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<h3>
Fabian Klötzl pushed to branch master
at <a href="https://salsa.debian.org/med-team/andi">Debian Med / andi</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/andi/commit/7c5591d20d77f99bafba587c2f2f1723e07c522b">7c5591d2</a></strong>
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<span>by Fabian Klötzl</span>
<i>at 2018-03-05T15:11:17+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">make unit tests reproducible
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<strong><a href="https://salsa.debian.org/med-team/andi/commit/cc25208fe3c40273e6166633951eba77f74c7019">cc25208f</a></strong>
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<span>by Fabian Klötzl</span>
<i>at 2018-03-05T15:16:50+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">document recent change
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<h4>3 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#1b219e8acbf9a435ab823eec62492cd0e972a8e9">
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debian/patches/0001-Make-unit-tests-reproducible.patch
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debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/andi/compare/ab7c981b3ccf459968f69a61e52818f70cc56eef...cc25208fe3c40273e6166633951eba77f74c7019#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">andi (0.12-2) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Derandomize unit tests. Fixes build failures.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Fabian Klötzl <kloetzl@evolbio.mpg.de> Mon, 05 Mar 2018 15:11:27 +0100</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">andi (0.12-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Team upload.</span>
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<li id="1b219e8acbf9a435ab823eec62492cd0e972a8e9">
<a href="https://salsa.debian.org/med-team/andi/compare/ab7c981b3ccf459968f69a61e52818f70cc56eef...cc25208fe3c40273e6166633951eba77f74c7019#1b219e8acbf9a435ab823eec62492cd0e972a8e9"><strong>debian/patches/0001-Make-unit-tests-reproducible.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From: Fabian Klötzl <kloetzl@evolbio.mpg.de></span>
</pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Date: Mon, 5 Mar 2018 14:43:06 +0100</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Subject: Make unit tests reproducible</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Applied-Upstream: https://github.com/EvolBioInf/andi/commit/394c3b4c3dfb8fd40530fd6815f300a273a309d2</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">---</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> test/low_homo.sh | 15 ++++++++++++---</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> test/nan.sh | 12 ++++++++++--</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> test/test_extra.sh | 15 ++++++++++++---</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> test/test_join.sh | 40 ++++++++++++++++++++++++++++++++--------</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> 4 files changed, 66 insertions(+), 16 deletions(-)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/test/low_homo.sh b/test/low_homo.sh</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gh" style="color: #999;">index 72d1693..11e889e 100755</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/low_homo.sh</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/low_homo.sh</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,8 +1,17 @@</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> #!/bin/bash -f</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./test/test_fasta -l 100000 > a.fa</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./test/test_fasta -l 100000 > b.fa</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./test/test_fasta -l 100 > both.fa</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SEED=${RANDOM_SEED:-0}</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SEED2=0</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SEED3=0</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if test $SEED -ne 0; then</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SEED=$((SEED + 1))</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SEED2=$((SEED + 2))</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SEED3=$((SEED + 3))</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+fi</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+./test/test_fasta -s $SEED -l 100000 > a.fa</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+./test/test_fasta -s $SEED2 -l 100000 > b.fa</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+./test/test_fasta -s $SEED3 -l 100 > both.fa</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> cat both.fa a.fa | awk -vRS='>' '{if($1 == "S0")print ">"$0 > "S0.fa"}'</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> cat both.fa b.fa | awk -vRS='>' '{if($1 == "S1")print ">"$0 > "S1.fa"}'</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/test/nan.sh b/test/nan.sh</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gh" style="color: #999;">index e0502d0..60db0e2 100755</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/nan.sh</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/nan.sh</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,15 @@</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> #!/bin/bash -f</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./test/test_fasta -l 10000 > a.fa</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./test/test_fasta -l 10000 > b.fa</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SEED=${RANDOM_SEED:-0}</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SEED2=0</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if test $SEED -ne 0; then</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SEED=$((SEED + 1))</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SEED2=$((SEED + 2))</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+fi</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+./test/test_fasta -s $SEED -l 10000 > a.fa</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+./test/test_fasta -s $SEED2 -l 10000 > b.fa</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> # this is expected to trigger the nan warning</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> ./src/andi -j a.fa b.fa 2>&1 | grep 'nan'</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/test/test_extra.sh b/test/test_extra.sh</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gh" style="color: #999;">index dbb23ea..c1c0641 100755</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/test_extra.sh</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/test_extra.sh</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -3,17 +3,26 @@</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> # Test if andi exists, and can be executed</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> ./src/andi --version > /dev/null || exit 1</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> </span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SEED=${RANDOM_SEED:-0}</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SEED2=0</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SEED3=0</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if test $SEED -ne 0; then</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SEED=$((SEED + 1))</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SEED2=$((SEED + 2))</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SEED3=$((SEED + 3))</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+fi</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> # Test andi for more than just two sequences at a time</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./test/test_fasta -l 100000 -d 0.01 -d 0.01 -d 0.01 -d 0.01 | ./src/andi > /dev/null || exit 1</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+./test/test_fasta -s $SEED -l 100000 -d 0.01 -d 0.01 -d 0.01 -d 0.01 | ./src/andi > /dev/null || exit 1</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> # Test low-memory mode</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./test/test_fasta -l 10000 > test_extra.fasta</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+./test/test_fasta -s $SEED2 -l 10000 > test_extra.fasta</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> ./src/andi test_extra.fasta > extra.out</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> ./src/andi test_extra.fasta --low-memory > extra_low_memory.out</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> diff extra.out extra_low_memory.out || exit 1</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> </span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> # Test file of filenames</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./test/test_fasta -l 10000 > test_extra.fasta</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+./test/test_fasta -s $SEED3 -l 10000 > test_extra.fasta</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> echo "$PWD/test_extra.fasta" > fof.txt</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> ./src/andi test_extra.fasta > extra.out</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> ./src/andi --file-of-filenames fof.txt > fof.out</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/test/test_join.sh b/test/test_join.sh</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gh" style="color: #999;">index 60e099a..33cc2c6 100755</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/test_join.sh</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/test_join.sh</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2,10 +2,19 @@</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> ./src/andi --help > /dev/null || exit 1</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> </span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SEED=${RANDOM_SEED:-0}</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SEED2=0</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SEED3=0</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if test $SEED -ne 0; then</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SEED=$((SEED + 1))</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SEED2=$((SEED + 2))</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SEED3=$((SEED + 3))</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+fi</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> # Simple join test</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./test/test_fasta -l 1000 -L 1000 -d 0.1 > p1.fasta</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./test/test_fasta -l 1000 -L 1000 -d 0.1 > p2.fasta</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./test/test_fasta -l 10000 -L 10000 -d 0.1 > p3.fasta</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p1.fasta</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+./test/test_fasta -s $SEED2 -l 1000 -L 1000 -d 0.1 > p2.fasta</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+./test/test_fasta -s $SEED3 -l 10000 -L 10000 -d 0.1 > p3.fasta</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> </span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> head -qn 2 p1.fasta p2.fasta p3.fasta > S0.fasta</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> tail -qn 2 p1.fasta p2.fasta p3.fasta > S1.fasta</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -25,9 +34,16 @@ if test $RES -ne 1; then</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> exit 1;</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> fi</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> </span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SEED=${RANDOM_SEED:-0}</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SEED2=0</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if test $SEED -ne 0; then</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SEED=$((SEED + 5))</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SEED2=$((SEED + 6))</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+fi</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> #unbalanced number of contigs</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./test/test_fasta -l 1000 -L 1000 -d 0.1 > p2.fasta</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./test/test_fasta -l 10000 -L 10000 -d 0.1 > p3.fasta</span></span>
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<td class="diff-line-num new new_line" data-linenumber="135" 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">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p2.fasta</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+./test/test_fasta -s $SEED2 -l 10000 -L 10000 -d 0.1 > p3.fasta</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> </span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> head -qn 2 p3.fasta > S0.fasta</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> tail -qn 2 p2.fasta p3.fasta > S1.fasta</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -47,11 +63,19 @@ if test $RES -ne 1; then</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> exit 1;</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> fi</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> </span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SEED=${RANDOM_SEED:-0}</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SEED2=0</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SEED3=0</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if test $SEED -ne 0; then</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SEED=$((SEED + 11))</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SEED2=$((SEED + 12))</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SEED3=$((SEED + 13))</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+fi</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> </span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> #unbalanced number of contigs 2</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./test/test_fasta -l 1000 -L 1000 -d 0.1 > p1.fasta</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./test/test_fasta -l 1000 -L 1000 -d 0.1 > p2.fasta</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./test/test_fasta -l 10000 -L 10000 -d 0.1 > p3.fasta</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p1.fasta</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+./test/test_fasta -s $SEED2 -l 1000 -L 1000 -d 0.1 > p2.fasta</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+./test/test_fasta -s $SEED3 -l 10000 -L 10000 -d 0.1 > p3.fasta</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> </span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> head -qn 2 p1.fasta p3.fasta > S0.fasta</span>
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<td class="diff-line-num new new_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> tail -qn 2 p1.fasta p2.fasta p3.fasta > S1.fasta</span></pre>
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<a href="https://salsa.debian.org/med-team/andi/compare/ab7c981b3ccf459968f69a61e52818f70cc56eef...cc25208fe3c40273e6166633951eba77f74c7019#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">0001-Make-unit-tests-reproducible.patch</span></pre>
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