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<h3>
Sascha Steinbiss pushed to branch master
at <a href="https://salsa.debian.org/med-team/ariba">Debian Med / ariba</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ariba/-/commit/7f99111f03696efebd8e40b5b9ed44a80d27f4ba">7f99111f</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-06-30T12:36:27+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">suggest SPAdes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ariba/-/commit/f1f2bff25061fa1440d6b5dfdf58ac50b5f5c14d">f1f2bff2</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-06-30T12:37:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add patch to fix test failures
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ariba/-/commit/b5606c2d0d45aaf9be20529fa3068da94d5ceb12">b5606c2d</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-06-30T12:37:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add patch to call SPAdes correctly
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ariba/-/commit/6f7ba3956df14a97e39ed1fe85734a5762322e0e">6f7ba395</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-06-30T12:37:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add upstream metadata
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ariba/-/commit/f5f3d044d5a992aa730445a0f6077462fc0b0b83">f5f3d044</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-06-30T12:37:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">use debhelper 13
</pre>
</li>
</ul>
<h4>6 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="#e9f91012ec087d39b35d3d6de757263ba1773128">
<span class="new-file">
+
debian/patches/run-debian-spades-wrapper.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#435da802d1cb574311690e482b233ea047b42ea6">
<span class="new-file">
+
debian/patches/support-pymummer-0.11.patch
</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/ariba/-/compare/fba3b82104d2b898e68321aacd0826328058006b...f5f3d044d5a992aa730445a0f6077462fc0b0b83#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">ariba (2.14.5+ds-2) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ariba (2.14.5+ds-2) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="2" 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="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line old" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> <span class="idiff left right">* Team upload.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> <span class="idiff left right">[ Andreas Tille ]</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Build-Depends: spades <!nocheck></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> * Depends: spades</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Suggests: spades</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></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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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> [ Sascha Steinbiss ]</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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Add patch to fix test failures.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> Closes: #963332</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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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Add patch to call SPAdes correctly.</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"> * Add upstream metadata.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Use debhelper 13.</span>
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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="LC7" class="line" lang="plaintext"> -- <span class="idiff left right">Andreas Tille <tille@debian.org> Mon, 22 Jun 2020 11:29:55</span> +0200</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"> -- <span class="idiff left right">Sascha Steinbiss <satta@debian.org> Tue, 30 Jun 2020 12:32:39</span> +0200</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">ariba (2.14.5+ds-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/ariba/-/compare/fba3b82104d2b898e68321aacd0826328058006b...f5f3d044d5a992aa730445a0f6077462fc0b0b83#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">@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Sascha Steinbiss <satta@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-biopython,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-all-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">@@ -47,8 +47,8 @@ Depends: ${misc:Depends},</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> python3-pysam (>= 0.9.1),</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> python3-matplotlib,</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> python3-tk,</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> fastaq (>= 3.12.0)<span class="idiff left right">,</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"><span class="idiff left right"> </span> spades</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> fastaq (>= 3.12.0)</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"><span class="idiff left right">Suggests:</span> spades</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext">Description: Antibiotic Resistance Identification By Assembly</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"> ARIBA is a tool that identifies antibiotic resistance genes by running local</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"> assemblies.</span>
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<a href="https://salsa.debian.org/med-team/ariba/-/compare/fba3b82104d2b898e68321aacd0826328058006b...f5f3d044d5a992aa730445a0f6077462fc0b0b83#e9f91012ec087d39b35d3d6de757263ba1773128"><strong>debian/patches/run-debian-spades-wrapper.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: run Debian SPAdes wrapper</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> Debian's /usr/bin/spades.py is not a Python script, but a wrapper</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> around a common executable only provided for compatibility reasons.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> Ariba is trying to execute it explicitly as a Python script.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> This patch just calls the executable without forcing it through the</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> Python interpreter.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Author: Sascha Steinbiss <satta@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Last-Update: 2020-06-30</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ariba/assembly.py</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ariba/assembly.py</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">@@ -140,7 +140,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> spades_out_seq_base = "contigs.fasta"</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> raise ValueError("Unknown spades_mode value: {}".format(self.spades_mode))</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;">- asm_cmd = ['python3', spades_exe, "-t", str(self.threads), "--pe1-1", self.reads1, "--pe1-2", self.reads2, "-o", self.assembler_dir] + \</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;">+ asm_cmd = [spades_exe, "-t", str(self.threads), "--pe1-1", self.reads1, "--pe1-2", self.reads2, "-o", self.assembler_dir] + \</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> spades_options</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> asm_ok,err = common.syscall(asm_cmd, verbose=True, verbose_filehandle=self.log_fh, shell=False, allow_fail=True)</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> if not asm_ok:</span></pre>
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<a href="https://salsa.debian.org/med-team/ariba/-/compare/fba3b82104d2b898e68321aacd0826328058006b...f5f3d044d5a992aa730445a0f6077462fc0b0b83#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">@@ -2,3 +2,5 @@ use_debian_packaged_libs_for_extension.patch</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">use_bwa_compatible_fermi-lite.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">add-testdata.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">disable-tests-with-internet-access.patch</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">support-pymummer-0.11.patch</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">run-debian-spades-wrapper.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/ariba/-/compare/fba3b82104d2b898e68321aacd0826328058006b...f5f3d044d5a992aa730445a0f6077462fc0b0b83#435da802d1cb574311690e482b233ea047b42ea6"><strong>debian/patches/support-pymummer-0.11.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: adapt test cases for new PyMUMmer version</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> pymummer 0.11 uses a different internal format which is incompatible</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> with the one assumed by Ariba. Note that ariba hard-requires an earlier</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> version than the one in Debian. However, since Debian has updated</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> pymummer now, we need to catch up even though upstream does not.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Author: Sascha Steinbiss <satta@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Last-Update: 2020-06-30</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ariba/tests/assembly_variants_test.py</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ariba/tests/assembly_variants_test.py</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -52,23 +52,23 @@</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> def test_get_variant_effect(self):</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> '''test _get_variant_effect'''</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> ref_seq = pyfastaq.sequences.Fasta('gene', 'GATCGCGAAGCGATGACCCATGAAGCGACCGAACGCTGA')</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;">- v1 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tT\t6\tx\tx\t39\t39\tx\tx\tgene\tcontig'))</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;">- v1 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tT\t6\tx\tx\t39\t39\tx\tx\tgene\tcontig'))</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v2 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\tA\t6\tx\tx\t39\t39\tx\tx\tgene\tcontig'))</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v3 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\tT\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v4 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tA\t6\tx\tx\t39\t39\tx\tx\tgene\tcontig'))</span></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;">- v5 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\t.\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))</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;">- v6 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tA\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))</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;">- v7 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tG\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))</span></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;">+ v1 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tT\t6\tx\tx\t39\t39\tx\t1\tgene\tcontig'))</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;">+ v1 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tT\t6\tx\tx\t39\t39\tx\t1\tgene\tcontig'))</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;">+ v2 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\tA\t6\tx\tx\t39\t39\tx\t1\tgene\tcontig'))</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v3 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\tT\t4\tx\tx\t39\t39\tx\t1\tgene\tcontig'))</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v4 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tA\t6\tx\tx\t39\t39\tx\t1\tgene\tcontig'))</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v5 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\t.\t4\tx\tx\t39\t39\tx\t1\tgene\tcontig'))</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v6 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tA\t4\tx\tx\t39\t39\tx\t1\tgene\tcontig'))</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v7 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tG\t4\tx\tx\t39\t39\tx\t1\tgene\tcontig'))</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> v7.qry_base = 'GAT'</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v8 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tG\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v8 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tG\t4\tx\tx\t39\t39\tx\t1\tgene\tcontig'))</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> v8.qry_base = 'TGA'</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v9 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tG\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v9 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tG\t4\tx\tx\t39\t39\tx\t1\tgene\tcontig'))</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> v9.qry_base = 'ATTCCT'</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v10 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\t.\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v10 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\t.\t4\tx\tx\t39\t39\tx\t1\tgene\tcontig'))</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> v10.ref_base = 'CGC'</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> v10.ref_end = 5</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v11 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\t.\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v11 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\t.\t4\tx\tx\t39\t39\tx\t1\tgene\tcontig'))</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> v11.ref_base = 'CGCGAA'</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> v11.ref_end = 8</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="p">@@ -93,9 +93,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> def test_filter_mummer_variants(self):</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> '''test filter_mummer_variants'''</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> ref_seq = pyfastaq.sequences.Fasta('gene', 'GATCGCGAAGCGATGACCCATGAAGCGACCGAACGCTGA')</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v1 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\tT\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))</span></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;">- v2 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tA\t6\tx\tx\t39\t39\tx\tx\tgene\tcontig'))</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v3 = pymummer.variant.Variant(pymummer.snp.Snp('12\tG\tT\t12\tx\tx\t39\t39\tx\tx\tgene\tcontig'))</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v1 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\tT\t4\tx\tx\t39\t39\tx\t1\tgene\tcontig'))</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v2 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tA\t6\tx\tx\t39\t39\tx\t1\tgene\tcontig'))</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v3 = pymummer.variant.Variant(pymummer.snp.Snp('12\tG\tT\t12\tx\tx\t39\t39\tx\t1\tgene\tcontig'))</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> mummer_variants = {'contig': [[v1, v2], v3]}</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> assembly_variants.AssemblyVariants._filter_mummer_variants(mummer_variants, ref_seq)</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> expected = {'contig': [[v1, v2]]}</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="p">@@ -110,13 +110,13 @@</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> ref_sequence_name = 'non_coding'</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> refdata_var_dict = refdata.metadata[ref_sequence_name]</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"><span class="gd" style="color: #000; background-color: #fdd;">- v0 = pymummer.variant.Variant(pymummer.snp.Snp('2\tT\tA\t2\tx\tx\t42\t42\tx\tx\tnon_coding\tcontig'))</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v0 = pymummer.variant.Variant(pymummer.snp.Snp('2\tT\tA\t2\tx\tx\t42\t42\tx\t1\tnon_coding\tcontig'))</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> # ref has A at position 3, which is variant type. This gives contig the wild type C. Shouldn't report</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;">- v1 = pymummer.variant.Variant(pymummer.snp.Snp('3\tA\tC\t3\tx\tx\t42\t42\tx\tx\tnon_coding\tcontig'))</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v1 = pymummer.variant.Variant(pymummer.snp.Snp('3\tA\tC\t3\tx\tx\t42\t42\tx\t1\tnon_coding\tcontig'))</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> # ref has T at position 5, which is wild type. This gives contig variant type A. Should report</span>
</pre>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v2 = pymummer.variant.Variant(pymummer.snp.Snp('5\tT\tA\t5\tx\tx\t42\t42\tx\tx\tnon_coding\tcontig'))</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v2 = pymummer.variant.Variant(pymummer.snp.Snp('5\tT\tA\t5\tx\tx\t42\t42\tx\t1\tnon_coding\tcontig'))</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> meta0 = sequence_metadata.SequenceMetadata('non_coding\t0\t0\tC3A\tid1\tref has variant type A')</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> meta2 = sequence_metadata.SequenceMetadata('non_coding\t0\t0\tT5A\tid1\tref has wild type T')</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="p">@@ -153,33 +153,33 @@</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> ref_sequence = refdata.sequence(ref_sequence_name)</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> refdata_var_dict = refdata.metadata[ref_sequence_name]</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v0 = pymummer.variant.Variant(pymummer.snp.Snp('6\tT\tA\t6\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="81" 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="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v1 = pymummer.variant.Variant(pymummer.snp.Snp('9\tA\tT\t9\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="82" 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="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v2 = pymummer.variant.Variant(pymummer.snp.Snp('18\tG\tT\t18\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="83" 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="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v3 = pymummer.variant.Variant(pymummer.snp.Snp('21\tC\tT\t21\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="84" 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="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v4 = pymummer.variant.Variant(pymummer.snp.Snp('7\tA\tT\t7\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="85" 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="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v5 = pymummer.variant.Variant(pymummer.snp.Snp('12\tA\tC\t11\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="87" 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="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v6 = pymummer.variant.Variant(pymummer.snp.Snp('4\tG\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="88" 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="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(v6.update_indel(pymummer.snp.Snp('5\tA\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))</span></span>
</pre>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="90" 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="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v7 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tA\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="91" 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">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(v7.update_indel(pymummer.snp.Snp('4\t.\tA\t5\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="92" 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">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="93" 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">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v8 = pymummer.variant.Variant(pymummer.snp.Snp('4\tG\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="94" 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">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(v8.update_indel(pymummer.snp.Snp('5\tA\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(v8.update_indel(pymummer.snp.Snp('6\tT\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="96" 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">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="97" 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">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v9 = pymummer.variant.Variant(pymummer.snp.Snp('4\tG\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="98" 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">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(v9.update_indel(pymummer.snp.Snp('5\tA\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="99" 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">
99
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(v9.update_indel(pymummer.snp.Snp('6\tT\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="100" 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">
100
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(v9.update_indel(pymummer.snp.Snp('7\tA\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="101" 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">
101
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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="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(v9.update_indel(pymummer.snp.Snp('8\tG\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(v9.update_indel(pymummer.snp.Snp('9\tA\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v10 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tA\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="105" 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">
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;">- self.assertTrue(v10.update_indel(pymummer.snp.Snp('4\t.\tT\t5\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="106" 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">
106
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(v10.update_indel(pymummer.snp.Snp('4\t.\tT\t6\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v0 = pymummer.variant.Variant(pymummer.snp.Snp('6\tT\tA\t6\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v1 = pymummer.variant.Variant(pymummer.snp.Snp('9\tA\tT\t9\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="109" 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">
109
</td>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v2 = pymummer.variant.Variant(pymummer.snp.Snp('18\tG\tT\t18\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="110" 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">
110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v3 = pymummer.variant.Variant(pymummer.snp.Snp('21\tC\tT\t21\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="111" 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">
111
</td>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v4 = pymummer.variant.Variant(pymummer.snp.Snp('7\tA\tT\t7\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="112" 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">
112
</td>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v5 = pymummer.variant.Variant(pymummer.snp.Snp('12\tA\tC\t11\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="113" 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">
113
</td>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="114" 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">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v6 = pymummer.variant.Variant(pymummer.snp.Snp('4\tG\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="115" 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">
115
</td>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue(v6.update_indel(pymummer.snp.Snp('5\tA\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="116" 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">
116
</td>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v7 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tA\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue(v7.update_indel(pymummer.snp.Snp('4\t.\tA\t5\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v8 = pymummer.variant.Variant(pymummer.snp.Snp('4\tG\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue(v8.update_indel(pymummer.snp.Snp('5\tA\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="122" 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">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue(v8.update_indel(pymummer.snp.Snp('6\tT\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="124" 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">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v9 = pymummer.variant.Variant(pymummer.snp.Snp('4\tG\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="125" 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">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue(v9.update_indel(pymummer.snp.Snp('5\tA\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue(v9.update_indel(pymummer.snp.Snp('6\tT\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="127" 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">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue(v9.update_indel(pymummer.snp.Snp('7\tA\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue(v9.update_indel(pymummer.snp.Snp('8\tG\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="129" 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">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue(v9.update_indel(pymummer.snp.Snp('9\tA\t.\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))</span></span>
</pre>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v10 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tA\t4\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig'))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="132" 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">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue(v10.update_indel(pymummer.snp.Snp('4\t.\tT\t5\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue(v10.update_indel(pymummer.snp.Snp('4\t.\tT\t6\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig')))</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> mummer_variants = [[v0], [v1], [v2], [v3], [v4], [v5], [v6], [v7], [v8], [v9], [v10]]</span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="p">@@ -306,8 +306,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> os.unlink(metadata_tsv)</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> </span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> nucmer_snp_file = os.path.join(data_dir, 'assembly_variants_test_get_variants_presence_absence.snps')</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v2 = pymummer.variant.Variant(pymummer.snp.Snp('14\tC\tA\t14\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig1'))</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v3 = pymummer.variant.Variant(pymummer.snp.Snp('15\tG\tC\t15\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig1'))</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v2 = pymummer.variant.Variant(pymummer.snp.Snp('14\tC\tA\t14\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig1'))</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v3 = pymummer.variant.Variant(pymummer.snp.Snp('15\tG\tC\t15\tx\tx\t42\t42\tx\t1\tpresence_absence\tcontig1'))</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> ref_nucmer_coords = {</span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> 'contig1': [pyfastaq.intervals.Interval(0, 30)],</span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="p">@@ -354,8 +354,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> os.unlink(metadata_tsv)</span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> nucmer_snp_file = os.path.join(data_dir, 'assembly_variants_test_get_variants_variants_only.snps')</span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v2 = pymummer.variant.Variant(pymummer.snp.Snp('14\tC\tA\t14\tx\tx\t42\t42\tx\tx\tvariants_only\tcontig1'))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- v3 = pymummer.variant.Variant(pymummer.snp.Snp('15\tG\tC\t15\tx\tx\t42\t42\tx\tx\tvariants_only\tcontig1'))</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v2 = pymummer.variant.Variant(pymummer.snp.Snp('14\tC\tA\t14\tx\tx\t42\t42\tx\t1\tvariants_only\tcontig1'))</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ v3 = pymummer.variant.Variant(pymummer.snp.Snp('15\tG\tC\t15\tx\tx\t42\t42\tx\t1\tvariants_only\tcontig1'))</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> ctg_nucmer_coords = {</span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> 'contig1': [pyfastaq.intervals.Interval(0, 41)],</span>
</pre>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps</span></span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="p">@@ -1,3 +1,3 @@</span></span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-9 A T 9 x x 42 42 x x variants_only contig1</span></span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-14 C A 14 x x 42 42 x x variants_only contig1</span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-15 G C 15 x x 42 42 x x variants_only contig1</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+9 A T 9 x x 42 42 x 1 variants_only contig1</span></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+14 C A 14 x x 42 42 x 1 variants_only contig1</span></span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+15 G C 15 x x 42 42 x 1 variants_only contig1</span></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="p">@@ -1,3 +1,3 @@</span></span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-9 A T 9 x x 42 42 x x presence_absence contig1</span></span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-14 C A 14 x x 42 42 x x presence_absence contig1</span></span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-15 G C 15 x x 42 42 x x presence_absence contig1</span></span>
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+9 A T 9 x x 42 42 x 1 presence_absence contig1</span></span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+14 C A 14 x x 42 42 x 1 presence_absence contig1</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+15 G C 15 x x 42 42 x 1 presence_absence contig1</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ariba/-/compare/fba3b82104d2b898e68321aacd0826328058006b...f5f3d044d5a992aa730445a0f6077462fc0b0b83#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/sanger-pathogens/ariba</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/sanger-pathogens/ariba/issues/new</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Repository: https://github.com/sanger-pathogens/ariba.git</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Repository-Browse: https://github.com/sanger-pathogens/ariba</span>
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1
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Reference:</span>
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2
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> - Author: ></span>
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3
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> Martin Hunt and Alison E. Mather and Leonor Sanchez-Buso and Andrew</span>
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