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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/snpeff">Debian Med / snpeff</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/7891daf027b4b1d1b8a4a01fd765fb5ad0816eae">7891daf0</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-06T20:55:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removing README.source about Mavenization
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/9a35e508be4088a8285d04c7802d87b195ecacb3">9a35e508</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-08T17:24:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refreshing classpath and dependencies
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/de0ec85971e844d7c3cafea1dd1f409f71330675">de0ec859</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-08T23:51:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Having the conffile provided by libsnpeff-java instead of snpeff, as the lib itself now needs it
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/65451ea236c5a555544b902323cf516045c0924a">65451ea2</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-08T23:51:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding autopkgtest
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/c2b3c1b3a7862bdfc2d7ba86fa4afb7418c9e023">c2b3c1b3</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-08T23:53:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating changelog
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<h4>11 changed files:</h4>
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<li class="file-stats">
<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
debian/README.Debian
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<li class="file-stats">
<a href="#cf9802e192b48f765b1b5c8268d550d89c933053">
<span class="deleted-file">
−
debian/README.source
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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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<li class="file-stats">
<a href="#421b2289d48481a6f602903ce0a8cba782533109">
<span class="new-file">
+
debian/libsnpeff-java.install
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<li class="file-stats">
<a href="#a48018bf42326f9230994db72d9d6d5753df88e3">
<span class="new-file">
+
debian/libsnpeff-java.maintscript
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<li class="file-stats">
<a href="#586be86c96c4f5565540f46cb13fca5585d2f3e5">
debian/libsnpeff-java.manifest
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<li class="file-stats">
<a href="#94bfc9b7b2edebd4dc49a7edd537fcb53d71efa6">
debian/patches/update_launching_script_and_config_file_for_Debian.patch
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<li class="file-stats">
<a href="#c010e67beab6a47730d0e8ec966e11bb2109a001">
debian/snpeff.install
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/snpeff/-/compare/8a6e5f9df6dcd3a9662b1c52c18ed6dac838599d...c2b3c1b3a7862bdfc2d7ba86fa4afb7418c9e023#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">When getting SnpEff from the upstream source repository, the configuration file</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">snpEff.config usually sits next to the jar; this is not the case for the Debian</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">packaging, because the jar is in /usr/share/java. So I am shipping a default</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">/etc/snpEff.config file and it will be copied into<span class="idiff left right"> ~/.snpEff/snpEff.config,</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">which will be used, if the latter does not exist and<span class="idiff left right"> if no other config file is</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">given in the command line invocation.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">/etc/<span class="idiff left right">snpeff/</span>snpEff.config file and it will be copied into</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"><span class="idiff left right">~/.snpEff/snpEff.config, </span>which will be used, if the latter does not exist and</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"><span class="idiff left right">if no other config file is </span>given in the command line invocation.</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">Moreover, by default data downloaded from the Internet by snpEff will be put</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">into ~/.snpEff/data. The users can change this by editing their per-user config</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">file ~/.snpEff/snpEff.config or by providing another config file on the command</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">line.</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> -- Pierre Gruet <pgt@debian.org> <span class="idiff left">Sun, 21</span> Feb 202<span class="idiff">1 15</span>:4<span class="idiff">5</span>:1<span class="idiff right">0</span> +0100</span></pre>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> -- Pierre Gruet <pgt@debian.org> <span class="idiff left">Tue, 08</span> Feb 202<span class="idiff">2 23</span>:4<span class="idiff">4</span>:1<span class="idiff right">8</span> +0100</span></pre>
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<a href="https://salsa.debian.org/med-team/snpeff/-/compare/8a6e5f9df6dcd3a9662b1c52c18ed6dac838599d...c2b3c1b3a7862bdfc2d7ba86fa4afb7418c9e023#cf9802e192b48f765b1b5c8268d550d89c933053"><strong>debian/README.source</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Information about snpeff</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"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">This package was debianized using the mh_make command</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">from the maven-debian-helper package.</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">The build system uses Maven but prevents it from downloading</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">anything from the Internet, making the build compliant with</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">the Debian policy.</span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/snpeff/-/compare/8a6e5f9df6dcd3a9662b1c52c18ed6dac838599d...c2b3c1b3a7862bdfc2d7ba86fa4afb7418c9e023#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</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">@@ -4,16 +4,20 @@ snpeff (5.1+dfsg-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Using tags instead of releases in d/watch</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Refreshing patches</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Refreshing d/copyright</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> * Updating dependencies list and related Maven rules, notably<span class="idiff left right"> switching</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> to junit5</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Updating <span class="idiff left right">classpath, </span>dependencies list and related Maven rules, notably</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> <span class="idiff left right">switching </span>to junit5</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * The path of the config file in the source has moved</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Using Debian-packaged biojava4 instead of biojava6, while upstream</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> previously used biojava3</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Disabling tests needing files that are not available</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Marking the doc package as Multi-Arch: foreign</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * Adding a Lintian override for a file with very-long-lines</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> * Removing README.source about Mavenization</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> * Having the conffile provided by libsnpeff-java instead of snpeff, as the</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> lib itself now needs it</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> * Adding autopkgtest based on unit tests</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> -- Pierre Gruet <pgt@debian.org> <span class="idiff left right">Sat, 29 Jan 2022 15:15:09</span> +0100</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> -- Pierre Gruet <pgt@debian.org> <span class="idiff left right">Tue, 08 Feb 2022 23:51:48</span> +0100</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">snpeff (4.3t+dfsg1-2) unstable; urgency=medium</span>
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<a href="https://salsa.debian.org/med-team/snpeff/-/compare/8a6e5f9df6dcd3a9662b1c52c18ed6dac838599d...c2b3c1b3a7862bdfc2d7ba86fa4afb7418c9e023#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">@@ -41,7 +41,9 @@ Rules-Requires-Root: no</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">Package: libsnpeff-java</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"> ${maven:Depends}</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> ${maven:Depends},</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> libbiojava4-java,</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> libhtsjdk-java</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">Suggests: ${maven:OptionalDepends},</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> libsnpeff-java-doc</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">Description: genetic variant annotation and effect prediction toolbox - lib</span>
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<a href="https://salsa.debian.org/med-team/snpeff/-/compare/8a6e5f9df6dcd3a9662b1c52c18ed6dac838599d...c2b3c1b3a7862bdfc2d7ba86fa4afb7418c9e023#421b2289d48481a6f602903ce0a8cba782533109"><strong>debian/libsnpeff-java.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">snpEff</span><span class="mf" style="color: #099;">.</span><span class="n" style="color: #333;">config</span> <span class="n" style="color: #333;">etc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">snpeff</span></span></pre>
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<a href="https://salsa.debian.org/med-team/snpeff/-/compare/8a6e5f9df6dcd3a9662b1c52c18ed6dac838599d...c2b3c1b3a7862bdfc2d7ba86fa4afb7418c9e023#a48018bf42326f9230994db72d9d6d5753df88e3"><strong>debian/libsnpeff-java.maintscript</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># Removing the conffile, which is now shipped in libsnpef-java</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">mv_conffile /etc/snpEff.config /etc/snpeff/snpEff.config 5.1+dfsg-1~ snpeff</span></pre>
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<a href="https://salsa.debian.org/med-team/snpeff/-/compare/8a6e5f9df6dcd3a9662b1c52c18ed6dac838599d...c2b3c1b3a7862bdfc2d7ba86fa4afb7418c9e023#586be86c96c4f5565540f46cb13fca5585d2f3e5"><strong>debian/libsnpeff-java.manifest</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">/usr/share/java/snpeff.jar:</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> Class-Path: /usr/share/java/apfloat.jar /usr/share/java/charts4j.jar /usr/share/java/commons-cli.jar /usr/share/java/trove4j.jar /usr/share/java/freemarker.jar /usr/share/java/distlib.jar /usr/share/java/htsjdk.jar /usr/share/java/commons-math3.jar /usr/share/java/commons-io.jar /usr/share/java/commons-codec.jar <span class="idiff left">/usr/share/java/log4j-1.2.jar </span>/usr/share/java/biojava4-core.jar /usr/share/java/biojava4-structure.jar<span class="idiff right"> /usr/share/java/scala-library.jar</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Class-Path: /usr/share/java/apfloat.jar /usr/share/java/charts4j.jar /usr/share/java/commons-cli.jar /usr/share/java/trove4j.jar /usr/share/java/freemarker.jar /usr/share/java/distlib.jar /usr/share/java/htsjdk.jar /usr/share/java/commons-math3.jar /usr/share/java/commons-io.jar /usr/share/java/commons-codec.jar /usr/share/java/biojava4-core.jar /usr/share/java/biojava4-structure.jar</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> Main-Class: org.snpeff.SnpEff</span></pre>
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<a href="https://salsa.debian.org/med-team/snpeff/-/compare/8a6e5f9df6dcd3a9662b1c52c18ed6dac838599d...c2b3c1b3a7862bdfc2d7ba86fa4afb7418c9e023#94bfc9b7b2edebd4dc49a7edd537fcb53d71efa6"><strong>debian/patches/update_launching_script_and_config_file_for_Debian.patch</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: Alter the launching script and the config file for a Debian install</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Alter the launching script, the config file and relevant Java</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> files for a Debian install:</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"> - Simplify the paths to account for a Debian installation.</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"> - Use the default /etc/snpEff.config file as configuration file if no<span class="idiff left right"> file was</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> given in the command line: it will be copied into<span class="idiff left right"> ~/.snpEff/snpEff.config,</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> which will be used as the configuration file is no<span class="idiff left right"> other is given on the</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> command line.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> - Use the default /etc/<span class="idiff left right">snpeff/</span>snpEff.config file as configuration file if no</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="idiff left right"> file was</span> given in the command line: it will be copied into</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="idiff left right"> ~/.snpEff/snpEff.config,</span> which will be used as the configuration file is no</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="idiff left right"> other is given on the</span> command line.</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> - By default, put data in ~/.snpEff/data.</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> - Correct bashisms in the launching script.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> - In Config.java, use per-user config file if available. Else use the file in</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> /etc/snpeff. Else (which should normally just concern the unit tests), use</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> default file which should be in the source tree.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> - Indicate path to effective config file in Java files.</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt@debian.org></span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="p">Last-Update: 202<span class="idiff left">1</span>-02-<span class="idiff right">21</span></span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">Last-Update: 202<span class="idiff left">2</span>-02-<span class="idiff right">07</span></span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff">--- a/scripts/snpEff</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/snpEff</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -49,7 +54,7 @@ Last-Update: 2021-02-21</td>
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<pre style="margin: 0;"> <span id="LC54" 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="LC55" 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="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if [ -d ~/.snpEff -a ! -e ~/.snpEff/snpEff.config ]; then</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;">+ cp /etc/snpEff.config ~/.snpEff/snpEff.config</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cp /etc/<span class="idiff left right">snpeff/</span>snpEff.config ~/.snpEff/snpEff.config</span></span>
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<pre style="margin: 0;"> <span id="LC58" 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="LC59" 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="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pass_args="$pass_args -c $HOME/.snpEff/snpEff.config"</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -69,3 +74,284 @@ Last-Update: 2021-02-21</td>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="diff"> #---</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"> # Database repository: A URL to the server where you can download databases (command: 'snpEff download dbName')</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/PromoterSequences.java</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/PromoterSequences.java</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="p">@@ -63,7 +63,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> genes = new HashSet<Gene>();</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> Log.info("Loading database");</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String configFile = HOME + "/snpEff/snpEff.config";</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String configFile = HOME + "/.snpEff/snpEff.config";</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> config = new Config(genomeName, configFile);</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> config.loadSnpEffectPredictor();</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> snpEffectPredictor = config.getSnpEffectPredictor();</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/SnpEff.java</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/SnpEff.java</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="p">@@ -163,7 +163,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> public SnpEff() {</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> genomeVer = ""; // Genome version</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- configFile = Config.DEFAULT_CONFIG_FILE; // Config file</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ configFile = Config.defaultConfigFile(); // Config file</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> verbose = false; // Be verbose</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> debug = false; // Debug mode</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> quiet = false; // Be quiet</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/Config.java</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/Config.java</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="p">@@ -16,6 +16,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> public class Config implements Serializable, Iterable<String> {</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> public static final String DEFAULT_CONFIG_FILE = "snpEff.config";</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static final String ETC_CONFIG_FILE = "/etc/snpeff/snpEff.config";</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static final String PREFERRED_CONFIG_FILE = Gpr.HOME + "/.snpEff/snpEff.config";</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> public static final String DEFAULT_DATA_DIR = "./data";</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> // Keys in properties file</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> public static final String KEY_BUNDLE_SUFIX = ".bundle";</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="p">@@ -94,7 +96,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> * Create a config (uses DEFAULT_CONFIG_FILE)</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> public Config(String genomeVersion) {</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;">- init(genomeVersion, DEFAULT_CONFIG_FILE, null, null);</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;">+ init(genomeVersion, defaultConfigFile(), null, null);</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> }</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> </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"><span class="p">@@ -197,6 +199,23 @@</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC123" 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="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * If Debian-preferred config file is available, give it.</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * else, if the config file in /etc/snpeff is available, give it.</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * Else, default to DEFAULT_CONFIG_FILE.</span></span>
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<pre style="margin: 0;">+<span id="LC127" 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="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public static String defaultConfigFile() {</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;">+ File preferred = new File(PREFERRED_CONFIG_FILE);</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ File etcFile = new File(ETC_CONFIG_FILE);</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;">+ if (preferred.exists()) {</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return PREFERRED_CONFIG_FILE;</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ } else if (etcFile.exists()) {</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return ETC_CONFIG_FILE;</span></span>
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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;">+ } else {</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return DEFAULT_CONFIG_FILE;</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> /**</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> * Get a list of URLs that can be used to download a database</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> * Use compatible versions from 'getDatabaseCompatibilityVersions()'</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdProtein.java</span></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;">+++ b/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdProtein.java</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="p">@@ -48,7 +48,7 @@</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> int totalOk = 0;</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> int totalWarnings = 0;</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> int totalNotFound = 0;</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String configFile = Config.DEFAULT_CONFIG_FILE;</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;">+ String configFile = Config.defaultConfigFile();</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> String proteinFile = "";</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> Map<String, String> proteinByTrId;</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> AutoHashMap<String, List<Transcript>> trByChromo;</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;">--- a/src/main/java/org/snpeff/snpEffect/testCases/integration/CompareEffects.java</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/CompareEffects.java</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="p">@@ -42,7 +42,7 @@</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> this.verbose = verbose;</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> this.snpEffectPredictor = snpEffectPredictor;</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> initRand();</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- config = new Config("testCase", Config.DEFAULT_CONFIG_FILE);</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ config = new Config("testCase", Config.defaultConfigFile());</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> }</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> </span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> public CompareEffects(String genomeName, long randSeed, boolean verbose) {</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="p">@@ -50,7 +50,7 @@</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> this.randSeed = randSeed;</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> this.verbose = verbose;</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> initRand();</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- config = new Config("testCase", Config.DEFAULT_CONFIG_FILE);</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ config = new Config("testCase", Config.defaultConfigFile());</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"> }</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> </span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> /**</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="p">@@ -124,7 +124,7 @@</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> </span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> public void initSnpEffPredictor() {</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> // Create a config and force out snpPredictor for hg37 chromosome Y</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- config = new Config(genomeName, Config.DEFAULT_CONFIG_FILE);</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ config = new Config(genomeName, Config.defaultConfigFile());</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> </span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> if (snpEffectPredictor == null) {</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> config.loadSnpEffectPredictor();</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/testCases/integration/CompareToEnsembl.java</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/CompareToEnsembl.java</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="p">@@ -57,7 +57,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> public CompareToEnsembl(String genomeName, boolean throwException) {</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> this.throwException = throwException;</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> if (verbose) Log.info("Loading predictor");</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- config = new Config(genomeName, Config.DEFAULT_CONFIG_FILE);</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ config = new Config(genomeName, Config.defaultConfigFile());</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> config.loadSnpEffectPredictor();</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> snpEffectPredictor = config.getSnpEffectPredictor();</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> genome = config.getGenome();</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/testCases/integration/CreateSpliceSiteTestCase.java</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/CreateSpliceSiteTestCase.java</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="p">@@ -33,7 +33,7 @@</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> */</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> public void run() {</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> Log.debug("Loading config files");</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Config config = new Config("testCase", Config.DEFAULT_CONFIG_FILE);</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Config config = new Config("testCase", Config.defaultConfigFile());</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"> config.loadSnpEffectPredictor();</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> </span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> for (Gene gint : config.getGenome().getGenes()) {</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesHgvsBase.java</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesHgvsBase.java</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="p">@@ -75,7 +75,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> */</span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> protected void initSnpEffPredictor(boolean addUtrs, boolean onlyPlusStrand) {</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> // Create a config and force out snpPredictor for hg37 chromosome Y</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (config == null) config = new Config("testCase", Config.DEFAULT_CONFIG_FILE);</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (config == null) config = new Config("testCase", Config.defaultConfigFile());</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> // Initialize factory</span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> int maxGeneLen = 1000;</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationBase.java</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationBase.java</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="p">@@ -95,7 +95,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"> String expectedResult = Gpr.readFile(resultFile).trim();</span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"> // Build</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Config config = new Config(genome, Config.defaultConfigFile());</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> SnpEffPredictorFactoryRefSeq factory = new SnpEffPredictorFactoryRefSeq(config);</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> factory.setFileName(refSeqFile);</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> factory.setVerbose(verbose);</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="p">@@ -118,7 +118,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"> * Build a genome from a embl file and compare results to 'expected' results</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> public SnpEffectPredictor buildEmbl(String genome, String emblFile) {</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Config config = new Config(genome, Config.defaultConfigFile());</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> SnpEffPredictorFactoryEmbl sepEmbl = new SnpEffPredictorFactoryEmbl(config, emblFile);</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> SnpEffectPredictor sep = sepEmbl.create();</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> return sep;</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="p">@@ -132,7 +132,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> * Build a genome from a genbank file and compare results to 'expected' results</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> public SnpEffectPredictor buildGeneBank(String genome, String genBankFile, boolean circularCorrectlargeGap) {</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Config config = new Config(genome, Config.defaultConfigFile());</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> SnpEffPredictorFactoryGenBank sepfg = new SnpEffPredictorFactoryGenBank(config, genBankFile);</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> sepfg.setVerbose(verbose);</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"> sepfg.setCircularCorrectLargeGap(circularCorrectlargeGap);</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"><span class="p">@@ -158,7 +158,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> public SnpEffectPredictor buildGff3AndCompare(String genome, String gff3File, String resultFile, boolean readSeqs, boolean createRandSequences) {</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> // Build</span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Config config = new Config(genome, Config.defaultConfigFile());</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"> SnpEffPredictorFactoryGff3 fgff3 = new SnpEffPredictorFactoryGff3(config);</span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> fgff3.setVerbose(verbose);</span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"> if (gff3File != null) fgff3.setFileName(gff3File);</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"><span class="p">@@ -195,7 +195,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"> String expectedResult = Gpr.readFile(resultFile).trim();</span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"> // Build</span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);</span></span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Config config = new Config(genome, Config.defaultConfigFile());</span></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"> SnpEffPredictorFactoryGtf22 fgtf22 = new SnpEffPredictorFactoryGtf22(config);</span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"> fgtf22.setFileName(gtf22);</span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> fgtf22.setVerbose(verbose);</span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationExonFrame.java</span></span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationExonFrame.java</span></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"><span class="p">@@ -50,7 +50,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> //---</span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> // Load database and check some numbers</span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"> //---</span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String configFile = Config.DEFAULT_CONFIG_FILE;</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String configFile = Config.defaultConfigFile();</span></span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> Config config = new Config(genomeName, configFile);</span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"> if (verbose) Log.info("Loading database");</span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"> SnpEffectPredictor snpEffectPredictor = config.loadSnpEffectPredictor();</span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationLof.java</span></span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationLof.java</span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"><span class="p">@@ -281,7 +281,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"> // Load database</span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> String genomeVer = "testHg3766Chr1";</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- config = new Config(genomeVer, Config.DEFAULT_CONFIG_FILE);</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ config = new Config(genomeVer, Config.defaultConfigFile());</span></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"> config.loadSnpEffectPredictor();</span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"> config.setTreatAllAsProteinCoding(true); // For historical reasons...</span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"> config.getSnpEffectPredictor().buildForest();</span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationNmd.java</span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationNmd.java</span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="p">@@ -25,7 +25,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> // Load database</span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"> String genomeVer = "testHg3766Chr1";</span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> Log.debug("Loading database '" + genomeVer + "'");</span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Config config = new Config(genomeVer, Config.DEFAULT_CONFIG_FILE);</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Config config = new Config(genomeVer, Config.defaultConfigFile());</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"> config.setTreatAllAsProteinCoding(true); // For historical reasons...</span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"> config.loadSnpEffectPredictor();</span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationVariant.java</span></span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationVariant.java</span></span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="p">@@ -225,7 +225,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"> public void test_25_exon_bases() {</span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"> Log.debug("Test");</span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Config config = new Config("testCase", Config.DEFAULT_CONFIG_FILE);</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Config config = new Config("testCase", Config.defaultConfigFile());</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"> config.loadSnpEffectPredictor();</span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"> String fastaFile = path("testCase.fa");</span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"><span class="p">@@ -283,7 +283,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"> String gtfFile = path("ENSMUSG00000005763.gtf");</span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"> String genome = "testMm37.61";</span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Config config = new Config(genome, Config.defaultConfigFile());</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"> SnpEffPredictorFactoryGtf22 fgtf22 = new SnpEffPredictorFactoryGtf22(config);</span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> fgtf22.setFileName(gtfFile);</span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> fgtf22.setReadSequences(false); // Don't read sequences</span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesBase.java</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesBase.java</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="p">@@ -254,7 +254,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"> protected void initSnpEffPredictor(Gene[] genesToAdd) {</span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"> // Create a config and force out snpPredictor</span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"> if (config == null || config.getGenome() == null || !config.getGenome().getGenomeName().equals(genomeName)) {</span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- config = new Config(genomeName, Config.DEFAULT_CONFIG_FILE);</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ config = new Config(genomeName, Config.defaultConfigFile());</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"> // Initialize factory</span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesBaseApply.java</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesBaseApply.java</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"><span class="p">@@ -44,7 +44,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"> protected void initSnpEffPredictor() {</span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"> // Create a config and force out snpPredictor</span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"> if (config == null || config.getGenome() == null || !config.getGenome().getGenomeName().equals(genomeName)) {</span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- config = new Config(genomeName, Config.DEFAULT_CONFIG_FILE);</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ config = new Config(genomeName, Config.defaultConfigFile());</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"> // Create predictor</span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesBuild.java</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesBuild.java</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="p">@@ -30,7 +30,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> };</span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"> // Build</span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Config config = new Config(genome, Config.defaultConfigFile());</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> SnpEffPredictorFactoryGff3 sefGff = new SnpEffPredictorFactoryGff3(config);</span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"> sefGff.setFileName(gff);</span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"> sefGff.setVerbose(verbose);</span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"><span class="p">@@ -68,7 +68,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> };</span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"> // Build</span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Config config = new Config(genome, Config.DEFAULT_CONFIG_FILE);</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Config config = new Config(genome, Config.defaultConfigFile());</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"> SnpEffPredictorFactoryGff3 sefGff = new SnpEffPredictorFactoryGff3(config);</span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"> sefGff.setFileName(gff);</span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"> sefGff.setFastaFile(fasta);</span></pre>
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<a href="https://salsa.debian.org/med-team/snpeff/-/compare/8a6e5f9df6dcd3a9662b1c52c18ed6dac838599d...c2b3c1b3a7862bdfc2d7ba86fa4afb7418c9e023#c010e67beab6a47730d0e8ec966e11bb2109a001"><strong>debian/snpeff.install</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="php"><span class="n" style="color: #333;">scripts</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">snpEff</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span></span></pre>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="php"><span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">snpEff</span><span class="mf" style="color: #099;">.</span><span class="n" style="color: #333;">config</span> <span class="n" style="color: #333;">etc</span></span></pre>
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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-headless, junit5, libsnpeff-java, quilt</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/snpeff/-/compare/8a6e5f9df6dcd3a9662b1c52c18ed6dac838599d...c2b3c1b3a7862bdfc2d7ba86fa4afb7418c9e023#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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/bash</span></span>
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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>snpeff</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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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="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="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="si" 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="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</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="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Push patches if some of them still have to be applied, but don't fail else.</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nv" style="color: #008080;">QUILT_PATCHES</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"debian/patches"</span> quilt push <span class="nt" style="color: #000080;">-a</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">true</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Copying config file in home dir.</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nv" style="color: #008080;">HOME</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</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 class="s2" style="color: #d14;">"</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"xxxxxxxx </span><span class="nv" style="color: #008080;">$HOME</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"xxxxxxxx </span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">readlink</span> <span class="nt" style="color: #000080;">-f</span> ~<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</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;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> ~/.snpEff</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;">cp</span> /etc/snpeff/snpEff.config ~/.snpEff</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="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/org/snpeff/snpEffect/testCases/"</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> src/main/java/org/snpeff/snpEffect/testCases/integration <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/org/snpeff/snpEffect/testCases/"</span></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;">cp</span> <span class="nt" style="color: #000080;">-a</span> src/main/java/org/snpeff/snpEffect/testCases/unity <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/org/snpeff/snpEffect/testCases/"</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> tests/ <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</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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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" 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;">mkdir </span>classes/</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell">javac <span class="nt" style="color: #000080;">-d</span> classes <span class="nt" style="color: #000080;">-cp</span> /usr/share/java/junit-jupiter-api.jar:/usr/share/java/snpeff.jar:/usr/share/java/biojava4-core.jar:/usr/share/java/biojava4-sequencing.jar:/usr/share/java/biojava4-structure.jar org/snpeff/snpEffect/testCases/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.java</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Only running unit tests, not integration ones (needing data from the Internet)</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell">java <span class="nt" style="color: #000080;">-jar</span> /usr/share/java/junit-platform-console-standalone.jar <span class="nt" style="color: #000080;">--class-path</span> /usr/share/java/snpeff.jar:/usr/share/java/biojava4-sequencing.jar:classes <span class="nt" style="color: #000080;">--select-package</span> org.snpeff.snpEffect.testCases.unity</span></pre>
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