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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/gasic">Debian Med / gasic</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/gasic/-/commit/a0b828af137c2497f3f65c199487648fcb5a2260">a0b828af</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-05-12T17:40:51+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove unnecessary example files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gasic/-/commit/de364d4792b916b513ea9d693eccebd920d6deea">de364d47</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-05-13T01:31:49+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix mason_simulator arguments
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gasic/-/commit/e611aaf5ce0a905a9f23e6e7a10c9bb922c0b8a9">e611aaf5</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-05-13T02:38:05+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add more autopkgtests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gasic/-/commit/c42123d62629d9621adc58482ee64bbc76aa0df1">c42123d6</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-05-13T02:39:51+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove removed binaries from include-binaries
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gasic/-/commit/ac007039bd1d4fd1d1905e7448f78838b52aba56">ac007039</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-05-13T15:10:46+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://salsa.debian.org/med-team/gasic
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gasic/-/commit/f2779eb9678c3d88f643a61755f330dcd35aefd9">f2779eb9</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-05-13T15:18:46+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
</pre>
</li>
</ul>
<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#968c4691073d4f7c0f089a3fa020a3aefa835489">
debian/patches/use_seqan_mason.patch
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<li class="file-stats">
<a href="#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242">
debian/source/include-binaries
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<li class="file-stats">
<a href="#d05d19370642bb823275fab19a195aeecd6e5147">
<span class="deleted-file">
−
debian/tests/data/genomes/dwv.fasta-e.gz
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<a href="#cb1e93dac244f64d65e82ae1ba6899e2353ded7f">
<span class="deleted-file">
−
debian/tests/data/genomes/dwv.fasta.fai.gz
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<a href="#34982f0eae38c31cbe7cb5bce48623223bcc0330">
<span class="deleted-file">
−
debian/tests/data/genomes/vdv-1-dwv-5.fasta.fai.gz
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<li class="file-stats">
<a href="#f08d736526f19dd4de1f351012feb69351b5f52a">
<span class="deleted-file">
−
debian/tests/data/genomes/vdv-1-dwv-9.fasta.fai.gz
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<li class="file-stats">
<a href="#bcb71e30c602e39499e35e155133da229c12f742">
<span class="deleted-file">
−
debian/tests/data/genomes/vdv1.fasta.fai.gz
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<li class="file-stats">
<a href="#ef6221b1e833200bf7d7d99d4a2ce8f564c9cad9">
<span class="new-file">
+
debian/tests/data/names
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<li class="file-stats">
<a href="#651cd058599fc98d53bb65150d3ba460bd5b02a9">
<span class="deleted-file">
−
debian/tests/data/names.gz
</span>
</a>
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/gasic/-/compare/0c51555761bd86d7ad4110ae12820383c0707064...f2779eb9678c3d88f643a61755f330dcd35aefd9#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gasic (0.0.r19-7) UNRELEASED; urgency=medium</span>
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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 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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Remove unnecessary example files</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"> * Fix mason_simulator arguments</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Add more autopkgtests</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Remove removed binaries from include-binaries</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Pranav Ballaney <ballaneypranav@gmail.com> Wed, 13 May 2020 15:13:02 +0530</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">gasic (0.0.r19-6) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Team upload</span>
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<li id="968c4691073d4f7c0f089a3fa020a3aefa835489">
<a href="https://salsa.debian.org/med-team/gasic/-/compare/0c51555761bd86d7ad4110ae12820383c0707064...f2779eb9678c3d88f643a61755f330dcd35aefd9#968c4691073d4f7c0f089a3fa020a3aefa835489"><strong>debian/patches/use_seqan_mason.patch</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +18,7 @@ Description: since there is a name conflict with mason and the Debian package</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ reportbug gasic</span></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">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+to propose enhancements.</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+""" % (out,ref))</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command = "/usr/lib/seqan/bin/mason_simulator <span class="idiff left right">illumina --illumina-read-length 10000 -o %s</span> %s"%(out,ref)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command = "/usr/lib/seqan/bin/mason_simulator <span class="idiff left right">--seq-technology illumina -n 10000 --illumina-read-length 72 -o %s -ir</span> %s"%(out,ref)</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> print("Executing:",command)</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> os.system(command)</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> # remove the needless SAM file</span></pre>
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<a href="https://salsa.debian.org/med-team/gasic/-/compare/0c51555761bd86d7ad4110ae12820383c0707064...f2779eb9678c3d88f643a61755f330dcd35aefd9#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242"><strong>debian/source/include-binaries</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">debian/tests/data/names.gz</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">debian/tests/data/genomes/vdv1.fasta.fai.gz</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests/data/genomes/dwv.fasta.gz</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">debian/tests/data/genomes/vdv1.fasta.gz</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">debian/tests/data/genomes/vdv1dwv9.fasta.gz</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">debian/tests/data/genomes/vdv1dwv5.fasta.gz</span></pre>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">debian/tests/data/genomes/vdv-1-dwv-9.fasta.fai.gz</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">debian/tests/data/genomes/vdv-1-dwv-5.fasta.fai.gz</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">debian/tests/data/genomes/dwv.fasta-e.gz</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">debian/tests/data/genomes/dwv.fasta.fai.gz</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">debian/tests/data/genomes/dwv.fasta.gz</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">debian/tests/data/reads/SRR059298_subset.fastq.gz</span></pre>
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<a href="https://salsa.debian.org/med-team/gasic/-/compare/0c51555761bd86d7ad4110ae12820383c0707064...f2779eb9678c3d88f643a61755f330dcd35aefd9#d05d19370642bb823275fab19a195aeecd6e5147"><strong>debian/tests/data/genomes/dwv.fasta-e.gz</strong>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">dwv</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">vdv1</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">vdv1dwv5</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">vdv1dwv9</span></pre>
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<a href="https://salsa.debian.org/med-team/gasic/-/compare/0c51555761bd86d7ad4110ae12820383c0707064...f2779eb9678c3d88f643a61755f330dcd35aefd9#651cd058599fc98d53bb65150d3ba460bd5b02a9"><strong>debian/tests/data/names.gz</strong>
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<a href="https://salsa.debian.org/med-team/gasic/-/compare/0c51555761bd86d7ad4110ae12820383c0707064...f2779eb9678c3d88f643a61755f330dcd35aefd9#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -15,13 +15,33 @@ cd "${AUTOPKGTEST_TMP}"</td>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[93m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mTest 0: Create Genome Indices</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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18
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>genomes</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">bwa index dwv.fasta</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">bwa index vdv1.fasta </span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell">bwa index vdv1dwv9.fasta</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">bwa index vdv1dwv5.fasta</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ..</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[92m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mPassed</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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19
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"><span class="idiff left right">bowtie-build dwv.fasta dwv.fasta</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"><span class="idiff left right">bowtie-build vdv1.fasta vdv1.fasta </span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"><span class="idiff left right">bowtie-build vdv1dwv9.fasta vdv1dwv9.fasta</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"><span class="idiff left right">bowtie-build vdv1dwv5.fasta vdv1dwv5.fasta</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-e</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\e</span></span><span class="s2" style="color: #d14;"><span class="idiff">[93m</span></span><span class="se" style="color: #d14;"><span class="idiff">\e</span></span><span class="s2" style="color: #d14;"><span class="idiff">[1mTest 1: run_mappers</span></span><span class="se" style="color: #d14;"><span class="idiff">\e</span></span><span class="s2" style="color: #d14;"><span class="idiff right">[0m"</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="29" 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">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="idiff left">run_mappers names reads/SRR059298_subset.fastq </span><span class="nt" style="color: #000080;"><span class="idiff">-i</span></span><span class="idiff"> ./genomes/%s.fasta </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff"> ./SAM/mapped_%s.sam </span><span class="nt" style="color: #000080;"><span class="idiff">-m</span></span><span class="idiff right"> bwa</span></span>
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<td class="diff-line-num new new_line" data-linenumber="30" 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">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-e</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\e</span></span><span class="s2" style="color: #d14;"><span class="idiff">[92m</span></span><span class="se" style="color: #d14;"><span class="idiff">\e</span></span><span class="s2" style="color: #d14;"><span class="idiff">[1mPassed</span></span><span class="se" style="color: #d14;"><span class="idiff">\e</span></span><span class="s2" style="color: #d14;"><span class="idiff right">[0m"</span></span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;"><span class="idiff left right">echo</span></span></span>
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24
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[93m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mTest 2: create_matrix</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell">create_matrix names <span class="nt" style="color: #000080;">-s</span> mason_illumina <span class="nt" style="color: #000080;">-m</span> bwa <span class="nt" style="color: #000080;">-r</span> genomes/%s.fasta <span class="nt" style="color: #000080;">-i</span> genomes/%s.fasta <span class="nt" style="color: #000080;">-t</span> ./SAM</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[92m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mPassed</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[93m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mTest 3: correct_abundances</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell">correct_abundances names <span class="nt" style="color: #000080;">-s</span> ./SAM/mapped_%s.sam <span class="nt" style="color: #000080;">-m</span> similarity_matrix.npy <span class="nt" style="color: #000080;">-o</span> results.txt</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[92m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mPassed</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[93m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mTest 4: quality_check</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell">quality_check ./SAM/mapped_vdv1.sam</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[92m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mPassed</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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26
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="shell"></span></pre>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell">run_mappers names reads/SRR059298_subset.fastq <span class="nt" style="color: #000080;">-i</span> ./genomes/%s.fasta <span class="nt" style="color: #000080;">-o</span> ./SAM/mapped_%s.sam <span class="nt" style="color: #000080;">-m</span> bowtie</span></pre>
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