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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/sumaclust">Debian Med / sumaclust</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sumaclust/-/commit/ba23c747cc86b7512c32fe768fe7d3cbe2f30bf2">ba23c747</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-04-03T16:41:05+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating fix_build patch after new upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sumaclust/-/commit/b5678dc0f1e690975f35eb01305b9e5a9917d7ab">b5678dc0</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-04-03T17:57:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Providing autopkgtests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sumaclust/-/commit/099bc8b2264a2f1efdbeb6b6bd4c48d1994507dd">099bc8b2</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-04-04T08:44:15+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding new uploader
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<li>
<strong><a href="https://salsa.debian.org/med-team/sumaclust/-/commit/d7a6b35e2cc87576446bc35be882d8ebd3cad269">d7a6b35e</a></strong>
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<span>by Pierre Gruet</span>
<i>at 2020-04-04T08:49:09+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Finalizing debian/changelog
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<h4>8 changed files:</h4>
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<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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<a href="#6dec30f8e16862dab64a62963e7c85766df0df63">
debian/patches/fix_build.patch
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<a href="#8ba9323f1a60d98416fe576221526ee5af6cf140">
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debian/tests/clusterIdenticalInputs
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debian/tests/clusterThreeInputs
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debian/tests/clusterTwoInputsTwoSuccessiveCalls
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<a href="#b184104d61b47be92fb6f22ba9e7bd6d1d1b7219">
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debian/tests/clusterTwoInputsTwoThresholds
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debian/tests/control
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/sumaclust/-/compare/57e9cf1041ecff94f17461f1ebb53f0ad732d111...d7a6b35e2cc87576446bc35be882d8ebd3cad269#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sumaclust (1.0.35-2) 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"> * Updating fix_build patch after new upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Providing autopkgtests</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Pierre Gruet <pgtdebian@free.fr> Sat, 04 Apr 2020 08:44:33 +0200</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">sumaclust (1.0.35-1) unstable; urgency=medium</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"> * New upstream version</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/sumaclust/-/compare/57e9cf1041ecff94f17461f1ebb53f0ad732d111...d7a6b35e2cc87576446bc35be882d8ebd3cad269#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: sumaclust</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Tim Booth <tbooth@ceh.ac.uk>,</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org>,</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Pierre Gruet <pgtdebian@free.fr></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12)</span>
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<li id="6dec30f8e16862dab64a62963e7c85766df0df63">
<a href="https://salsa.debian.org/med-team/sumaclust/-/compare/57e9cf1041ecff94f17461f1ebb53f0ad732d111...d7a6b35e2cc87576446bc35be882d8ebd3cad269#6dec30f8e16862dab64a62963e7c85766df0df63"><strong>debian/patches/fix_build.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,22 +2,19 @@ Description: Fix Build</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/952093</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"> https://bugs.debian.org/954262</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: <span class="idiff left right">Wed, 01 Apr 2020 14:36:2</span>7 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: <span class="idiff left right">Fri, 03 Apr 2020 16:40:1</span>7 +0200</span></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">--- a/Makefile</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;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">@@ -1,<span class="idiff left right">6 +1,6</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -1,<span class="idiff left right">4 +1,4</span> @@</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;">-PREFIX=/usr/local</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+PREFIX=/usr</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS=-I$(PREFIX)/include</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS=-I$(PREFIX)/include -I$(CURDIR)/sumalibs</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> EXEC = sumaclust</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> CFLAGS=-I$(PREFIX)/include</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/global.mk</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/global.mk</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="p">@@ -8,9 +8,9 @@</span><span class="idiff left right"> LDFLAGS:=$(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -8,9 +8,9 @@</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> ifeq ($(CC),gcc)</span>
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<a href="https://salsa.debian.org/med-team/sumaclust/-/compare/57e9cf1041ecff94f17461f1ebb53f0ad732d111...d7a6b35e2cc87576446bc35be882d8ebd3cad269#8ba9323f1a60d98416fe576221526ee5af6cf140"><strong>debian/tests/clusterIdenticalInputs</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># autopkgtest check: Run sumaclust on two identical chains with a threshold of </span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># 1 to check that only one cluster is created.</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># (C) 2020 Pierre Gruet.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">WORKDIR</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span><span class="si" style="color: #d14;">)</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: #008080;">$WORKDIR</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$WORKDIR</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOF</span><span class="sh" style="color: #d14;"> > inputIdentical.fasta</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="sh" style="color: #d14;">>SEQ_TEST1</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="sh" style="color: #d14;">CCAGATCTAGCTAGCTAGCTACAGCATCGACATCAGCACTCAGCACTCAG</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="sh" style="color: #d14;">>SEQ_TEST2</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="sh" style="color: #d14;">CCAGATCTAGCTAGCTAGCTACAGCATCGACATCAGCACTCAGCACTCAG</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="no" style="color: #008080;">EOF</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">sumaclust <span class="nt" style="color: #000080;">-t</span> 1. inputIdentical.fasta 2>&1 | <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-n</span> <span class="s1" style="color: #d14;">'/clusters/ s/.*Done : 100 \% *//p'</span> | <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-n</span> <span class="s1" style="color: #d14;">'s/ clusters.*//p'</span> | <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-q</span> <span class="s2" style="color: #d14;">"1"</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-ne</span> 0 <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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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">exit </span>1</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/sumaclust/-/compare/57e9cf1041ecff94f17461f1ebb53f0ad732d111...d7a6b35e2cc87576446bc35be882d8ebd3cad269#97b481542ead40b78e73a7740d187472e1a420a0"><strong>debian/tests/clusterThreeInputs</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># autopkgtest check: Run sumaclust on three different chains with a threshold </span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># of 0.97 to check that only two clusters are created.</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># (C) 2020 Pierre Gruet.</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">WORKDIR</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span><span class="si" style="color: #d14;">)</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: #008080;">$WORKDIR</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$WORKDIR</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOF</span><span class="sh" style="color: #d14;"> > inputThreeDifferent.fasta</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="sh" style="color: #d14;">>SEQ_TEST1</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="sh" style="color: #d14;">CCAGATCTAGCTAGCTAGCTACAGCATCGACATCAGCACTCAGCACTCAG</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="sh" style="color: #d14;">>SEQ_TEST2</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="sh" style="color: #d14;">TCAGATCTAGCTAGCTAGCTACAGCATCGACATCAGCACTCAGCACTCAG</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="sh" style="color: #d14;">>SEQ_TEST3</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="sh" style="color: #d14;">TTTCAGATCTAGCAAGCGAGCTGACTTACAGCATCGACATCAGCACTCAGCACTCAGTGAT</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="no" style="color: #008080;">EOF</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">sumaclust <span class="nt" style="color: #000080;">-t</span> 0.97 inputThreeDifferent.fasta 2>&1 | <span class="se" style="color: #d14;">\</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-n</span> <span class="s1" style="color: #d14;">'/clusters/ s/.*Done : 100 \% *//p'</span> | <span class="se" style="color: #d14;">\</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-n</span> <span class="s1" style="color: #d14;">'s/ clusters.*//p'</span> | <span class="se" style="color: #d14;">\</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-q</span> <span class="s2" style="color: #d14;">"2"</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-ne</span> 0 <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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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">exit </span>1</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"></span></pre>
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<li id="51fee6c9caa89d5921761cf9c46278a8c59e1b46">
<a href="https://salsa.debian.org/med-team/sumaclust/-/compare/57e9cf1041ecff94f17461f1ebb53f0ad732d111...d7a6b35e2cc87576446bc35be882d8ebd3cad269#51fee6c9caa89d5921761cf9c46278a8c59e1b46"><strong>debian/tests/clusterTwoInputsTwoSuccessiveCalls</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># autopkgtest check: Run sumaclust on two different chains with a threshold of </span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># 0.97, and then do a second run based on the output of the first one.</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Check that the chains are the same in the two output files, which is a kind </span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># of idempotency test.</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># (C) 2020 Pierre Gruet.</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nv" style="color: #008080;">WORKDIR</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: #008080;">$WORKDIR</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</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;">$WORKDIR</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOF</span><span class="sh" style="color: #d14;"> > inputTwoDifferent.fasta</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="sh" style="color: #d14;">>SEQ_TEST1</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="sh" style="color: #d14;">CCAGATCTAGCTAGCTAGCTACAGCATCGACATCAGCACTCAGCACTCAG</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="sh" style="color: #d14;">>SEQ_TEST2</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="sh" style="color: #d14;">CCAGATGATCTAGCTAGCTAGCTACAGCATTTGAACATCAGCACTGGATCAG</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="no" style="color: #008080;">EOF</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">sumaclust <span class="nt" style="color: #000080;">-t</span> 0.97 inputTwoDifferent.fasta <span class="o" style="font-weight: 600;">></span> outputTwoDifferent.fasta 2>&1</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell">sumaclust <span class="nt" style="color: #000080;">-t</span> 0.97 outputTwoDifferent.fasta <span class="o" style="font-weight: 600;">></span> outputTwoDifferent2.fasta 2>&1</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-n</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'2p;4p'</span> outputTwoDifferent.fasta <span class="o" style="font-weight: 600;">></span> extract</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;">sed</span> <span class="nt" style="color: #000080;">-n</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'2p;4p'</span> outputTwoDifferent2.fasta <span class="o" style="font-weight: 600;">></span> extract2</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell">diff extract extract2</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-ne</span> 0 <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="LC30" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">exit </span>1</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"></span></pre>
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<li id="b184104d61b47be92fb6f22ba9e7bd6d1d1b7219">
<a href="https://salsa.debian.org/med-team/sumaclust/-/compare/57e9cf1041ecff94f17461f1ebb53f0ad732d111...d7a6b35e2cc87576446bc35be882d8ebd3cad269#b184104d61b47be92fb6f22ba9e7bd6d1d1b7219"><strong>debian/tests/clusterTwoInputsTwoThresholds</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># autopkgtest check: Run sumaclust on two different chains with two different </span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># thresholds: 0.9 and 0.8. The first run must result in 2 clusters, the second </span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># one must result in 1 cluster.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># (C) 2020 Pierre Gruet.</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nv" style="color: #008080;">WORKDIR</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span><span class="si" style="color: #d14;">)</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: #008080;">$WORKDIR</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$WORKDIR</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOF</span><span class="sh" style="color: #d14;"> > inputTwoDifferent.fasta</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="sh" style="color: #d14;">>SEQ_TEST1</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="sh" style="color: #d14;">CCAGATCTAGCTAGCTAGCTACAGCATCGACATCAGCACTCAGCACTCAG</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="sh" style="color: #d14;">>SEQ_TEST2</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="sh" style="color: #d14;">CCAGATGATCTAGCTAGCTAGCTACAGCATTTGAACATCAGCACTGGATCAG</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="no" style="color: #008080;">EOF</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">sumaclust <span class="nt" style="color: #000080;">-t</span> 0.9 inputTwoDifferent.fasta 2>&1 | <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-n</span> <span class="s1" style="color: #d14;">'/clusters/ s/.*Done : 100 \% *//p'</span> | <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-n</span> <span class="s1" style="color: #d14;">'s/ clusters.*//p'</span> | <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-q</span> <span class="s2" style="color: #d14;">"2"</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-ne</span> 0 <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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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">exit </span>1</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell">sumaclust <span class="nt" style="color: #000080;">-t</span> 0.8 inputTwoDifferent.fasta 2>&1 | <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-n</span> <span class="s1" style="color: #d14;">'/clusters/ s/.*Done : 100 \% *//p'</span> | <span class="se" style="color: #d14;">\</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-n</span> <span class="s1" style="color: #d14;">'s/ clusters.*//p'</span> | <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-q</span> <span class="s2" style="color: #d14;">"1"</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-ne</span> 0 <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="LC35" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">exit </span>1</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/sumaclust/-/compare/57e9cf1041ecff94f17461f1ebb53f0ad732d111...d7a6b35e2cc87576446bc35be882d8ebd3cad269#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: clusterIdenticalInputs, clusterThreeInputs, clusterTwoInputsTwoSuccessiveCalls, clusterTwoInputsTwoThresholds</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span></pre>
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