<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="#490a82a2fa527c129de4e49174e3ee693da72117">
<span class="new-file">
+
debian/patches/fix-myfunctions-example-file.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#0ddc2310a98e93221ce234f9be58d879d176994a">
<span class="new-file">
+
debian/patches/replace-biopython-trie-with-pygtrie.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
<span class="new-file">
+
debian/salsa-ci.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#eebd58f645086af566297cb3d59c9fa7b409ce14">
debian/seqmagick.1
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
</span>
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
</span>
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/9179005c3920850ee3759fcac0cbbe4e57098829...e1d5a7e31df79d7d068bac7ec502ca4ef5ceb49d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="plaintext">seqmagick (0.8.0-2) UNRELEASED; urgency=medium</span>
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<td class="diff-line-num new new_line" data-linenumber="2" 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">
2
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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="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> [ Steffen Moeller ]</span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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">
4
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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="plaintext"> * Remove autogenerated version string and egg-info</span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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">
5
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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="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" 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">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> [ Nilesh Patra ]</span>
</pre>
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<td class="diff-line-num new new_line" 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="plaintext"> * Encode for adding support to utf-8</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> * Replcae Bio.trie with pygtrie</span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> * Update Depends</span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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="LC10" class="line" lang="plaintext"> * Add autopkgtests</span>
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<td class="diff-line-num new old_line" data-linenumber="1" 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="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">
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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="LC11" class="line" lang="plaintext"> * Fix manpage</span>
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<td class="diff-line-num new new_line" data-linenumber="12" 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="LC12" class="line" lang="plaintext"> * Standards-Version: 4.5.0 (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext"> * Add salsa-ci file (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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="LC15" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="16" 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="LC16" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> Repository-Browse.</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"> -- Nilesh Patra <npatra974@gmail.com> Sun, 16 Aug 2020 20:44:11 +0530</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">seqmagick (0.8.0-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/9179005c3920850ee3759fcac0cbbe4e57098829...e1d5a7e31df79d7d068bac7ec502ca4ef5ceb49d#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -3,22 +3,25 @@ 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"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python3-all,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-setuptools,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3-nose,</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> python3-biopython</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.4.1</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> python3-biopython,</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> python3-pygtrie</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/seqmagick</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/seqmagick.git</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Homepage: https://github.com/fhcrc/seqmagick/</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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18
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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: seqmagick</span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> python3-biopython</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> python3-biopython,</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> python3-pygtrie</span>
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22
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Description: imagemagick-like frontend to Biopython SeqIO</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> Seqmagick is a little utility to expose the file format conversion</span>
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24
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> in BioPython in a convenient way.</span>
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<li id="490a82a2fa527c129de4e49174e3ee693da72117">
<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/9179005c3920850ee3759fcac0cbbe4e57098829...e1d5a7e31df79d7d068bac7ec502ca4ef5ceb49d#490a82a2fa527c129de4e49174e3ee693da72117"><strong>debian/patches/fix-myfunctions-example-file.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Nilesh Patra <npatra974@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: Encode hash result in hash_starts_numeric to support unicode</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/fhcrc/seqmagick/pull/85</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last Changed: August 16, 2020</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/examples/apply-function/myfunctions.py</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/examples/apply-function/myfunctions.py</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -14,6 +14,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> their sha-1 hash.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> for record in records:</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- seq_hash = hashlib.sha1(str(record.seq)).hexdigest()</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ seq_hash = hashlib.sha1(str(record.seq).encode('utf-8')).hexdigest()</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> if seq_hash[0].isdigit():</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> yield record</span></pre>
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<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/9179005c3920850ee3759fcac0cbbe4e57098829...e1d5a7e31df79d7d068bac7ec502ca4ef5ceb49d#0ddc2310a98e93221ce234f9be58d879d176994a"><strong>debian/patches/replace-biopython-trie-with-pygtrie.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Nilesh Patra <npatra974@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: Replace deprecated Biopython trie functionality with pygtrie</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/fhcrc/seqmagick/pull/86</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Changed: August 16, 2020</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/seqmagick/subcommands/quality_filter.py</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/seqmagick/subcommands/quality_filter.py</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -11,16 +11,29 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> import time</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> from Bio import SeqIO</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-try:</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- from Bio import trie, triefind</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-except ImportError:</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- trie = None</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- triefind = None</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import pygtrie as trie</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> from Bio.SeqIO import QualityIO</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> from seqmagick import fileformat, __version__</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> from .common import typed_range, FileType</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+def trie_match(string, trie):</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ def has_prefix(teststring, trie):</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for key in trie.keys():</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if key.startswith(teststring):</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return True</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return False</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ longest = None</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(len(string)):</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ substr = string[:i + 1]</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if not has_prefix(substr, trie):</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ break</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if trie.has_key(substr):</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ longest = substr</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return longest</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> # Default minimummean quality score</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> DEFAULT_MEAN_SCORE = 25.0</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="p">@@ -626,7 +639,7 @@</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> self.trie = trie</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> def filter_record(self, record):</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- m = triefind.match(str(record.seq), self.trie)</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ m = trie_match(str(record.seq), self.trie)</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> if m:</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> if self.listener:</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> self.listener(</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="p">@@ -646,7 +659,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> Any additional columns are ignored</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tr = trie.trie()</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tr = trie.StringTrie()</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> reader = csv.reader(fp)</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> if header:</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="p">@@ -680,10 +693,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> raise ValueError("--quality-window-mean-qual specified without "</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> "--quality-window")</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if trie is None or triefind is None:</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- raise ValueError(</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'Missing Bio.trie and/or Bio.triefind modules. Cannot continue')</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> filters = []</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> input_type = fileformat.from_handle(arguments.sequence_file)</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> output_type = fileformat.from_handle(arguments.output_file)</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/seqmagick/test/test_subcommands_quality_filter.py</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/seqmagick/test/test_subcommands_quality_filter.py</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="p">@@ -7,8 +7,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> from seqmagick.subcommands import quality_filter</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> </span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from Bio import triefind</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> IS_PYPY = hasattr(sys, 'pypy_version_info')</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> </span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="p">@@ -194,7 +192,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> [i.id for i in actual])</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-@unittest.skipIf(IS_PYPY, "Bio.trie not available on pypy.")</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> class PrimerBarcodeFilterTestCase(unittest.TestCase):</span>
</pre>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> def setUp(self):</span>
</pre>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> self.sequences = [</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="p">@@ -240,7 +237,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> self.assertEqual(events, [1, 5])</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-@unittest.skipIf(IS_PYPY, "Bio.trie not available on pypy.")</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> class BarcodePrimerTrieTestCase(unittest.TestCase):</span>
</pre>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> def setUp(self):</span>
</pre>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> self.barcode_str = """p1d1bc205,TACTAGCG,CATTGCCTATG</span>
</pre>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="p">@@ -258,9 +254,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> res = quality_filter.parse_barcode_file(self.fp, primer='CATTGCCTATG')</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> self.assertEqual(9, len(list(res.keys())))</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> self.assertEqual('p1d1bc210', res['TACAGTCGCATTGCCTATG'])</span>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(None, triefind.match('TACAGTCGCATTGCCTAT', res))</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(None, quality_filter.trie_match('TACAGTCGCATTGCCTAT', res))</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> self.assertEqual('TACAGTCGCATTGCCTATG',</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- triefind.match('TACAGTCGCATTGCCTATGCTACCTA', res))</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ quality_filter.trie_match('TACAGTCGCATTGCCTATGCTACCTA', res))</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> </span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> def test_primer_in_file(self):</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> res = quality_filter.parse_barcode_file(self.fp, primer=None)</span></pre>
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<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/9179005c3920850ee3759fcac0cbbe4e57098829...e1d5a7e31df79d7d068bac7ec502ca4ef5ceb49d#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">biopython_1.71_dual_coding_support.patch</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">fix-myfunctions-example-file.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">replace-biopython-trie-with-pygtrie.patch </span></pre>
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<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/9179005c3920850ee3759fcac0cbbe4e57098829...e1d5a7e31df79d7d068bac7ec502ca4ef5ceb49d#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>
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<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/9179005c3920850ee3759fcac0cbbe4e57098829...e1d5a7e31df79d7d068bac7ec502ca4ef5ceb49d#eebd58f645086af566297cb3d59c9fa7b409ce14"><strong>debian/seqmagick.1</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">@@ -5,7 +5,7 @@ seqmagick \- Manipulate sequence files</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">usage: seqmagick [\-h] [\-V] [\-v] [\-q]</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"><span class="idiff left right">{help,convert,info,mogrify,primer\-trim,quality\-filter,extract\-ids,backtrans\-align}</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"><span class="idiff left right">help, convert, info, mogrify, primer\-trim, quality\-filter, extract\-ids, backtrans\-align</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">\&...</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">.SH DESCIPTION</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Seqmagick is a little utility to expose the file format conversion</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">@@ -13,7 +13,7 @@ in BioPython in a convenient way.</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">.SS "positional arguments:"</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"><span class="idiff left right">{help,convert,info,mogrify,primer\-trim,quality\-filter,extract\-ids,backtrans\-align}</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"><span class="idiff left right">help, convert, info, mogrify, primer\-trim, quality\-filter, extract\-ids, backtrans\-align</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">help</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Detailed help for actions using help <action></span>
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<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/9179005c3920850ee3759fcac0cbbe4e57098829...e1d5a7e31df79d7d068bac7ec502ca4ef5ceb49d#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/9179005c3920850ee3759fcac0cbbe4e57098829...e1d5a7e31df79d7d068bac7ec502ca4ef5ceb49d#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>seqmagick</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">TEST_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TEST_DIR</span><span class="k" style="font-weight: 600;">}</span>/examples <span class="nt" style="color: #000080;">-a</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>f <span class="k" style="font-weight: 600;">in</span> <span class="sb" style="color: #d14;">`</span>find examples/ <span class="nt" style="color: #000080;">-name</span> <span class="s1" style="color: #d14;">'*.sh'</span><span class="sb" style="color: #d14;">`</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cd</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">dirname</span> <span class="nv" style="color: #008080;">$f</span><span class="sb" style="color: #d14;">`</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> /bin/bash <span class="k" style="font-weight: 600;">*</span>.sh</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd</span> -</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'PASS'</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span></pre>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/9179005c3920850ee3759fcac0cbbe4e57098829...e1d5a7e31df79d7d068bac7ec502ca4ef5ceb49d#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Bug-Database: https://github.com/fhcrc/seqmagick/issues</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Bug-Submit: https://github.com/fhcrc/seqmagick/issues/new</span>
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1
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Registry:</span>
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2
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> - Name: bio.tools</span>
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3
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Entry: NA</span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,3 +9,5 @@ Registry:</td>
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7
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> Entry: seqmagick</span>
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8
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> - Name: SciCrunch</span>
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9
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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">
11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> Entry: NA</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Repository: https://github.com/fhcrc/seqmagick.git</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Repository-Browse: https://github.com/fhcrc/seqmagick</span></pre>
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