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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/alter-sequence-alignment">Debian Med / alter-sequence-alignment</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/alter-sequence-alignment/-/commit/cb6b5e033a23add9c88e4fd602f622b15eeb3ee8">cb6b5e03</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-16T16:34:49+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/alter-sequence-alignment/-/commit/74542cabf767e3068f91cc4d9ff68624af6b7b16">74542cab</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-16T16:35:12+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/alter-sequence-alignment/-/commit/a409cf3df289a98ed19fba066b599c6643ff0593">a409cf3d</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-16T16:35:12+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/alter-sequence-alignment/-/commit/e2d16f137eee0cd8d0f4d89070d78dc59b8655dd">e2d16f13</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-16T16:35:22+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/alter-sequence-alignment/-/commit/6c81a9fb56c7d9108e4d94697684b888204e14d7">6c81a9fb</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-16T16:35:22+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Rules-Requires-Root: no
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/alter-sequence-alignment/-/commit/cfe0b3242cf9d4889dc74742bd2425a9bc0776e9">cfe0b324</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-16T16:35:34+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Submit.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/alter-sequence-alignment/-/commit/22073afa95842928a9f5a0667ddeb58f877ddb44">22073afa</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-16T11:42:28+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set CLASSPATH
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/alter-sequence-alignment/-/commit/f4e1fb17243f50d690365bc4d51ee067131d5b08">f4e1fb17</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-16T11:42:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
<span class="new-file">
+
debian/salsa-ci.yml
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
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+
debian/tests/control
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
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+
debian/tests/run-unit-test
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/alter-sequence-alignment/-/compare/784dd949b12436812afb9d12c1bb8d093476f855...f4e1fb17243f50d690365bc4d51ee067131d5b08#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">alter-sequence-alignment (1.3.4-4) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team Upload.</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Remove substvars</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"> [ Nilesh Patra ]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Add autopkgtests</span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> * Standards-Version: 4.5.0 (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Add salsa-ci file (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Submit.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Mon, 16 Nov 2020 16:35:35 +0530</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">alter-sequence-alignment (1.3.4-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> * Replace python-markdown by markdown</span>
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<a href="https://salsa.debian.org/med-team/alter-sequence-alignment/-/compare/784dd949b12436812afb9d12c1bb8d093476f855...f4e1fb17243f50d690365bc4d51ee067131d5b08#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: java</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> javahelper,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> maven-debian-helper,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libproperties-maven-plugin-java,</span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
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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">@@ -13,10 +13,11 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libargs4j-java,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> rename,</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> markdown</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.1</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.0</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/alter-sequence-alignment</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/alter-sequence-alignment.git</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Homepage: http://sing.ei.uvigo.es/ALTER/</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Package: alter-sequence-alignment</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Architecture: all</span>
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<a href="https://salsa.debian.org/med-team/alter-sequence-alignment/-/compare/784dd949b12436812afb9d12c1bb8d093476f855...f4e1fb17243f50d690365bc4d51ee067131d5b08#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>
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<a href="https://salsa.debian.org/med-team/alter-sequence-alignment/-/compare/784dd949b12436812afb9d12c1bb8d093476f855...f4e1fb17243f50d690365bc4d51ee067131d5b08#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @, default-jdk</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/alter-sequence-alignment/-/compare/784dd949b12436812afb9d12c1bb8d093476f855...f4e1fb17243f50d690365bc4d51ee067131d5b08#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" 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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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"alter-sequence-alignment"</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">CUR_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</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="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;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</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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9
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<pre style="margin: 0;">+<span id="LC9" 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;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CUR_DIR</span><span class="k" style="font-weight: 600;">}</span>/alter-lib/src/main/java/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CUR_DIR</span><span class="k" style="font-weight: 600;">}</span>/alter-web/src/main/resources/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Test 1"</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">alter-sequence-alignment <span class="nt" style="color: #000080;">-i</span> muscle.aln <span class="nt" style="color: #000080;">-ia</span> <span class="nt" style="color: #000080;">-of</span> FASTA <span class="nt" style="color: #000080;">-oo</span> Linux <span class="nt" style="color: #000080;">-op</span> MUSCLE <span class="nt" style="color: #000080;">-o</span> test1</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> test1 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ./test1</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;">echo</span> <span class="s2" style="color: #d14;">"PASS"</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="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Test 2"</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">alter-sequence-alignment <span class="nt" style="color: #000080;">-i</span> tcoffee.aln <span class="nt" style="color: #000080;">-ia</span> <span class="nt" style="color: #000080;">-of</span> MSF <span class="nt" style="color: #000080;">-oo</span> Linux <span class="nt" style="color: #000080;">-op</span> TCoffee <span class="nt" style="color: #000080;">-o</span> test2</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> test2 <span class="o" style="font-weight: 600;">]</span> <span class="o" 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="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ./test2</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Test converter"</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;">cat</span> <span class="o" style="font-weight: 600;">></span>TestAlter.java <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">HERE</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="sh" style="color: #d14;">import es.uvigo.ei.sing.alter.converter.Converter;</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="sh" style="color: #d14;">import es.uvigo.ei.sing.alter.converter.DefaultFactory;</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="sh" style="color: #d14;">import es.uvigo.ei.sing.alter.parser.ParseException;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="sh" style="color: #d14;">import java.io.IOException;</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="sh" style="color: #d14;">import java.nio.file.Files;</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="sh" style="color: #d14;">import java.nio.file.Paths;</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="sh" style="color: #d14;">public class TestAlter {</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="sh" style="color: #d14;"> public static void main(String[] args) throws IOException {</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="sh" style="color: #d14;"> Converter converter = new DefaultFactory().getConverter(</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="sh" style="color: #d14;"> "Linux", // Input operating system (Linux, MacOS or Windows)</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="sh" style="color: #d14;"> "clustal", // Input program (Clustal, MAFFT, MUSCLE, PROBCONS or TCoffee)</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"><span class="sh" style="color: #d14;"> "NEXUS", // Input format (ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR)</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="sh" style="color: #d14;"> false, // Autodetect format (other input options are omitted)</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"><span class="sh" style="color: #d14;"> false, // Collapse sequences to haplotypes</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="sh" style="color: #d14;"> true, // Treat gaps as missing data when collapsing</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"><span class="sh" style="color: #d14;"> false, // Count missing data as differences when collapsing</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"><span class="sh" style="color: #d14;"> 0, // Connection limit (sequences differing at <= l sites will be collapsed) (default is l=0)</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="sh" style="color: #d14;"> "windows", // Output operating system (Linux, MacOS or Windows)</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"><span class="sh" style="color: #d14;"> "general", // Output program (jModelTest, MrBayes, PAML, PAUP, PhyML,</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"><span class="sh" style="color: #d14;"> // ProtTest, RAxML, TCS, CodABC,</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="sh" style="color: #d14;"> // BioEdit, MEGA, dnaSP, Se-Al, Mesquite, SplitsTree, Clustal, MAFFT,</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"><span class="sh" style="color: #d14;"> // MUSCLE, PROBCONS, TCoffee, Gblocks, SeaView, trimAl or GENERAL)</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"><span class="sh" style="color: #d14;"> "aln", // Output format (ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR)</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"><span class="sh" style="color: #d14;"> false, // Low case output</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"><span class="sh" style="color: #d14;"> false, // Output residue numbers (only ALN format)</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"><span class="sh" style="color: #d14;"> false, // Sequential output (only NEXUS and PHYLIP formats)</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"><span class="sh" style="color: #d14;"> false, // Output match characters</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"><span class="sh" style="color: #d14;"> "MyConverterApp" // identifier for log messages</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"><span class="sh" style="color: #d14;"> );</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell"></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="shell"><span class="sh" style="color: #d14;"> try {</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell"><span class="sh" style="color: #d14;"> String inputSequence = new String(Files.readAllBytes(Paths.get("clustal.nex")));</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"><span class="sh" style="color: #d14;"> String converted = converter.convert(inputSequence);</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell"></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell"><span class="sh" style="color: #d14;"> System.out.println("converted file:");</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"><span class="sh" style="color: #d14;"> System.out.println(converted);</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell"></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell"><span class="sh" style="color: #d14;"> } catch (ParseException e) {</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"><span class="sh" style="color: #d14;"> System.err.println("the input file seems to contain errors");</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="shell"><span class="sh" style="color: #d14;"> e.printStackTrace();</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="shell"><span class="sh" style="color: #d14;"> }</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="shell"></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="shell"><span class="sh" style="color: #d14;"> }</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="shell"><span class="sh" style="color: #d14;">}</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="shell"></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="shell"><span class="no" style="color: #008080;">HERE</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="shell"></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="shell"><span class="nv" style="color: #008080;">CLASSPATH</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">".:/usr/share/java/alter-lib.jar:/usr/share/java/alter.jar"</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="shell">javac TestAlter.java</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="shell">java TestAlter</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ./TestAlter<span class="k" style="font-weight: 600;">*</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span></span></pre>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/alter-sequence-alignment/-/compare/784dd949b12436812afb9d12c1bb8d093476f855...f4e1fb17243f50d690365bc4d51ee067131d5b08#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Bug-Submit: https://github.com/sing-group/ALTER/issues/new</span>
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1
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Reference:</span>
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2
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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"> Daniel Glez-Peña and Daniel Gómez-Blanco and Miguel Reboiro-Jato and</span>
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