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<h3>
Andreas Tille pushed to branch debian/unstable
at <a href="https://salsa.debian.org/med-team/sga">Debian Med / sga</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sga/commit/1db0055649883266b47206397c9a0bbca847680e">1db00556</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-02T18:20:15Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use 2to3 to port to Python3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sga/commit/51d61e2d10d202d0953f5cd1b7f26d2ea02fb821">51d61e2d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-02T18:21:00Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adjust (Build-)Depends
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sga/commit/0d89879e383e9c6da8b6842d294a3275083c920c">0d89879e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-02T18:21:23Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sga/commit/2b4b5b8b3294ad1f52579e1e75f36a8847b36f5b">2b4b5b8b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-02T18:21:26Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sga/commit/db1be50f6f9938c7dd87870deb7a97f374c177e5">db1be50f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-02T18:21:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Secure URI in copyright format
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sga/commit/9f9ad8bdf13d8f3b7f90ceea5c0abbe5d4bb01e4">9f9ad8bd</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-02T18:21:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Trim trailing whitespace.
Fixes lintian: file-contains-trailing-whitespace
See https://lintian.debian.org/tags/file-contains-trailing-whitespace.html for more details.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sga/commit/b9723af48bd14597a7557eb1e7019565bb212916">b9723af4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-02T18:21:29Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set fields Upstream-Contact in debian/copyright.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sga/commit/79cdf7b832460c03fd346a46f57000304488b1dc">79cdf7b8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-02T18:21:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove obsolete fields Name, Contact from debian/upstream/metadata.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sga/commit/424abe8d350549bd96232876639f6784c0baef63">424abe8d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-02T18:41:23Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">s/python/python3/
</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
<span class="new-file">
+
debian/patches/2to3.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</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/sga/compare/1dc3d29ba6f22edfc01969b55ac9ec4c114e20e1...424abe8d350549bd96232876639f6784c0baef63#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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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sga (0.10.15-5) 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">
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<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"> * Use 2to3 to port to Python3</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">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Closes: 938472</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">
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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"> * debhelper-compat 12</span>
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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">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Standards-Version: 4.4.0</span>
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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"> * Secure URI in copyright format</span>
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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"> * Trim trailing whitespace.</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"> * Set fields Upstream-Contact in debian/copyright.</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"> * Remove obsolete fields Name, Contact from debian/upstream/metadata.</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">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
</pre>
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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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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 02 Sep 2019 20:18:33 +0200</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"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">sga (0.10.15-4) unstable; urgency=medium</span>
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2
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<td class="diff-line-num new_line" data-linenumber="15" 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="LC15" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="16" 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="LC16" class="line" lang="plaintext"> * debhelper 11</span>
</pre>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/sga/compare/1dc3d29ba6f22edfc01969b55ac9ec4c114e20e1...424abe8d350549bd96232876639f6784c0baef63#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">11</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/sga/compare/1dc3d29ba6f22edfc01969b55ac9ec4c114e20e1...424abe8d350549bd96232876639f6784c0baef63#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">@@ -4,7 +4,7 @@ Uploaders: Michael R. Crusoe <michael.crusoe@gmail.com>,</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 11~</span>),</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> libsparsehash-dev,</span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> zlib1g-dev | libz-dev,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libbamtools-dev,</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">@@ -13,10 +13,10 @@ Build-Depends: debhelper (>= 11~),</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"># Run-Time Depends</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"># (to prevent building on architectures where it won't be installable)</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> samtools,</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> python,</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> python-ruffus,</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> python-pysam</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> python<span class="idiff left right">3</span>,</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-ruffus,</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-pysam</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.0</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/sga</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/sga.git</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Homepage: https://github.com/jts/sga</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="26" 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">@@ -26,9 +26,9 @@ Architecture: any</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> samtools,</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> python,</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> python-ruffus,</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> python-pysam</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> python<span class="idiff left right">3</span>,</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-ruffus,</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-pysam</span>
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">Recommends: abyss (>= 2.0.2-1)</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">Description: de novo genome assembler that uses string graphs</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> The major goal of SGA is to be very memory efficient, which is achieved by</span>
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<a href="https://salsa.debian.org/med-team/sga/compare/1dc3d29ba6f22edfc01969b55ac9ec4c114e20e1...424abe8d350549bd96232876639f6784c0baef63#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: http<span class="idiff left right">s</span>://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Upstream-Name: sga</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Source: https://github.com/jts/sga</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Upstream-Contact: http://groups.google.com/group/sga-users</span>
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4
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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5
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Files: *</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Copyright: 2009-2012 Jared T. Simpson <js18@sanger.ac.uk></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -87,4 +88,3 @@ License: Expat</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext"> ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"> CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE</span>
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89
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"> SOFTWARE.</span></pre>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/sga/compare/1dc3d29ba6f22edfc01969b55ac9ec4c114e20e1...424abe8d350549bd96232876639f6784c0baef63#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use 2to3 to port to Python3</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/938472</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Mon, 02 Sep 2019 20:18:33 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/bin/sga-astat.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/bin/sga-astat.py</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#! /usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> # sga-astat.py - Compute Myers' a-statistic for a set of contigs using read alignments</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> # in a bam file</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -30,20 +30,20 @@</span> genomeSize = 0</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> arrivalRate = 0</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> def usage():</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'usage: sga-astat.py in.bam'</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'Compute Myers\' a-statistic for a set of contigs using the read alignments in in.bam'</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'Options:'</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ' -m=INT only compute a-stat for contigs at least INT bases in length'</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ' -b=INT use the longest INT contigs to perform the initial estimate'</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ' of the arrival rate (default: ' + str(numContigsForInitialEstimate) + ')' </span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ' -n=INT perform INT bootstrap iterations of the estimate'</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ' -g=INT use INT as the genome size instead of estimating it'</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ' --no-duplicates do not use duplicate reads to calculate statistics'</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;">+ print('usage: sga-astat.py in.bam')</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;">+ print('Compute Myers\' a-statistic for a set of contigs using the read alignments in in.bam')</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;">+ print('Options:')</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;">+ print(' -m=INT only compute a-stat for contigs at least INT bases in length')</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;">+ print(' -b=INT use the longest INT contigs to perform the initial estimate')</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;">+ print(' of the arrival rate (default: ' + str(numContigsForInitialEstimate) + ')') </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;">+ print(' -n=INT perform INT bootstrap iterations of the estimate')</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;">+ print(' -g=INT use INT as the genome size instead of estimating it')</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;">+ print(' --no-duplicates do not use duplicate reads to calculate statistics')</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> </span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> opts, args = getopt.gnu_getopt(sys.argv[1:], 'm:b:n:g:', ['help', 'no-duplicates'])</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-except getopt.GetoptError, err:</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print str(err)</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+except getopt.GetoptError as err:</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(str(err))</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> usage()</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> sys.exit(2)</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="p">@@ -63,7 +63,7 @@</span> for (oflag, oarg) in opts:</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> sys.exit(1)</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> if len(args) == 0:</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'Error: a BAM file must be provided\n'</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('Error: a BAM file must be provided\n')</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> usage()</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> sys.exit(2)</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> </span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="p">@@ -172,7 +172,7 @@</span> sumUnique = 0</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> sumRepeat = 0</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> for cd in contigData:</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> if cd.len >= minLength and cd.nlen > 0:</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print '%s\t%d\t%d\t%d\t%f\t%f' % (cd.name, cd.len, cd.nlen, cd.n, cd.n / (cd.nlen * arrivalRate), cd.astat)</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('%s\t%d\t%d\t%d\t%f\t%f' % (cd.name, cd.len, cd.nlen, cd.n, cd.n / (cd.nlen * arrivalRate), cd.astat))</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> if cd.bUnique:</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> sumUnique += cd.len</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;">--- a/src/bin/sga-preqc-report.py</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/bin/sga-preqc-report.py</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="p">@@ -1,8 +1,8 @@</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> """Generate a readable report from preqc output.</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> """</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> </span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import print_function, division</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" 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="LC75" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> import sys, os.path</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> import matplotlib as MPL</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="p">@@ -458,7 +458,7 @@</span> def plot_mean_quality_scores(ax, data, l</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> 'mean_quality' in d[QUALITY_SCORE_NAME] ):</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> names.append(d['name'])</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> mean_quality = d[QUALITY_SCORE_NAME]['mean_quality']</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- indices = range(0, len(mean_quality))</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ indices = list(range(0, len(mean_quality)))</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> marker = d['plot_marker'] if( use_markers ) else None</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> ax.plot(indices, mean_quality, '-',</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> marker=marker, color=d['plot_color'])</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="p">@@ -478,7 +478,7 @@</span> def plot_q30_quality_scores(ax, data, le</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> 'fraction_q30' in d[QUALITY_SCORE_NAME] ):</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> names.append(d['name'])</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> q30_fraction = d[QUALITY_SCORE_NAME]['fraction_q30']</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- indices = range(0, len(q30_fraction))</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ indices = list(range(0, len(q30_fraction)))</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> marker = d['plot_marker'] if( use_markers ) else None</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> ax.plot(indices, q30_fraction, '-',</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> marker=marker, color=d['plot_color'])</span></pre>
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<a href="https://salsa.debian.org/med-team/sga/compare/1dc3d29ba6f22edfc01969b55ac9ec4c114e20e1...424abe8d350549bd96232876639f6784c0baef63#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -6,3 +6,4 @@</td>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">0006-remove-google-addsense.patch</span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">gcc-7.patch</span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">no_privacy_breach_url.patch</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">2to3.patch</span></pre>
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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">@@ -53,4 +53,3 @@ override_dh_installman:</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="make"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"generate sga merge commands from a list of files"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="make"> <span class="nt" style="color: #000080;">--output</span> <span class="nv" style="color: #008080;">$(mandir)</span>/sga-mergeDriver.1 <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="make"> <span class="nv" style="color: #008080;">$(bindir)</span>/sga-mergeDriver</span></pre>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="make"></span></pre>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/sga/compare/1dc3d29ba6f22edfc01969b55ac9ec4c114e20e1...424abe8d350549bd96232876639f6784c0baef63#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Contact: http://groups.google.com/group/sga-users</span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">FAQ: https://github.com/jts/sga/wiki/FAQ</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Name: SGA (String Graph Assembler)</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> Author: Jared T. Simpson and Richard Durbin</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> DOI: 10.1101/gr.126953.111</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> Eprint: http://genome.cshlp.org/content/22/3/549.full.pdf</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> Journal: Genome Res</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> Number: 3</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> Pages: 549-555</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> PMID: 22156294</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> Title: Efficient de novo assembly of large genomes using compressed data structures.</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> Type: article</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> URL: http://genome.cshlp.org/content/22/3/549.abstract</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> Volume: 22</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> Year: 2012</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> <span class="idiff left right"> </span>Author: Jared T. Simpson and Richard Durbin</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> <span class="idiff left right"> </span>DOI: 10.1101/gr.126953.111</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> <span class="idiff left right"> </span>Eprint: http://genome.cshlp.org/content/22/3/549.full.pdf</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> <span class="idiff left right"> </span>Journal: Genome Res</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> <span class="idiff left right"> </span>Number: 3</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> <span class="idiff left right"> </span>Pages: 549-555</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> <span class="idiff left right"> </span>PMID: 22156294</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> <span class="idiff left right"> </span>Title: Efficient de novo assembly of large genomes using compressed data structures.</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> <span class="idiff left right"> </span>Type: article</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> <span class="idiff left right"> </span>URL: http://genome.cshlp.org/content/22/3/549.abstract</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> <span class="idiff left right"> </span>Volume: 22</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">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> <span class="idiff left right"> </span>Year: 2012</span>
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17
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<td class="diff-line-num new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Repository: git://github.com/jts/sga.git</span>
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<td class="diff-line-num old_line" data-linenumber="18" 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">
18
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<td class="diff-line-num new_line" data-linenumber="16" 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">
16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Repository-Browse: https://github.com/jts/sga/tree/master/src</span>
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<td class="diff-line-num old_line" data-linenumber="19" 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">
19
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Bug-Database: https://github.com/jts/sga/issues</span>
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20
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<td class="diff-line-num new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Bug-Submit: https://github.com/jts/sga/issues/new</span>
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<td class="diff-line-num old_line" data-linenumber="21" 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">
21
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Registry:</span>
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<td class="diff-line-num old old_line" data-linenumber="22" 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">
22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"><span class="idiff left right"> </span>- Name: OMICtools</span>
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<td class="diff-line-num old old_line" data-linenumber="23" 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">
23
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<td class="diff-line-num new_line old" data-linenumber="20" 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="LC23" class="line" lang="plaintext"> <span class="idiff left right"> </span>Entry: OMICS_00028</span>
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<td class="diff-line-num old old_line" data-linenumber="24" 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">
24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"><span class="idiff left right"> </span>- Name: bio.tools</span>
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<td class="diff-line-num old old_line" data-linenumber="25" 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">
25
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<td class="diff-line-num new_line old" data-linenumber="20" 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="LC25" class="line" lang="plaintext"> <span class="idiff left right"> </span>Entry: SGA</span>
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<td class="diff-line-num old old_line" data-linenumber="26" 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">
26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"><span class="idiff left right"> </span>- Name: SciCrunch</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> <span class="idiff left right"> </span>Entry: SCR_001982</span></pre>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">- Name: OMICtools</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> Entry: OMICS_00028</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">- Name: bio.tools</span>
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<td class="diff-line-num new new_line" data-linenumber="23" 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">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> Entry: SGA</span>
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<td class="diff-line-num new old_line" data-linenumber="28" 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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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">- Name: SciCrunch</span>
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<td class="diff-line-num new old_line" data-linenumber="28" 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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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> Entry: SCR_001982</span></pre>
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