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<h3>
Sascha Steinbiss pushed to branch master
at <a href="https://salsa.debian.org/med-team/sspace">Debian Med / sspace</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sspace/commit/8e30a522d2723ca1b4a29ea0b96ee20dadb4b593">8e30a522</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2019-12-20T13:44:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bump Standards-Version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sspace/commit/8ca82b3c8a78cece18446687d4921f0c517efa53">8ca82b3c</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2019-12-20T13:44:28Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove debugging code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sspace/commit/4a26d3b34e33c8ebc139701919302d2a99553b6a">4a26d3b3</a></strong>
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<span>by Sascha Steinbiss</span>
<i>at 2019-12-20T13:44:33Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">use python3 dep
</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#159455bee6fdb73e8d11536e0452e47e714f8375">
<span class="deleted-file">
−
debian/patches/debug.patch
</span>
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#7163a2f4b02f1d500909e51d8a4afc1a59ff4e95">
debian/tests/example-tests
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/sspace/compare/5233f8b03b7dd384bdff3b0631dbf5238cf96dd0...4a26d3b34e33c8ebc139701919302d2a99553b6a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new_line" data-linenumber="1" 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="LC1" class="line" lang="plaintext">sspace (2.1.1+dfsg-5) unstable; 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 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"> [ Andreas Tille ]</span>
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Use 2to3 to port to Python3</span>
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<td class="diff-line-num new_line" data-linenumber="5" 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="LC5" class="line" lang="plaintext"> Closes: #938565</span>
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<td class="diff-line-num new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<td class="diff-line-num old old_line" data-linenumber="6" 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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<td class="diff-line-num new_line old" data-linenumber="7" 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="LC6" class="line" lang="plaintext"> * Standards-Version: 4.4.0</span>
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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * Remove trailing whitespace in debian/changelog</span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> * Fix permission of fasta file</span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></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"> [ Sascha Steinbiss ]</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"> * Bump Standards-Version.</span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 06 Sep 2019 12:03:56 +0200</span>
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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">sspace (2.1.1+dfsg-4) unstable; urgency=medium</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/sspace/compare/5233f8b03b7dd384bdff3b0631dbf5238cf96dd0...4a26d3b34e33c8ebc139701919302d2a99553b6a#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" 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="6" 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">@@ -6,10 +6,10 @@ Section: science</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> recode,</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> python,</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> python<span class="idiff left right">3</span>,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> asciidoctor,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> bowtie</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/sspace</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/sspace.git</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Homepage: https://github.com/nsoranzo/sspace_basic</span>
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<a href="https://salsa.debian.org/med-team/sspace/compare/5233f8b03b7dd384bdff3b0631dbf5238cf96dd0...4a26d3b34e33c8ebc139701919302d2a99553b6a#159455bee6fdb73e8d11536e0452e47e714f8375"><strong>debian/patches/debug.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/PairingAndScaffolding.pl</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/PairingAndScaffolding.pl</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">@@ -821,7 +821,7 @@</span> sub mapReadsWithBowtie{</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> my $procline = "bowtie -p $threads -v $gaps -m 1 bowtieoutput/$bowtieout --suppress 6,7 -f $singlereads --quiet --refidx |";</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> die "Contig file ($contigFile) not found. Exiting...\n" if(!(-e $contigFile));</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> &printMessage("\n=>".getDate().": Building Bowtie index for contigs\n");</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- system("bowtie-build $contigFile bowtieoutput/$bowtieout --quiet --noref") == 0 || die "\nBowtie-build error; $?"; # returns exit status values</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ system("bowtie-build $contigFile bowtieoutput/$bowtieout --quiet --noref") == 0 || die "\nBowtie-build error\n\tbowtie-build $contigFile bowtieoutput/$bowtieout --quiet --noref; $?"; # returns exit status values</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> #Treat the output of Bowtie differently if multithreading is used or not</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> readBowtieOneThread($procline) if($threads <= 1);</span></pre>
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<a href="https://salsa.debian.org/med-team/sspace/compare/5233f8b03b7dd384bdff3b0631dbf5238cf96dd0...4a26d3b34e33c8ebc139701919302d2a99553b6a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">shebangs.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">2to3.patch</span></pre>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">debug.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/sspace/compare/5233f8b03b7dd384bdff3b0631dbf5238cf96dd0...4a26d3b34e33c8ebc139701919302d2a99553b6a#7163a2f4b02f1d500909e51d8a4afc1a59ff4e95"><strong>debian/tests/example-tests</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">@@ -17,12 +17,6 @@ else</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">CMD</span><span class="o" style="font-weight: 600;">=</span>sspace</span>
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</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">
19
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-x</span></span>
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<td class="diff-line-num old old_line" data-linenumber="21" 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">
21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell">which python</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell">python</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell">which bowtie-build</span>
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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell">bowtie-build <span class="nt" style="color: #000080;">--help</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;">ls</span> <span class="nt" style="color: #000080;">-l</span></span>
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26
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="nv" style="color: #008080;">$CMD</span> <span class="nt" style="color: #000080;">-l</span> libraries.txt <span class="nt" style="color: #000080;">-s</span> contigs_abyss.fasta</span>
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<td class="diff-line-num old_line" data-linenumber="27" 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">
27
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="28" 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">
28
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> standard_output.final.evidence <span class="o" style="font-weight: 600;">]</span></span>
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