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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/bowtie">Debian Med / bowtie</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie/commit/9c2d1ce50b468111f3676e7a73601c3cc797c467">9c2d1ce5</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-01-07T12:09:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">try out "make simple-test"
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie/commit/014701beb183d1c6f43615f8ec7edd455fa24d25">014701be</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-01-07T12:11:13+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">R-U: autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie/commit/ca149dd08c93cd4537c02c84f03a098b05c83a15">ca149dd0</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-01-07T13:07:52+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Run upstream's tests in addition to our own
Remove obsolete fields Contact from debian/upstream/metadata.
</pre>
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<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#0a860cdba9fc7bcf6b28c442b89b1e1f2c4add92">
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+
debian/patches/simple-test
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bowtie/compare/fbfe4d2485a081c5ae467d7912586387ab8d2d3e...ca149dd08c93cd4537c02c84f03a098b05c83a15#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bowtie (1.2.3+dfsg-3) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * `make simple-test` in addition to our own tests</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Remove obsolete fields Contact from debian/upstream/metadata.</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"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Tue, 07 Jan 2020 12:11:17 +0100</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">bowtie (1.2.3+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Use python3 in (Build-)Depends in d/control</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/bowtie/compare/fbfe4d2485a081c5ae467d7912586387ab8d2d3e...ca149dd08c93cd4537c02c84f03a098b05c83a15#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +12,9 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libtbb-dev,</span>
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<td class="diff-line-num old_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"> python3,</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"> seqan-dev,</span>
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<td class="diff-line-num old old_line" data-linenumber="15" 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="15" 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="LC15" class="line" lang="plaintext"> zlib1g-dev</span>
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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> libclone-perl,</span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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="LC17" class="line" lang="plaintext"> libtest-deep-perl</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Standards-Version: 4.4.0</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/bowtie</span>
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18
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/bowtie.git</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">@@ -20,6 +22,7 @@ Homepage: http://bowtie-bio.sourceforge.net/</td>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Package: bowtie</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Architecture: alpha any-amd64 arm64 mips64el ppc64 ppc64el s390x sparc64</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Multi-Arch: foreign</span>
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23
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> python3</span>
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<a href="https://salsa.debian.org/med-team/bowtie/compare/fbfe4d2485a081c5ae467d7912586387ab8d2d3e...ca149dd08c93cd4537c02c84f03a098b05c83a15#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">@@ -16,3 +16,4 @@ enable_arm64.patch</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">reproducible.patch</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">gcc-64bit.patch</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">build-as-Cpp03.patch</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">simple-test</span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie/compare/fbfe4d2485a081c5ae467d7912586387ab8d2d3e...ca149dd08c93cd4537c02c84f03a098b05c83a15#0a860cdba9fc7bcf6b28c442b89b1e1f2c4add92"><strong>debian/patches/simple-test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: Sys::Info isn't packaged for Debian, so work around it</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bowtie.orig/scripts/test/simple_tests.pl</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bowtie/scripts/test/simple_tests.pl</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -14,8 +14,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> use DNA;</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> use Clone qw(clone);</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> use Test::Deep;</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;">-use Sys::Info;</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-use Sys::Info::Constants qw( :device_cpu );</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> my $bowtie = "";</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> my $bowtie_build = "";</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -1130,9 +1128,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> while(<FA>) { print $_; }</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> close(FA);</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> if($do_build) {</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;">- my $info = Sys::Info->new;</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;">- my $cpu = $info->device('CPU');</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;">- my $nthreads = int(rand($cpu->count || 1)) + 1;</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;">+ my $nthreads = 2;</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> my $build_args = "";</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> $build_args .= " -C " if $color;</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> my $cmd = "$bowtie_build $idx_type --threads $nthreads --quiet --sanity $build_args $fa .simple_tests.tmp";</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -1285,7 +1281,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> my $tmpfafn = ".simple_tests.pl.fa";</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> my $last_ref = undef;</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> foreach my $large_idx (undef,1) {</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- foreach my $debug_mode (1,undef) {</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ foreach my $debug_mode (undef) {</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> for (my $ci = 0; $ci < scalar(@cases); $ci++) {</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> my $c = $cases[$ci];</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> last unless defined($c);</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;">--- bowtie.orig/Makefile</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;">+++ bowtie/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="p">@@ -438,12 +438,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> done</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> .PHONY: simple-test</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-simple-test: allall perl-deps</span></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;">- eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \</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;">+simple-test: all</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> ./scripts/test/simple_tests.pl --bowtie=./bowtie --bowtie-build=./bowtie-build</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> .PHONY: random-test</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-random-test: all perl-deps</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+random-test: all</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> ./scripts/test/random_bowtie_tests.sh</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> </span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/bowtie/compare/fbfe4d2485a081c5ae467d7912586387ab8d2d3e...ca149dd08c93cd4537c02c84f03a098b05c83a15#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -44,10 +44,9 @@ override_dh_auto_clean:</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> # print DEB_BUILD_OPTIONS</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> $(info $$DEB_BUILD_OPTIONS is [${DEB_BUILD_OPTIONS}])</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> make simple-test</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> ln -s debian/tests</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> sh debian/tests/run-unit-test test_at_build_time</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> <span class="idiff left right">unset LD_PRELOAD && </span>sh debian/tests/run-unit-test test_at_build_time</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> rm -f tests examples[0-9].out</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext">endif</span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie/compare/fbfe4d2485a081c5ae467d7912586387ab8d2d3e...ca149dd08c93cd4537c02c84f03a098b05c83a15#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">@@ -5,13 +5,13 @@ if [ "$1" = "test_at_build_time" ] ; then</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">PATH</span><span class="o" style="font-weight: 600;">=</span>.:<span class="nv" style="color: #008080;">$PATH</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>bowtie</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">A<span class="idiff left right">DT</span>TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">A<span class="idiff left right">UTOPKGTEST_</span>TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span>/tests</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> debian/tests/example<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span>/tests</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/bowtie/examples/indexes <span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span>/tests</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> debian/tests/example<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span>/tests</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/bowtie/examples/indexes <span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell">check_result <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/bowtie/compare/fbfe4d2485a081c5ae467d7912586387ab8d2d3e...ca149dd08c93cd4537c02c84f03a098b05c83a15#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Contact: Ben Langmead <blangmea@jhsph.edu></span>
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2
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> author: ></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Ben Langmead and Cole Trapnell and Mihai Pop and Steven L Salzberg</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> title: ></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> Ultrafast and memory-efficient alignment of short DNA sequences to</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> the human genome</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> journal: Genome Biology</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> volume: 10</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> pages: R25</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> year: 2009</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> DOI: 10.1186/gb-2009-10-3-r25</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> URL: http://genomebiology.com/2009/10/3/R25</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> eprint: http://genomebiology.com/content/pdf/gb-2009-10-3-r25.pdf</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> author: "Ben Langmead and Cole Trapnell and Mihai Pop and Steven L Salzberg\n"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> title: "Ultrafast and memory-efficient alignment of short DNA sequences to the human\</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> \ genome\n"</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> journal: Genome Biology</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> volume: 10</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> pages: R25</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> year: 2009</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> DOI: 10.1186/gb-2009-10-3-r25</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> URL: http://genomebiology.com/2009/10/3/R25</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">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> eprint: http://genomebiology.com/content/pdf/gb-2009-10-3-r25.pdf</span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
15
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<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">
12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Registry:</span>
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<td class="diff-line-num old old_line" data-linenumber="16" 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">
16
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<td class="diff-line-num new_line old" data-linenumber="13" 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="LC16" class="line" lang="plaintext"><span class="idiff left right"> </span>- Name: SciCrunch</span>
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<td class="diff-line-num old old_line" data-linenumber="17" 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">
17
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<td class="diff-line-num new_line old" data-linenumber="13" 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="LC17" class="line" lang="plaintext"> <span class="idiff left right"> </span>Entry: SCR_005476</span>
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<td class="diff-line-num old old_line" data-linenumber="18" 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">
18
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<td class="diff-line-num new_line old" data-linenumber="13" 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="LC18" class="line" lang="plaintext"><span class="idiff left right"> </span>- Name: OMICtools</span>
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<td class="diff-line-num old old_line" data-linenumber="19" 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">
19
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<td class="diff-line-num new_line old" data-linenumber="13" 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="LC19" class="line" lang="plaintext"> <span class="idiff left right"> </span>Entry: OMICS_00653</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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<td class="diff-line-num new_line old" data-linenumber="13" 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="LC20" class="line" lang="plaintext"><span class="idiff left right"> </span>- Name: bio.tools</span>
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<td class="diff-line-num old old_line" data-linenumber="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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<td class="diff-line-num new_line old" data-linenumber="13" 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="LC21" class="line" lang="plaintext"> <span class="idiff left right"> </span>Entry: bowtie</span>
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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
22
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<td class="diff-line-num new_line old" data-linenumber="13" 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="LC22" class="line" lang="plaintext"><span class="idiff left right"> </span>- Name: conda:bioconda</span>
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<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
23
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<td class="diff-line-num new_line old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> <span class="idiff left right"> </span>Entry: bowtie</span></pre>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">- Name: SciCrunch</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Entry: SCR_005476</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">- Name: OMICtools</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> Entry: OMICS_00653</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">- Name: bio.tools</span>
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<td class="diff-line-num new new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> Entry: bowtie</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">- Name: conda:bioconda</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> Entry: bowtie</span></pre>
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