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GitLab

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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/c815b41298d37f2bbc1455afa90deaf44e4db433">c815b412</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2020-12-04T17:06:49+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Deleting pom.xml patch, using d/maven.rules and d/maven.ignoreRules instead

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/b98871be8686c1049d434e82e617c8bc9daf3368">b98871be</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2020-12-04T17:07:47+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Attempting to git rid of akka using java.util.concurrent

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/cb1c0e773c9c086da2d77b747e28289b32a82e7b">cb1c0e77</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2020-12-04T17:08:46+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Switching to biojava4

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/c753fcadbdfdf417482f0e5d10f74a4a6e6b311f">c753fcad</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2020-12-04T17:09:19+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Taking samtools in libhtsjdk-java

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/e576b57421bfdf941a560ce1f32e360e64220a61">e576b574</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2020-12-04T17:10:07+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding scala as a dependency in the pom

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/dcf7f6dacbe9618c9e752b36f9183b1a46462894">dcf7f6da</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2020-12-04T17:11:08+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating build-dependencies

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/e8d6c062965531d811be6301a0221b64fc0216cb">e8d6c062</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2020-12-04T17:11:34+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">export LC_ALL=C.UTF-8

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/7b981b72947027ab2f35a3c788a1bc62194808df">7b981b72</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2020-12-04T17:12:17+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 13

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/240cf46fd9cad263b15b1cc53c3180e4c4697cb6">240cf46f</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2020-12-04T17:12:41+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards version 4.5.1

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/5e5ade1a52c783b6859d40da008c1b5e770af5da">5e5ade1a</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2020-12-04T17:15:01+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removing binary package snpsift, of which source is not in this package

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/fe681da29377fe736e7e4b41ed4f8d3584faa201">fe681da2</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2020-12-08T21:43:12+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reordering binary packages to put Maven stuff in the first one

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/0f8c0f43359d775f709e86de8c3d11906aa3a70d">0f8c0f43</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2020-12-08T21:43:33+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Having the unit tests run

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/678aa07c79bc433ed9f46d01b6fea4692d8198c7">678aa07c</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2020-12-08T21:43:56+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding a manifest for the main class and the classpath of the jar

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/e2e4ae63615ae8ea7e350bd60809637d08c8c9e6">e2e4ae63</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2020-12-08T21:46:23+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop d/maven.cleanIgnoreRules and d/maven.publishedRules which do nothing

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/531438dafeddff7865ac36953d4638a98ed59f26">531438da</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2020-12-09T21:19:25+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cleaning maven files in debian/

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/70555d6eae0edf3fe882da7213d779ed68f2c773">70555d6e</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2020-12-09T23:00:15+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Deleting rules linked to snpeff itself in d/maven.rules

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/301b16b7d5c73a326d8427165ced89359792c793">301b16b7</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2020-12-10T07:43:39+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Changing the section of the package to java

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/94094d57c976240df0f7095f30cfde0e9dcf8ef5">94094d57</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2020-12-10T23:47:11+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Having the complete version number in pom and in the name of the jar

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/0772e188d7e0fad41547fc151ff3be89ba8e9a16">0772e188</a></strong>

<div>

<span>by Pierre Gruet</span>

<i>at 2020-12-10T23:47:30+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update todo in d/changelog

</pre>

</li>

</ul>

<h4>19 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#586be86c96c4f5565540f46cb13fca5585d2f3e5">

<span class="new-file">

+

debian/libsnpeff-java.manifest

</span>

</a>

</li>

<li class="file-stats">

<a href="#8f26a3ee4710acd4172b137f1a6174dcf0808341">

debian/libsnpeff-java.poms

</a>

</li>

<li class="file-stats">

<a href="#5f7c96eb17e78b0de55008d54b51e8dee2f412bc">

<span class="deleted-file">

−

debian/maven.cleanIgnoreRules

</span>

</a>

</li>

<li class="file-stats">

<a href="#26121dc92cd4cd9822d2e9e2b619b799bf9a51f4">

debian/maven.ignoreRules

</a>

</li>

<li class="file-stats">

<a href="#d006b76813d91cccc2a85e222d10982eb5d52728">

<span class="deleted-file">

−

debian/maven.properties

</span>

</a>

</li>

<li class="file-stats">

<a href="#24b90c28b48ee27d2ecad460d66ac6959df5c033">

<span class="deleted-file">

−

debian/maven.publishedRules

</span>

</a>

</li>

<li class="file-stats">

<a href="#58530b38acb0fa3a65612c676abaea46c4a3f2f3">

debian/maven.rules

</a>

</li>

<li class="file-stats">

<a href="#dad1c764ef97fe56bf2081424eccb7987e4361c8">

<span class="new-file">

+

debian/patches/adapting_to_htsjdk.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#090dbfdd4da905a27df6ad036a69314ac3c39e2d">

<span class="new-file">

+

debian/patches/adding_scala_in_pom.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#e55e63231c28bebd84d729b0952e9a5a0f9db6d9">

<span class="new-file">

+

debian/patches/depending_on_biojava4.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#5d4bc5bec9cccce49eb00b14a49d6fa0feedbf70">

<span class="new-file">

+

debian/patches/fix_tests.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#e06a2c9f813d324237c5cdc37eb8277d157ffacb">

<span class="deleted-file">

−

debian/patches/pom_xml.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#aaf074da7d5fb997bc41e660dff8a9bc83c39576">

<span class="new-file">

+

debian/patches/prepare_to_put_package_version_in_pom.xml

</span>

</a>

</li>

<li class="file-stats">

<a href="#17563e1f4545f161f646a7b847a908f665bb1c7d">

<span class="new-file">

+

debian/patches/replacing_akka_with_java_util_concurrent.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

<li class="file-stats">

<a href="#8756c63497c8dc39f7773438edf53b220c773f67">

debian/rules

</a>

</li>

<li class="file-stats">

<a href="#f6c6956cf73acf73842e03af1a6088b689674ca7">

<span class="deleted-file">

−

debian/snpeff.poms

</span>

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/snpeff/-/compare/ddb09726588ba978ba10bc1b27e077b785cb86ee...0772e188d7e0fad41547fc151ff3be89ba8e9a16#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1

</td>

<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">snpeff (4.3t+dfsg-1) UNRELEASED; urgency=<span class="idiff left right">low</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">snpeff (4.3t+dfsg-1) UNRELEASED; urgency=<span class="idiff left right">medium</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

</td>

<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">  * Initial release (Closes: #<bug>)</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

</td>

<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">  TODO:</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5

</td>

<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">     apfloat 1.6.3:</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

</td>

<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">       https://github.com/mtommila/apfloat</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

7

</td>

<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">       http://www.apfloat.org/apfloat_java/maven.html</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

</td>

<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">     charts4j 1.3:</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

</td>

<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">       https://mvnrepository.com/artifact/com.googlecode.charts4j/charts4j/1.3</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

</td>

<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">     com.typesafe.akka:akka-actor 2.0.1</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

</td>

<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">     distlib 0.9.1:</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

</td>

<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">       https://sourceforge.net/projects/statdistlib/?source=navbar</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">    - replace name of the jar SnpEff.jar to snpeff.jar (Java policy)</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">    - fill in debian/copyright, maybe remove the html/ folder.</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">    - complete the binary package snpeff, add manpage, ...</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">    - check my patch replacing akka with java.util.concurrent.</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">    - snpsift is to package elsewhere on its own.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

</td>

<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

</td>

<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> -- <span class="idiff left right">Andreas Tille <tille@debian.org>  Wed, 22 Apr 2020 15:04:51 +02</span>00</span></pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- <span class="idiff left right">Pierre Gruet <pgtdebian@free.fr>  Thu, 10 Dec 2020 22:40:03 +01</span>00</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/snpeff/-/compare/ddb09726588ba978ba10bc1b27e077b785cb86ee...0772e188d7e0fad41547fc151ff3be89ba8e9a16#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

</td>

<td class="diff-line-num new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: snpeff</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

</td>

<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

</td>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

</td>

<td class="diff-line-num new_line old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">Section: <span class="idiff left right">science</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Section: <span class="idiff left right">java</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

</td>

<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

</td>

<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

</td>

<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">               javahelper,</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

</td>

<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">               default-jdk,</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

</td>

<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">               default-jdk-doc,</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

</td>

<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">               maven-debian-helper,</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

</td>

<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">               libmaven-assembly-plugin-java,</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

</td>

<td class="diff-line-num new_line old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">               libtrove-java,</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">               libtrove<span class="idiff left right">3</span>-java,</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

</td>

<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">               liblog4j1.2-java,</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

</td>

<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">               libhtsjdk-java,</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

</td>

<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">               libbiojava4-java,</span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +18,6 @@ Build-Depends: debhelper-compat (= 12),</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

</td>

<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">               libcommons-io-java,</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

</td>

<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">               libcommons-cli-java,</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

</td>

<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">               libcommons-math3-java,</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

21

</td>

<td class="diff-line-num new_line old" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">               libcommons-cli-java-doc,</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

</td>

<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">               libfreemarker-java,</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

</td>

<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">               libmaven-javadoc-plugin-java,</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

</td>

<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">               junit4-doc,</span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,18 +26,26 @@ Build-Depends: debhelper-compat (= 12),</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

27

</td>

<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

26

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">               libcommons-math3-java-doc,</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

28

</td>

<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

27

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">               libfreemarker-java-doc,</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

29

</td>

<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

28

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">               liblog4j1.2-java-doc,</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

30

</td>

<td class="diff-line-num new_line old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">               libtrove-java-doc</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

31

</td>

<td class="diff-line-num new_line old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">Standards-Version: 4.5.0</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

29

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">               libhtsjdk-java-doc,</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

30

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">               libbiojava4-java-doc,</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

31

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">               libtrove3-java-doc,</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

32

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">               libcharts4j-java,</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

33

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">               libapfloat-java,</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

34

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">               libdistlib-java,</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

35

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">               scala-library</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

36

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">Standards-Version: 4.5.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

32

</td>

<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

37

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/snpeff</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

33

</td>

<td class="diff-line-num new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

38

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/snpeff.git</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

34

</td>

<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">Homepage: http://snpeff.sourceforge.net/</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

35

</td>

<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">Rules-Requires-Root: no</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

36

</td>

<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

37

</td>

<td class="diff-line-num new_line old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">Package: <span class="idiff left right">snpeff</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

42

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">Package: <span class="idiff left right">libsnpeff-java</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

38

</td>

<td class="diff-line-num new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">Architecture: all</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

39

</td>

<td class="diff-line-num new_line old" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">Depends: ${java:Depends},</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

40

</td>

<td class="diff-line-num new_line old" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">         ${misc:Depends}</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

41

</td>

<td class="diff-line-num new_line old" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">Description: genetic variant annotation and effect prediction toolbox</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">Depends: ${misc:Depends},</span>

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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">         ${maven:Depends}</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">Suggests: ${maven:OptionalDepends},</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">          libsnpeff-java-doc</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Description: genetic variant annotation and effect prediction toolbox - lib</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> SnpEff is a variant annotation and effect prediction tool. It annotates</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> and predicts the effects of variants on genes (such as amino acid</span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> changes).</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -51,15 +58,29 @@ Description: genetic variant annotation and effect prediction toolbox</td>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"> calculates the effects they produce on known genes (e.g. amino acid</span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"> changes). A list of effects and annotations that SnpEff can calculate</span>

</pre>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"> can be found here.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> .</span>

</pre>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> This package contains the library.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext">Package: <span class="idiff left right">libsnpeff-java</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">Package: <span class="idiff left right">snpeff</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext">Architecture: all</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">Depends: ${misc:Depends},</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">         ${maven:Depends}</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">Suggests: ${maven:OptionalDepends},</span>

</pre>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">          libsnpeff-java-doc</span>

</pre>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext">Description: Snp Effect</span>

</pre>

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62

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<td class="diff-line-num new_line old" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext"> Variant annotation and effect prediction package.</span>

</pre>

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66

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">Depends: ${java:Depends},</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">         ${misc:Depends},</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

68

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">         libsnpeff-java (= ${binary:Version})</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">Description: genetic variant annotation and effect prediction toolbox - tool</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> SnpEff is a variant annotation and effect prediction tool. It annotates</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

71

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> and predicts the effects of variants on genes (such as amino acid</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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72

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> changes).</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> .</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> The inputs are predicted variants (SNPs, insertions, deletions and</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> MNPs). The input file is usually obtained as a result of a sequencing</span>

</pre>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> experiment, and it is usually in variant call format (VCF).</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> .</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> SnpEff analyzes the input variants. It annotates the variants and</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> calculates the effects they produce on known genes (e.g. amino acid</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> changes). A list of effects and annotations that SnpEff can calculate</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

81

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> can be found here.</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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82

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> .</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> This package contains the command line tool.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

63

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<td class="diff-line-num new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

84

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext">Package: libsnpeff-java-doc</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

65

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<td class="diff-line-num new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="plaintext">Architecture: all</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -72,14 +93,3 @@ Description: Documentation for Snp Effect</td>

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<td class="diff-line-num old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext"> Variant annotation and effect prediction package.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

73

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext"> .</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

74

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<td class="diff-line-num new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"> This package contains the API documentation of libsnpeff-java.</span></pre>

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<td class="diff-line-num old old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

76

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<td class="diff-line-num new_line old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext">Package: snpsift</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

77

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<td class="diff-line-num new_line old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">Architecture: all</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

78

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<td class="diff-line-num new_line old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext">Depends: ${java:Depends},</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

79

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext">         ${misc:Depends}</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext">Description: annotates genomic variants using databases</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext"> SnpSift annotates genomic variants using databases, filters, and</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

82

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<td class="diff-line-num new_line old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext"> manipulates genomic annotated variants. Once you annotated your files</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

83

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<td class="diff-line-num new_line old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext"> using SnpEff, you can use SnpSift to help you filter large genomic</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext"> datasets in order to find the most significant variants for your</span>

</pre>

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext"> experiment.</span></pre>

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<br>

</li>

<li id="586be86c96c4f5565540f46cb13fca5585d2f3e5">

<a href="https://salsa.debian.org/med-team/snpeff/-/compare/ddb09726588ba978ba10bc1b27e077b785cb86ee...0772e188d7e0fad41547fc151ff3be89ba8e9a16#586be86c96c4f5565540f46cb13fca5585d2f3e5"><strong>debian/libsnpeff-java.manifest</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">/usr/share/java/SnpEff.jar:</span>

</pre>

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2

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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/log4j-1.2.jar /usr/share/java/biojava4-core.jar /usr/share/java/biojava4-structure.jar /usr/share/java/scala-library.jar</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Main-Class: org.snpeff.SnpEff</span></pre>

</td>

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</table>

<br>

</li>

<li id="8f26a3ee4710acd4172b137f1a6174dcf0808341">

<a href="https://salsa.debian.org/med-team/snpeff/-/compare/ddb09726588ba978ba10bc1b27e077b785cb86ee...0772e188d7e0fad41547fc151ff3be89ba8e9a16#8f26a3ee4710acd4172b137f1a6174dcf0808341"><strong>debian/libsnpeff-java.poms</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">@@ -25,4 +25,4 @@</td>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">#   --site-xml=<location>: Optional, the location for site.xml if it needs to be installed.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">#     Empty by default. [mh_install]</span>

</pre>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">#</span>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">pom.xml<span class="idiff left right"> --has-package-version</span></span></pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">pom.xml</span></pre>

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</li>

<li id="5f7c96eb17e78b0de55008d54b51e8dee2f412bc">

<a href="https://salsa.debian.org/med-team/snpeff/-/compare/ddb09726588ba978ba10bc1b27e077b785cb86ee...0772e188d7e0fad41547fc151ff3be89ba8e9a16#5f7c96eb17e78b0de55008d54b51e8dee2f412bc"><strong>debian/maven.cleanIgnoreRules</strong>

deleted

</a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"></span></pre>

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<br>

</li>

<li id="26121dc92cd4cd9822d2e9e2b619b799bf9a51f4">

<a href="https://salsa.debian.org/med-team/snpeff/-/compare/ddb09726588ba978ba10bc1b27e077b785cb86ee...0772e188d7e0fad41547fc151ff3be89ba8e9a16#26121dc92cd4cd9822d2e9e2b619b799bf9a51f4"><strong>debian/maven.ignoreRules</strong></a>

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1

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">com.googlecode.charts4j charts4j * * * *</span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">com.typesafe.akka akka-actor * * * *</span></pre>

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4

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">distlib distlib * * * *</span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">org.apache.maven.plugins maven-assembly-plugin * * * *</span>

</pre>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">org.apache.maven.plugins maven-javadoc-plugin * * * *</span>

</pre>

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7

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">org.apfloat apfloat * * * *</span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">org.biojava biojava3-core * * * *</span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">org.biojava biojava3-structure * * * *</span>

</pre>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">samtools samtools * * * *</span></pre>

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<li id="d006b76813d91cccc2a85e222d10982eb5d52728">

<a href="https://salsa.debian.org/med-team/snpeff/-/compare/ddb09726588ba978ba10bc1b27e077b785cb86ee...0772e188d7e0fad41547fc151ff3be89ba8e9a16#d006b76813d91cccc2a85e222d10982eb5d52728"><strong>debian/maven.properties</strong>

deleted

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;"># Include here properties to pass to Maven during the build.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;"># For example:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;"># maven.test.skip=true</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;"># project.build.sourceEncoding=UTF-8</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC5" class="line" lang="properties"></span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="24b90c28b48ee27d2ecad460d66ac6959df5c033">

<a href="https://salsa.debian.org/med-team/snpeff/-/compare/ddb09726588ba978ba10bc1b27e077b785cb86ee...0772e188d7e0fad41547fc151ff3be89ba8e9a16#24b90c28b48ee27d2ecad460d66ac6959df5c033"><strong>debian/maven.publishedRules</strong>

deleted

</a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">org.snpeff SnpEff jar s/.*/debian/ * *</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="58530b38acb0fa3a65612c676abaea46c4a3f2f3">

<a href="https://salsa.debian.org/med-team/snpeff/-/compare/ddb09726588ba978ba10bc1b27e077b785cb86ee...0772e188d7e0fad41547fc151ff3be89ba8e9a16#58530b38acb0fa3a65612c676abaea46c4a3f2f3"><strong>debian/maven.rules</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

</td>

<td class="diff-line-num new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">junit junit jar s/4\..*/4.x/ * *</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

</td>

<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">org.snpeff SnpEff jar * * *</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

</td>

<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">org.snpeff SnpEff jar s/.*/debian/ * *</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

</td>

<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">log4j log4j * s/1\.2\..*/1.2.x/ * *</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

</td>

<td class="diff-line-num new_line old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">net.sf.trove4j trove4j * s/.*/2.x/ * *</span></pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">net.sf.trove4j trove4j * s/.*/debian/ * *</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">org.apfloat apfloat jar s/.*/debian/ * *</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">distlib distlib jar s/.*/debian/ * *</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">com.googlecode.charts4j charts4j jar s/.*/debian/ * *</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">commons-cli commons-cli jar s/.*/debian/ * *</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">junit junit jar s/4\..*/4.x/ * *</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">org.freemarker freemarker jar s/.*/debian/ * *</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">org.apache.commons commons-math3 jar s/.*/debian/ * *</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">commons-io commons-io jar s/.*/debian/ * *</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">commons-codec commons-codec jar s/.*/debian/ * *</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">s/samtools/com.github.samtools/ s/samtools/htsjdk/ jar s/.*/debian/ * *</span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">org.scala-lang scala-library jar s/2\..*/2.11.x/ * *</span></pre>

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<br>

</li>

<li id="dad1c764ef97fe56bf2081424eccb7987e4361c8">

<a href="https://salsa.debian.org/med-team/snpeff/-/compare/ddb09726588ba978ba10bc1b27e077b785cb86ee...0772e188d7e0fad41547fc151ff3be89ba8e9a16#dad1c764ef97fe56bf2081424eccb7987e4361c8"><strong>debian/patches/adapting_to_htsjdk.patch</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: adapting the program to use samtools from htsjdk</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> Imports in Java headers have to be changed.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> SAMFileReader has to be changed to SamReader.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Origin: htsjdk-api.patch of Sascha Steinbiss for fastqc</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Last-Update: 2020-12-04</span></span>

</pre>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff">--- a/src/main/java/org/snpeff/coverage/CountReads.java</span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/coverage/CountReads.java</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">@@ -1,6 +1,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> package org.snpeff.coverage;</span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> import java.io.File;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import java.io.IOException;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> import java.util.ArrayList;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> import java.util.Collection;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> import java.util.HashSet;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -22,9 +23,12 @@</span></span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> import org.snpeff.util.Timer;</span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> import org.snpeff.vcf.VcfEntry;</span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import net.sf.samtools.SAMFileReader;</span></span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import net.sf.samtools.SAMFileReader.ValidationStringency;</span></span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import net.sf.samtools.SAMRecord;</span></span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import htsjdk.samtools.SamInputResource;</span></span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import htsjdk.samtools.SamReader;</span></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import htsjdk.samtools.SamReaderFactory;</span></span>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import htsjdk.samtools.ValidationStringency;</span></span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import htsjdk.samtools.SAMRecord;</span></span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import htsjdk.samtools.util.RuntimeIOException;</span></span>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> /**</span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff">  * Count how many reads map (from many SAM/BAM files) onto markers</span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="p">@@ -197,35 +201,40 @@</span></span>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff">   * Count all markers from a SAM/BAM file</span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff">   */</span>

</pre>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff">  void countSamFile(String fileName) {</span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         // Open file</span></span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         int readNum = 1;</span></span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         SAMFileReader sam = new SAMFileReader(new File(fileName));</span></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         sam.setValidationStringency(ValidationStringency.SILENT);</span></span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         for (SAMRecord samRecord : sam) {</span></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                 try {</span></span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         if (!samRecord.getReadUnmappedFlag()) { // Mapped?</span></span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                 Chromosome chr = genome.getOrCreateChromosome(samRecord.getReferenceName());</span></span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                 if (chr != null) {</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                         // Create a marker from read</span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                         Marker read = new Marker(chr, samRecord.getAlignmentStart(), samRecord.getAlignmentEnd(), false, "");</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                         readLengthCount++;</span></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                         readLengthSum += read.size();</span></span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                         countMarker(fileName, read);</span></span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                 }</span></span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         }</span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         if (verbose) Gpr.showMark(readNum, SHOW_EVERY);</span></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         readNum++;</span></span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                 } catch (Exception e) {</span></span>

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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         countExceptions++;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         if (countExceptions < 10) e.printStackTrace();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         else if (countExceptions == 10) System.err.println("Not showing more exceptions!");</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                 }</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         sam.close();</span></span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                try {</span></span>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        // Open file</span></span>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        int readNum = 1;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        SamInputResource sir = SamInputResource.of(new File(fileName));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        SamReader sam = srf.open(sir);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        for (SAMRecord samRecord : sam) {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                try {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        if (!samRecord.getReadUnmappedFlag()) { // Mapped?</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                Chromosome chr = genome.getOrCreateChromosome(samRecord.getReferenceName());</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                if (chr != null) {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                        // Create a marker from read</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                        Marker read = new Marker(chr, samRecord.getAlignmentStart(), samRecord.getAlignmentEnd(), false, "");</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                        readLengthCount++;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                        readLengthSum += read.size();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

84

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                        countMarker(fileName, read);</span></span>

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<pre style="margin: 0;">+<span id="LC86" 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="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        if (verbose) Gpr.showMark(readNum, SHOW_EVERY);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        readNum++;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                } catch (Exception e) {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        countExceptions++;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        if (countExceptions < 10) e.printStackTrace();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        else if (countExceptions == 10) System.err.println("Not showing more exceptions!");</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        sam.close();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                } catch (final IOException e) {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        throw new RuntimeIOException(e);</span></span>

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<pre style="margin: 0;">+<span id="LC101" 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="LC102" class="line" lang="diff">         }</span>

</pre>

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff">         /**</span>

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdCount.java</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdCount.java</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="p">@@ -11,9 +11,11 @@</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> import org.snpeff.util.Gpr;</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> import org.snpeff.util.Timer;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import net.sf.samtools.AbstractBAMFileIndex;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import net.sf.samtools.BAMIndexMetaData;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import net.sf.samtools.SAMFileReader;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import htsjdk.samtools.AbstractBAMFileIndex;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import htsjdk.samtools.BAMIndexMetaData;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import htsjdk.samtools.SamInputResource;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import htsjdk.samtools.SamReader;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import htsjdk.samtools.SamReaderFactory;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> </span>

</pre>

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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">  * Count reads from a BAM file given a list of intervals</span>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="p">@@ -42,8 +44,10 @@</span></span>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff">         int countTotalReads(String samFileName) {</span>

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff">                 try {</span>

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff">                         if (verbose) Timer.showStdErr("Counting reads on file: " + samFileName);</span>

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        SAMFileReader samReader = new SAMFileReader(new File(samFileName));</span></span>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        AbstractBAMFileIndex index = (AbstractBAMFileIndex) samReader.getIndex();</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;">+                        SamInputResource sir = SamInputResource.of(new File(samFileName));</span></span>

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        SamReaderFactory srf = SamReaderFactory.makeDefault();</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;">+                        SamReader samReader = srf.open(sir);</span></span>

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        AbstractBAMFileIndex index = (AbstractBAMFileIndex) samReader.indexing().getIndex();</span></span>

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff">                         int count = 0;</span>

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff">                         for (int i = 0; i < index.getNumberOfReferences(); i++) {</span>

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff">                                 BAMIndexMetaData meta = index.getMetaData(i);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdPdb.java</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;">+++ b/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdPdb.java</span></span>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="p">@@ -35,7 +35,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> import org.snpeff.util.Gpr;</span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> import org.snpeff.util.Timer;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import net.sf.samtools.util.RuntimeEOFException;</span></span>

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import htsjdk.samtools.util.RuntimeEOFException;</span></span>

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> /**</span>

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff">  * PDB distance analysis</span>

</pre>

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/net/sf/samtools/tabix/TabixReader.java</span></span>

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/net/sf/samtools/tabix/TabixReader.java</span></span>

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="p">@@ -41,7 +41,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> import org.snpeff.interval.Variant;</span>

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> import org.snpeff.util.Gpr;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import net.sf.samtools.util.BlockCompressedInputStream;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import htsjdk.samtools.util.BlockCompressedInputStream;</span></span>

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> public class TabixReader implements Iterable<String> {</span>

</pre>

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> </span></pre>

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<br>

</li>

<li id="090dbfdd4da905a27df6ad036a69314ac3c39e2d">

<a href="https://salsa.debian.org/med-team/snpeff/-/compare/ddb09726588ba978ba10bc1b27e077b785cb86ee...0772e188d7e0fad41547fc151ff3be89ba8e9a16#090dbfdd4da905a27df6ad036a69314ac3c39e2d"><strong>debian/patches/adding_scala_in_pom.patch</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Adding the scala library as a dependency</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: no</span></span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2020-12-04</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/pom.xml</span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pom.xml</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -118,6 +118,11 @@</span></span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff">         <scope>system</scope></span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff">         <systemPath>/usr/share/java/biojava4-structure.jar</systemPath></span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff">     </dependency></span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    <dependency></span></span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      <groupId>org.scala-lang</groupId></span></span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      <artifactId>scala-library</artifactId></span></span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      <version>2.11.x</version></span></span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    </dependency></span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff">   </dependencies></span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff">   <repositories></span></pre>

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<br>

</li>

<li id="e55e63231c28bebd84d729b0952e9a5a0f9db6d9">

<a href="https://salsa.debian.org/med-team/snpeff/-/compare/ddb09726588ba978ba10bc1b27e077b785cb86ee...0772e188d7e0fad41547fc151ff3be89ba8e9a16#e55e63231c28bebd84d729b0952e9a5a0f9db6d9"><strong>debian/patches/depending_on_biojava4.patch</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Adapt pom and imports to biojava4</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2020-12-02</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/pom.xml</span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pom.xml</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -106,13 +106,17 @@</span></span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff">     </dependency></span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff">     <dependency></span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff">          <groupId>org.biojava</groupId></span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         <artifactId>biojava3-core</artifactId></span></span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         <version>3.0.7</version></span></span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+         <artifactId>biojava4-core</artifactId></span></span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+         <version>debian</version></span></span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        <scope>system</scope></span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        <systemPath>/usr/share/java/biojava4-core.jar</systemPath></span></span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff">     </dependency></span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff">     <dependency></span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff">          <groupId>org.biojava</groupId></span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         <artifactId>biojava3-structure</artifactId></span></span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         <version>3.0.7</version></span></span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+         <artifactId>biojava4-structure</artifactId></span></span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+         <version>debian</version></span></span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        <scope>system</scope></span></span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        <systemPath>/usr/share/java/biojava4-structure.jar</systemPath></span></span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff">     </dependency></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff">   </dependencies></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/pdb/DistanceResult.java</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/pdb/DistanceResult.java</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="p">@@ -1,6 +1,6 @@</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> package org.snpeff.pdb;</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

34

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.biojava.bio.structure.AminoAcid;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.structure.AminoAcid;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> import org.snpeff.interval.Chromosome;</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> import org.snpeff.interval.Transcript;</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> import org.snpeff.util.Gpr;</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/pdb/PdbFile.java</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/pdb/PdbFile.java</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="p">@@ -4,10 +4,10 @@</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> import java.io.IOException;</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> import java.io.InputStream;</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> </span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.biojava.bio.structure.Structure;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.biojava.bio.structure.io.FileParsingParameters;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.biojava.bio.structure.io.PDBFileParser;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.biojava3.core.util.InputStreamProvider;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.structure.Structure;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.structure.io.FileParsingParameters;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.structure.io.PDBFileParser;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.core.util.InputStreamProvider;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> /**</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff">  * A structure that reads PDB files</span>

</pre>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdPdb.java</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdPdb.java</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="p">@@ -15,16 +15,16 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> import java.util.Set;</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> import java.util.zip.GZIPOutputStream;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.biojava.bio.structure.AminoAcid;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.biojava.bio.structure.Atom;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.biojava.bio.structure.Calc;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.biojava.bio.structure.Chain;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.biojava.bio.structure.Compound;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.biojava.bio.structure.DBRef;</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.biojava.bio.structure.Group;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

70

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.biojava.bio.structure.Structure;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

71

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.biojava.bio.structure.StructureException;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

72

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.biojava.bio.structure.io.PDBFileReader;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

73

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.structure.AminoAcid;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

74

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.structure.Atom;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

75

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.structure.Calc;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

76

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.structure.Chain;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

77

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.structure.Compound;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

78

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.structure.DBRef;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

79

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.structure.Group;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

80

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.structure.GroupType;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

81

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.structure.Structure;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

82

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.structure.io.PDBFileReader;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> import org.snpeff.SnpEff;</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

84

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> import org.snpeff.interval.Gene;</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

85

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> import org.snpeff.interval.Transcript;</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="p">@@ -171,7 +171,7 @@</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff">                          if (debug) Gpr.debug("\tMapping OK    :\t" + trId + "\terror: " + err);</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> </span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff">                          int trAaLen = tr.protein().length();</span>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         int pdbAaLen = chain.getAtomGroups("amino").size();</span></span>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                         int pdbAaLen = chain.getAtomGroups(GroupType.AMINOACID).size();</span></span>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff">                          for (IdMapperEntry idm : idmapsOri) {</span>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff">                                  if (trId.equals(idm.trId) && pdbId.equals(idm.pdbId)) {</span>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="p">@@ -261,12 +261,8 @@</span></span>

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff">          for (Atom atom1 : aa1.getAtoms())</span>

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff">                  for (Atom atom2 : aa2.getAtoms()) {</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;">-                         try {</span></span>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                        double dist = Calc.getDistance(atom1, atom2);</span></span>

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                        distMin = Math.min(distMin, dist);</span></span>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                } catch (StructureException e) {</span></span>

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                        throw new RuntimeException(e);</span></span>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                }</span></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;">+                                double dist = Calc.getDistance(atom1, atom2);</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;">+                                distMin = Math.min(distMin, dist);</span></span>

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff">                         }</span>

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff">                 return distMin;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="p">@@ -307,14 +303,14 @@</span></span>

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff">          * I.e.: Organism matches</span>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff">          */</span>

</pre>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff">         boolean filterPdbChain(Chain chain) {</span>

</pre>

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                if (chain.getHeader() == null) return false;</span></span>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                if (chain.getCompound() == null) return false;</span></span>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff">                 // Try 'ORGANISM_SCINETIFIC'</span>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                String orgs = chain.getHeader().getOrganismScientific();</span></span>

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                String orgs = chain.getCompound().getOrganismScientific();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff">                 if (orgs != null && orgs.indexOf(pdbOrganismScientific) >= 0) return true;</span>

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff">                 // Try 'ORGANISM_COMMON'</span>

</pre>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                orgs = chain.getHeader().getOrganismCommon();</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;">+                orgs = chain.getCompound().getOrganismCommon();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff">                 if (orgs == null) return false;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff">                 // Multiple organisms?</span></pre>

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<br>

</li>

<li id="5d4bc5bec9cccce49eb00b14a49d6fa0feedbf70">

<a href="https://salsa.debian.org/med-team/snpeff/-/compare/ddb09726588ba978ba10bc1b27e077b785cb86ee...0772e188d7e0fad41547fc151ff3be89ba8e9a16#5d4bc5bec9cccce49eb00b14a49d6fa0feedbf70"><strong>debian/patches/fix_tests.patch</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: bringing corrections in failing tests</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> Deactivating tests requiring files that do not exist.</span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> Correcting an assertEquals to care for tiny numerical differences.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>

</pre>

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5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Forwarded: no</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Last-Update: 2020-12-08</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">--- a/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesGenomicSequences.java</span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesGenomicSequences.java</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -4,6 +4,7 @@</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> import java.util.Random;</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> import org.junit.Assert;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.junit.Ignore;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> import org.junit.Test;</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> import org.snpeff.binseq.GenomicSequences;</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> import org.snpeff.interval.Chromosome;</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -56,6 +57,7 @@</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff">   * Create many small chromosomes, check that they are saved in only one sequences.bin file</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff">   * Test that we can recover the exact sequences</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff">   */</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        @Ignore("relies on a file that does not exist")</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff">  @Test</span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff">  public void test_01() {</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff">          Gpr.debug("Test");</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="p">@@ -115,6 +117,7 @@</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff">   * and the large ones are saved into separate files</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff">   * Test that we can recover the exact sequences</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff">   */</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        @Ignore("relies on a file that does not exist")</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff">  @Test</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff">  public void test_02() {</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff">          Gpr.debug("Test");</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesZzz.java</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesZzz.java</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="p">@@ -3,6 +3,7 @@</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> import java.util.List;</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> import org.junit.Assert;</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.junit.Ignore;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> import org.junit.Test;</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> import org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase;</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> import org.snpeff.util.Gpr;</span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="p">@@ -68,6 +69,7 @@</span></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff">   * at GRCh38 chr1:1232300 includes NM_016176.3:c.-562A>C and NM_016547.2:c.-562A>C.</span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff">   *</span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff">   */</span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        @Ignore("it seems the file does not contain testHg38Chr1")</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff">  @Test</span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff">  public void test_06_hgvs_upstream_negative_strand() {</span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff">          Gpr.debug("Test");</span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesCytoBands.java</span></span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesCytoBands.java</span></span>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="p">@@ -1,6 +1,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> package org.snpeff.snpEffect.testCases.unity;</span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> import org.junit.Assert;</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;">+import org.junit.Ignore;</span></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> import org.junit.Test;</span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> import org.snpeff.interval.Chromosome;</span>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> import org.snpeff.interval.CytoBands;</span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="p">@@ -22,6 +23,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff">  /**</span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff">   * Test that we can load cytobands</span>

</pre>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff">   */</span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        @Ignore("seems to rely on a file which does not exist")</span></span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff">  @Test</span>

</pre>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff">  public void test01() {</span>

</pre>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff">          Gpr.debug("Test");</span>

</pre>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="p">@@ -39,6 +41,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff">  /**</span>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff">   * Query cytobands</span>

</pre>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff">   */</span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        @Ignore("seems to rely on a file which does not exist")</span></span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff">  @Test</span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff">  public void test02() {</span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff">          Gpr.debug("Test");</span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesGenePvalueList.java</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesGenePvalueList.java</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="p">@@ -134,7 +134,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff">          // Check pvalues</span>

</pre>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff">          double pvalue = gpl.score(ScoreSummary.Z_SCORES);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         Assert.assertEquals(0.01651203260896289, pvalue);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+         Assert.assertEquals(0.01651203260896289, pvalue, 1.E-13);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff">  }</span>

</pre>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff">  /**</span></pre>

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<br>

</li>

<li id="e06a2c9f813d324237c5cdc37eb8277d157ffacb">

<a href="https://salsa.debian.org/med-team/snpeff/-/compare/ddb09726588ba978ba10bc1b27e077b785cb86ee...0772e188d7e0fad41547fc151ff3be89ba8e9a16#e06a2c9f813d324237c5cdc37eb8277d157ffacb"><strong>debian/patches/pom_xml.patch</strong>

deleted

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">FIXME: I've found this on my hard disk some time ago - no idea what I was approaching</span></span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff">--- a/pom.xml</span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pom.xml</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="p">@@ -1,194 +1,143 @@</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"></span></span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  <modelVersion>4.0.0</modelVersion></span></span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  <groupId>org.snpeff</groupId></span></span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  <artifactId>SnpEff</artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  <packaging>jar</packaging></span></span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  <name>Snp Effect</name></span></span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  <description>Variant annotation and effect prediction package.</description></span></span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  <url>http://snpeff.sourceforge.net/</url></span></span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  <licenses></span></span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    <license></span></span>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <name>GNU LESSER GENERAL PUBLIC LICENSE, Version 3.0</name></span></span>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <url>http://www.gnu.org/licenses/lgpl-3.0.txt</url></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <distribution>repo</distribution></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    </license></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  </licenses></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  <!--</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<?xml version='1.0' encoding='UTF-8'?></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <modelVersion>4.0.0</modelVersion></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <groupId>org.snpeff</groupId></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <artifactId>SnpEff</artifactId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <version>4.3</version></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <packaging>jar</packaging><properties></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+         </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                 <debian.hasPackageVersion/></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+         </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                 <debian.mavenRules>org.snpeff SnpEff jar s/.*/debian/ * *</debian.mavenRules></span></span>

</pre>

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</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+         </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                 <debian.originalVersion>4.3</debian.originalVersion></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+         </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                 <debian.package>libsnpeff-java</debian.package></span></span>

</pre>

</td>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </properties></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <name>Snp Effect</name></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <description>Variant annotation and effect prediction package.</description></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <url>http://snpeff.sourceforge.net/</url></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <licenses></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+         <license></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                 <name>GNU LESSER GENERAL PUBLIC LICENSE, Version 3.0</name></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                 <url>http://www.gnu.org/licenses/lgpl-3.0.txt</url></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                 <distribution>repo</distribution></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+         </license></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </licenses></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <!--</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff">   <scm></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff">     <url>https://snpeff.svn.sourceforge.net/svnroot/snpeff/SnpEffect/</url></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff">     <connection>https://snpeff.svn.sourceforge.net/svnroot/snpeff/SnpEffect/</connection></span>

</pre>

</td>

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff">   </scm></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff">   --></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  <developers></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    <developer></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <id>pcingola</id></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <name>Pablo Cingolani</name></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <email>pcingola@users.sourceforge.net</email></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    </developer></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  </developers></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  <dependencies></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    <dependency></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <groupId>org.apfloat</groupId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <artifactId>apfloat</artifactId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <version>1.6.3</version></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    </dependency></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    <dependency></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <groupId>com.googlecode.charts4j</groupId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <artifactId>charts4j</artifactId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <version>1.3</version></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    </dependency></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    <dependency></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <groupId>commons-cli</groupId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <artifactId>commons-cli</artifactId></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <version>1.2</version></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    </dependency></span></span>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    <dependency></span></span>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <groupId>com.typesafe.akka</groupId></span></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;">-      <artifactId>akka-actor</artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <version>2.0.1</version></span></span>

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    </dependency></span></span>

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    <dependency></span></span>

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <groupId>junit</groupId></span></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;">-      <artifactId>junit</artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <version>4.4</version></span></span>

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    </dependency></span></span>

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    <dependency></span></span>

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <groupId>net.sf.trove4j</groupId></span></span>

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <artifactId>trove4j</artifactId></span></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;">-      <version>3.0.2</version></span></span>

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    </dependency></span></span>

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    <dependency></span></span>

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <groupId>org.freemarker</groupId></span></span>

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <artifactId>freemarker</artifactId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <version>2.3.19</version></span></span>

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    </dependency></span></span>

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    <dependency></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <groupId>distlib</groupId></span></span>

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<pre style="margin: 0;">-<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <artifactId>distlib</artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <version>0.9.1</version></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    </dependency></span></span>

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    <dependency></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <groupId>samtools</groupId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <artifactId>samtools</artifactId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <version>1.107</version></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    </dependency></span></span>

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    <dependency></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <groupId>org.apache.commons</groupId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <artifactId>commons-math3</artifactId></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <version>3.2</version></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    </dependency></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    <dependency></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <groupId>commons-io</groupId></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <artifactId>commons-io</artifactId></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <version>2.4</version></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    </dependency></span></span>

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <dependency></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                <groupId>commons-codec</groupId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                <artifactId>commons-codec</artifactId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                <version>1.10</version></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </dependency></span></span>

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<pre style="margin: 0;">-<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    <dependency></span></span>

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <groupId>log4j</groupId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC128" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <artifactId>log4j</artifactId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <version>1.2.15</version></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <exclusions></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <exclusion></span></span>

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-          <groupId>com.sun.jdmk</groupId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-          <artifactId>jmxtools</artifactId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </exclusion></span></span>

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<pre style="margin: 0;">-<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <exclusion></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-          <groupId>com.sun.jmx</groupId></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC137" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-          <artifactId>jmxri</artifactId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </exclusion></span></span>

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      </exclusions></span></span>

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<pre style="margin: 0;">-<span id="LC140" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    </dependency></span></span>

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    <dependency></span></span>

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <groupId>org.biojava</groupId></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <artifactId>biojava3-core</artifactId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <version>3.0.7</version></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    </dependency></span></span>

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<pre style="margin: 0;">-<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    <dependency></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <groupId>org.biojava</groupId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <artifactId>biojava3-structure</artifactId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <version>3.0.7</version></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    </dependency></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC151" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  </dependencies></span></span>

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<pre style="margin: 0;">-<span id="LC152" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  <repositories></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    <repository></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <id>central</id></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC156" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <name>Central Repository</name></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC157" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <url>http://repo.maven.apache.org/maven2</url></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC158" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <layout>default</layout></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <snapshots></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <enabled>false</enabled></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC161" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      </snapshots></span></span>

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    </repository></span></span>

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<pre style="margin: 0;">-<span id="LC163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    <repository></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC164" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <id>hadoop-bam</id></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC165" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <name>Hadoop-BAM</name></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC166" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <url>http://hadoop-bam.sourceforge.net/maven/</url></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC167" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    </repository></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    <repository></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC169" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <id>ncimvn-public</id></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <name>Public NIH repository</name></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <url>https://ncimvn.nci.nih.gov/nexus/content/groups/public/</url></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    </repository></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC173" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    <repository></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC174" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <id>typesafe</id></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC175" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <name>Typesafe Repository</name></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <url>http://repo.typesafe.com/typesafe/releases/</url></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC177" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    </repository></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC178" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  </repositories></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC179" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC180" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  <build></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC181" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    <plugins></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC182" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <plugin></span></span>

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<pre style="margin: 0;">-<span id="LC183" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <groupId>org.apache.maven.plugins</groupId></span></span>

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<pre style="margin: 0;">-<span id="LC184" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <artifactId>maven-compiler-plugin</artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC185" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <version>2.3.2</version></span></span>

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<pre style="margin: 0;">-<span id="LC186" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <configuration></span></span>

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<pre style="margin: 0;">-<span id="LC187" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-          <source>1.8</source></span></span>

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<pre style="margin: 0;">-<span id="LC188" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-          <target>1.8</target></span></span>

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<pre style="margin: 0;">-<span id="LC189" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-          <encoding>ISO-8859-1</encoding></span></span>

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<pre style="margin: 0;">-<span id="LC190" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-          <showDeprecation>true</showDeprecation></span></span>

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<pre style="margin: 0;">-<span id="LC191" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-          <showWarnings>true</showWarnings></span></span>

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<pre style="margin: 0;">-<span id="LC192" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </configuration></span></span>

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<pre style="margin: 0;">-<span id="LC193" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      </plugin></span></span>

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <plugin></span></span>

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<pre style="margin: 0;">-<span id="LC195" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <groupId>org.apache.maven.plugins</groupId></span></span>

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<pre style="margin: 0;">-<span id="LC196" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <artifactId>maven-resources-plugin</artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC197" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <version>2.4.3</version></span></span>

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<pre style="margin: 0;">-<span id="LC198" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <configuration></span></span>

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<pre style="margin: 0;">-<span id="LC199" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-          <encoding>ISO-8859-1</encoding></span></span>

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<pre style="margin: 0;">-<span id="LC200" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </configuration></span></span>

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<pre style="margin: 0;">-<span id="LC201" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      </plugin></span></span>

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<pre style="margin: 0;">-<span id="LC202" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <plugin></span></span>

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<pre style="margin: 0;">-<span id="LC203" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <groupId>org.apache.maven.plugins</groupId></span></span>

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<pre style="margin: 0;">-<span id="LC204" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <artifactId>maven-assembly-plugin</artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC205" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <version>2.2-beta-5</version></span></span>

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<pre style="margin: 0;">-<span id="LC206" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <configuration></span></span>

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<pre style="margin: 0;">-<span id="LC207" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-          <descriptorRefs></span></span>

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<pre style="margin: 0;">-<span id="LC208" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            <descriptorRef>jar-with-dependencies</descriptorRef></span></span>

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<pre style="margin: 0;">-<span id="LC209" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-          </descriptorRefs></span></span>

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<pre style="margin: 0;">-<span id="LC210" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-          <archive></span></span>

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<pre style="margin: 0;">-<span id="LC211" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            <manifest></span></span>

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-              <mainClass>org.snpeff.SnpEff</mainClass></span></span>

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<pre style="margin: 0;">-<span id="LC213" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            </manifest></span></span>

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<pre style="margin: 0;">-<span id="LC214" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-          </archive></span></span>

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </configuration></span></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;">-      </plugin></span></span>

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<pre style="margin: 0;">-<span id="LC217" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      <plugin></span></span>

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <groupId>org.apache.maven.plugins</groupId></span></span>

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<pre style="margin: 0;">-<span id="LC219" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <artifactId>maven-javadoc-plugin</artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <version>2.8.1</version></span></span>

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<pre style="margin: 0;">-<span id="LC221" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <configuration></span></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;">-          <encoding>ISO-8859-1</encoding></span></span>

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<pre style="margin: 0;">-<span id="LC223" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </configuration></span></span>

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<pre style="margin: 0;">-<span id="LC224" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      </plugin></span></span>

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<pre style="margin: 0;">-<span id="LC225" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    </plugins></span></span>

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<pre style="margin: 0;">-<span id="LC226" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  </build></span></span>

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<pre style="margin: 0;">-<span id="LC227" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  <version>4.3</version></span></span>

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<pre style="margin: 0;">-<span id="LC228" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</project></span></span>

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<pre style="margin: 0;">-<span id="LC229" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        <developers></span></span>

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<pre style="margin: 0;">-<span id="LC230" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                <developer></span></span>

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<pre style="margin: 0;">-<span id="LC231" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <id>pcingola</id></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;">+                        <name>Pablo Cingolani</name></span></span>

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<pre style="margin: 0;">-<span id="LC233" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <email>pcingola@users.sourceforge.net</email></span></span>

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<pre style="margin: 0;">-<span id="LC234" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                </developer></span></span>

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<pre style="margin: 0;">-<span id="LC235" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        </developers></span></span>

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<pre style="margin: 0;">-<span id="LC236" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        <dependencies></span></span>

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<pre style="margin: 0;">-<span id="LC237" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                <dependency></span></span>

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<pre style="margin: 0;">-<span id="LC238" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <groupId>commons-cli</groupId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC239" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <artifactId>commons-cli</artifactId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC240" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <version>debian</version></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC241" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                </dependency></span></span>

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<pre style="margin: 0;">-<span id="LC242" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                <dependency></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC243" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <groupId>junit</groupId></span></span>

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<pre style="margin: 0;">-<span id="LC244" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <artifactId>junit</artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC245" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <version>4.x</version></span></span>

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<pre style="margin: 0;">-<span id="LC246" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                </dependency></span></span>

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<pre style="margin: 0;">-<span id="LC247" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                <dependency></span></span>

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<pre style="margin: 0;">-<span id="LC248" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <groupId>net.sf.trove4j</groupId></span></span>

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<pre style="margin: 0;">-<span id="LC249" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <artifactId>trove4j</artifactId></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;">+                        <version>2.x</version></span></span>

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<pre style="margin: 0;">-<span id="LC251" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                </dependency></span></span>

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<pre style="margin: 0;">-<span id="LC252" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                <dependency></span></span>

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<pre style="margin: 0;">-<span id="LC253" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <groupId>org.freemarker</groupId></span></span>

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<pre style="margin: 0;">-<span id="LC254" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <artifactId>freemarker</artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC255" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <version>debian</version></span></span>

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<pre style="margin: 0;">-<span id="LC256" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                </dependency></span></span>

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<pre style="margin: 0;">-<span id="LC257" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                <dependency></span></span>

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<pre style="margin: 0;">-<span id="LC258" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <groupId>org.apache.commons</groupId></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;">+                        <artifactId>commons-math3</artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC260" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <version>debian</version></span></span>

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<pre style="margin: 0;">-<span id="LC261" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                </dependency></span></span>

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<pre style="margin: 0;">-<span id="LC262" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                <dependency></span></span>

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<pre style="margin: 0;">-<span id="LC263" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <groupId>commons-io</groupId></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;">+                        <artifactId>commons-io</artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC265" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <version>debian</version></span></span>

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<pre style="margin: 0;">-<span id="LC266" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                </dependency></span></span>

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<pre style="margin: 0;">-<span id="LC267" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                <dependency></span></span>

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<pre style="margin: 0;">-<span id="LC268" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <groupId>commons-codec</groupId></span></span>

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<pre style="margin: 0;">-<span id="LC269" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <artifactId>commons-codec</artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC270" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <version>debian</version></span></span>

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<pre style="margin: 0;">-<span id="LC271" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                </dependency></span></span>

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<pre style="margin: 0;">-<span id="LC272" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                <dependency></span></span>

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<pre style="margin: 0;">-<span id="LC273" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <groupId>log4j</groupId></span></span>

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<pre style="margin: 0;">-<span id="LC274" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <artifactId>log4j</artifactId></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;">+                        <version>1.2.x</version></span></span>

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<pre style="margin: 0;">-<span id="LC276" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <exclusions></span></span>

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<pre style="margin: 0;">-<span id="LC277" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                <exclusion></span></span>

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<pre style="margin: 0;">-<span id="LC278" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        <groupId>com.sun.jdmk</groupId></span></span>

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<pre style="margin: 0;">-<span id="LC279" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        <artifactId>jmxtools</artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC280" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                </exclusion></span></span>

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<pre style="margin: 0;">-<span id="LC281" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                <exclusion></span></span>

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<pre style="margin: 0;">-<span id="LC282" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        <groupId>com.sun.jmx</groupId></span></span>

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<pre style="margin: 0;">-<span id="LC283" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        <artifactId>jmxri</artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC285" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        </exclusions></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;">+                </dependency></span></span>

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<pre style="margin: 0;">-<span id="LC287" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        </dependencies></span></span>

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<pre style="margin: 0;">-<span id="LC288" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        <repositories></span></span>

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<pre style="margin: 0;">-<span id="LC289" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                <repository></span></span>

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<pre style="margin: 0;">-<span id="LC290" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <id>central</id></span></span>

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<pre style="margin: 0;">-<span id="LC291" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <name>Central Repository</name></span></span>

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<pre style="margin: 0;">-<span id="LC292" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <url>http://repo.maven.apache.org/maven2</url></span></span>

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<pre style="margin: 0;">-<span id="LC293" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <layout>default</layout></span></span>

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<pre style="margin: 0;">-<span id="LC294" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <snapshots></span></span>

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<pre style="margin: 0;">-<span id="LC295" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                <enabled>false</enabled></span></span>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        </snapshots></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;">+                </repository></span></span>

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                <repository></span></span>

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<pre style="margin: 0;">-<span id="LC299" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <id>hadoop-bam</id></span></span>

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<pre style="margin: 0;">-<span id="LC300" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <name>Hadoop-BAM</name></span></span>

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<pre style="margin: 0;">-<span id="LC301" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <url>http://hadoop-bam.sourceforge.net/maven/</url></span></span>

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<pre style="margin: 0;">-<span id="LC302" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                </repository></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;">+                <repository></span></span>

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<pre style="margin: 0;">-<span id="LC304" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <id>ncimvn-public</id></span></span>

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<pre style="margin: 0;">-<span id="LC305" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <name>Public NIH repository</name></span></span>

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<pre style="margin: 0;">-<span id="LC306" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <url>https://ncimvn.nci.nih.gov/nexus/content/groups/public/</url></span></span>

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<pre style="margin: 0;">-<span id="LC307" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                </repository></span></span>

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<pre style="margin: 0;">-<span id="LC308" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                <repository></span></span>

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<pre style="margin: 0;">-<span id="LC309" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <id>typesafe</id></span></span>

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<pre style="margin: 0;">-<span id="LC310" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <name>Typesafe Repository</name></span></span>

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<pre style="margin: 0;">-<span id="LC311" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <url>http://repo.typesafe.com/typesafe/releases/</url></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;">+                </repository></span></span>

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<pre style="margin: 0;">-<span id="LC313" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        </repositories></span></span>

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<pre style="margin: 0;">-<span id="LC314" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        <build></span></span>

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<pre style="margin: 0;">-<span id="LC315" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                <plugins></span></span>

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<pre style="margin: 0;">-<span id="LC316" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        <plugin></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;">+                                <groupId>org.apache.maven.plugins</groupId></span></span>

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<pre style="margin: 0;">-<span id="LC318" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                <artifactId>maven-compiler-plugin</artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC319" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                <version>2.3.2</version></span></span>

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<pre style="margin: 0;">-<span id="LC320" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                <configuration></span></span>

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<pre style="margin: 0;">-<span id="LC321" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        <source>1.8</source></span></span>

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<pre style="margin: 0;">-<span id="LC322" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        <target>1.8</target></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;">+                                        <encoding>ISO-8859-1</encoding></span></span>

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<pre style="margin: 0;">-<span id="LC324" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        <showDeprecation>true</showDeprecation></span></span>

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<pre style="margin: 0;">-<span id="LC325" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        <showWarnings>true</showWarnings></span></span>

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<pre style="margin: 0;">-<span id="LC326" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                </configuration></span></span>

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<pre style="margin: 0;">-<span id="LC330" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                <artifactId>maven-resources-plugin</artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC332" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                <configuration></span></span>

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<pre style="margin: 0;">-<span id="LC333" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        <encoding>ISO-8859-1</encoding></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;">+                                </configuration></span></span>

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<pre style="margin: 0;">-<span id="LC335" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        </plugin></span></span>

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<pre style="margin: 0;">-<span id="LC336" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                </plugins></span></span>

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<pre style="margin: 0;">-<span id="LC337" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        </build></span></span>

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<pre style="margin: 0;">-<span id="LC338" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</project></span></span>

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<pre style="margin: 0;">-<span id="LC339" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span></pre>

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<br>

</li>

<li id="aaf074da7d5fb997bc41e660dff8a9bc83c39576">

<a href="https://salsa.debian.org/med-team/snpeff/-/compare/ddb09726588ba978ba10bc1b27e077b785cb86ee...0772e188d7e0fad41547fc151ff3be89ba8e9a16#aaf074da7d5fb997bc41e660dff8a9bc83c39576"><strong>debian/patches/prepare_to_put_package_version_in_pom.xml</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="xml">Description: Preparing pom.xml to receive the right version number</span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="xml"> Upstream provides a pom.xml with a version number that does not wholly</span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="xml"> corresponds to the package upstream version. We put a @VERSION@ in the pom, </span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="xml"> which will be replaced by the correct version number in debian/rules.</span>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="xml">Author: Pierre Gruet <span class="nt" style="color: #000080;"><pgtdebian</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">@free.fr</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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6

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="xml">Forwarded: not-needed</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="xml">Last-Update: 2020-12-10</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="xml"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="xml">--- a/pom.xml</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="xml">+++ b/pom.xml</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="xml">@@ -199,5 +199,5 @@</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="xml">       <span class="nt" style="color: #000080;"></plugin></span></span>

</pre>

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13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="xml">     <span class="nt" style="color: #000080;"></plugins></span></span>

</pre>

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14

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14" class="line" lang="xml">   <span class="nt" style="color: #000080;"></build></span></span>

</pre>

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15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="xml">-  <span class="nt" style="color: #000080;"><version></span>4.3<span class="nt" style="color: #000080;"></version></span></span>

</pre>

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16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="xml">+  <span class="nt" style="color: #000080;"><version></span>@VERSION@<span class="nt" style="color: #000080;"></version></span></span>

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17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="xml"> <span class="nt" style="color: #000080;"></project></span></span></pre>

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<br>

</li>

<li id="17563e1f4545f161f646a7b847a908f665bb1c7d">

<a href="https://salsa.debian.org/med-team/snpeff/-/compare/ddb09726588ba978ba10bc1b27e077b785cb86ee...0772e188d7e0fad41547fc151ff3be89ba8e9a16#17563e1f4545f161f646a7b847a908f665bb1c7d"><strong>debian/patches/replacing_akka_with_java_util_concurrent.patch</strong></a>

<hr>

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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: replacing akka using java.util.concurrent</span></span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: no</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2020-12-04</span></span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- /dev/null</span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/akka/ConcurrentFactory.java</span></span>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -0,0 +1,6 @@</span></span>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+package org.snpeff.akka;</span></span>

</pre>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+public interface ConcurrentFactory {</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        public ConcurrentActor create();</span></span>

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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</span></span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/akka/ConcurrentActor.java</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -0,0 +1,4 @@</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+package org.snpeff.akka;</span></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;">+</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+public abstract class ConcurrentActor {</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/akka/ConcurrentProperties.java</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="p">@@ -0,0 +1,14 @@</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+package org.snpeff.akka;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+public class ConcurrentProperties {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        public ConcurrentProperties(ConcurrentFactory pFactory) {</span></span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                this.factory = pFactory;</span></span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        }</span></span>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        public ConcurrentFactory getFactory() {</span></span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                return factory;</span></span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        }</span></span>

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<pre style="margin: 0;">+<span id="LC36" 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="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        private ConcurrentFactory factory;</span></span>

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<pre style="margin: 0;">+<span id="LC38" 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="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/akka/Master.java</span></span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/akka/Master.java</span></span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="p">@@ -8,10 +8,12 @@</span></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> import org.snpeff.akka.msg.Work;</span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> import org.snpeff.util.Gpr;</span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import akka.actor.ActorRef;</span></span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import akka.actor.Props;</span></span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import akka.actor.UntypedActor;</span></span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import akka.routing.SmallestMailboxRouter;</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import java.util.concurrent.CompletionService;</span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import java.util.concurrent.ExecutionException;</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import java.util.concurrent.ExecutorCompletionService;</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;">+import java.util.concurrent.Executors;</span></span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import java.util.concurrent.ExecutorService;</span></span>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import java.util.concurrent.Future;</span></span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> /**</span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff">  * Master: Distributes the jobs to all workers, sends the results to 'listener'</span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="p">@@ -21,7 +23,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff">  * @param <TI></span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff">  * @param <TO></span>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff">  */</span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-public abstract class Master<TI, TO> extends UntypedActor implements Iterable<TI>, Iterator<TI> {</span></span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+public abstract class Master<TI, TO> extends ConcurrentActor implements Iterable<TI>, Iterator<TI> {</span></span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff">  public static int LOAD_FACTOR = 3; // Number of works distributed per worker</span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="p">@@ -40,15 +42,17 @@</span></span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff">  protected int countInputObjects; // Count number of input objects</span>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff">  protected int numWorkers; // Number of workers (threads)</span>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff">  protected int sentWorks; // Number of workers still working</span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- protected ActorRef workerRouter;</span></span>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff">  protected HashMap<Long, Result<TO>> worksBySerial;</span>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        protected ExecutorService pool;</span></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        protected CompletionService<Result<TO>> completion;</span></span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        protected ConcurrentProperties props;</span></span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff">  /**</span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff">   * Constructor</span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff">   * @param numWorkers: How may workers will be used</span>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff">   * @param listener : Listener</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"><span class="gd" style="color: #000; background-color: #fdd;">- public Master(Props props, int numWorkers) {</span></span>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public Master(ConcurrentProperties props, int numWorkers) {</span></span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff">          // Initialize </span>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff">          sentWorks = 0;</span>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff">          this.numWorkers = numWorkers;</span>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="p">@@ -58,9 +62,10 @@</span></span>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff">          showEvery = DEFAULT_SHOW_EVERY;</span>

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff">          countInputObjects = 1;</span>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         // Create router</span></span>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         SmallestMailboxRouter router = new SmallestMailboxRouter(numWorkers);</span></span>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         workerRouter = getContext().actorOf(props.withRouter(router), "workerRouter");</span></span>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                this.props = props;</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;">+         // Create workers</span></span>

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                pool = Executors.newFixedThreadPool(numWorkers);</span></span>

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                completion = new ExecutorCompletionService<Result<TO>>(pool);</span></span>

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff">  }</span>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff">         @Override</span>

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="p">@@ -124,43 +129,54 @@</span></span>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff">          * Master-receive: Handle-messages</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">         @SuppressWarnings("unchecked")</span>

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        @Override</span></span>

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        public void onReceive(Object message) {</span></span>

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                //---</span></span>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                // Message specific processing</span></span>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                //---</span></span>

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                if (message instanceof StartMaster) {</span></span>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        if (debug) Gpr.debug("Start");</span></span>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        // Process start message</span></span>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        StartMaster start = (StartMaster) message;</span></span>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        startMaster(start);</span></span>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                } else if (message instanceof Result) {</span></span>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        // Process results </span></span>

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        sentWorks--;</span></span>

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        Result<TO> result = (Result<TO>) message;</span></span>

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        if (debug) Gpr.debug("Result: " + result.serialNumber);</span></span>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        processResults(result);</span></span>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                } else unhandled(message);</span></span>

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                //---</span></span>

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                // Distribute some work</span></span>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                //---</span></span>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                int threshold = LOAD_FACTOR * numWorkers; // We want all the workers to have some work at all times</span></span>

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                if (sentWorks < threshold) {</span></span>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        // Send all works to workers</span></span>

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        for (Work<TI> work : this.iterableWork()) {</span></span>

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                sentWorks++;</span></span>

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                workerRouter.tell(work, getSelf());</span></span>

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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                if (debug) Gpr.debug("Sent: " + work.serialNumber);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                if (sentWorks >= threshold) break; // Enough, wait until we get some results</span></span>

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        }</span></span>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                public void get(Object message) {</span></span>

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        // Nothing else to do? => Stop</span></span>

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        if ((sentWorks == 0) && !hasNext()) shutdown(); // Shutdown all agents (including router)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                }</span></span>

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        }</span></span>

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<pre style="margin: 0;">+<span id="LC143" 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="LC144" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        // Message specific processing</span></span>

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<pre style="margin: 0;">+<span id="LC145" 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="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        if (message instanceof StartMaster) {</span></span>

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                if (debug) Gpr.debug("Start");</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC148" 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="LC149" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                // Process start message</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                StartMaster start = (StartMaster) message;</span></span>

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                startMaster(start);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        } else throw new RuntimeException("Message of unknown type received by Master.");</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        while ((sentWorks != 0) || hasNext()) {</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                //---</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                // Distribute some work</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                //---</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                int threshold = LOAD_FACTOR * numWorkers; // We want all the workers to have some work at all times</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                if (sentWorks < threshold) {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        // Send all works to workers</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        for (Work<TI> work : this.iterableWork()) {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                sentWorks++;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                Worker wrker = (Worker)(props.getFactory().create());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                wrker.setMessage(work);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                completion.submit(wrker);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                if (debug) Gpr.debug("Sent: " + work.serialNumber);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                if (sentWorks >= threshold) break; // Enough, wait until we get some results</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        }</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        //Process results.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        try {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                Future<Result<TO>> result = completion.take();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                sentWorks--;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                if (debug) Gpr.debug("Result: " + result.get().serialNumber);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                processResults(result.get());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        } catch (ExecutionException e) {</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                System.out.println(e.getMessage());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                System.exit(1);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        } catch (InterruptedException e) {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                System.out.println(e.getMessage());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                System.exit(1);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        // Nothing else to do? => Stop</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        if ((sentWorks == 0) && !hasNext()) pool.shutdown(); // Shutdown all agents</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff">         /**</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff">          * Output all contents of a result</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="p">@@ -203,14 +219,6 @@</span></span>

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff">         }</span>

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff">         /**</span>

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         * Shut down all agents</span></span>

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         */</span></span>

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        protected void shutdown() {</span></span>

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                if (debug) Gpr.debug("Shutting down");</span></span>

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                getContext().system().shutdown();</span></span>

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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        }</span></span>

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        /**</span></span>

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff">          * This is executed when the 'start' message arrives (at the beginning of the processing)</span>

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff">          * @param startMaster</span>

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff">          */</span>

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/akka/Worker.java</span></span>

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/akka/Worker.java</span></span>

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="p">@@ -3,7 +3,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> import org.snpeff.akka.msg.Result;</span>

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"> import org.snpeff.akka.msg.Work;</span>

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import akka.actor.UntypedActor;</span></span>

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import java.util.concurrent.Callable;</span></span>

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> /**</span>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff">  * Worker: Performs a simple work and get the data back</span>

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="p">@@ -13,12 +13,13 @@</span></span>

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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff">  * </span>

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff">  * @author pablocingolani</span>

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff">  */</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;">-public class Worker<TI, TO> extends UntypedActor {</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;">+public class Worker<TI, TO> extends ConcurrentActor implements Callable<Result<TO>> {</span></span>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff">         private static int WORKER_ID = 0;</span>

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff">         private static String WORKER_ID_MUTEX = "WORKER_ID_MUTEX";</span>

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff">         protected int id;</span>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        protected Object message;</span></span>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff">         public static int getId() {</span>

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff">                 synchronized (WORKER_ID_MUTEX) {</span>

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"><span class="p">@@ -28,6 +29,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff">         public Worker() {</span>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff">                 id = getId();</span>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                message=null;</span></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"> </span>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff">         /**</span>

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="p">@@ -57,11 +59,16 @@</span></span>

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff">         @SuppressWarnings("unchecked")</span>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff">         @Override</span>

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        public void onReceive(Object message) {</span></span>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        public Result<TO> call() {</span></span>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                Result<TO> result;</span></span>

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff">                 if (message instanceof Work) {</span>

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff">                         // Perform some kind of calculation</span>

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        Result<TO> result = calculate((Work<TI>) message);</span></span>

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        getSender().tell(result, getSelf());</span></span>

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                } else unhandled(message);</span></span>

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        result = calculate((Work<TI>) message);</span></span>

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                } else throw new RuntimeException("Message received by Worker does not require any work.");</span></span>

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                return result;</span></span>

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff">         }</span>

</pre>

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</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;">+</span></span>

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        public void setMessage(Object pMessage) {</span></span>

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                this.message = pMessage;</span></span>

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC263" 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="LC264" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/akka/vcf/MasterVcf.java</span></span>

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/akka/vcf/MasterVcf.java</span></span>

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"><span class="p">@@ -5,7 +5,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> import org.snpeff.fileIterator.VcfFileIterator;</span>

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"> import org.snpeff.vcf.VcfEntry;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import akka.actor.Props;</span></span>

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.snpeff.akka.ConcurrentProperties;</span></span>

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"> /**</span>

</pre>

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff">  * A master that prcess VCF files</span>

</pre>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff">         protected String addHeader[]; // Add lines to VCF header before showing it</span>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff">         protected VcfFileIterator vcfFileIterator;</span>

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        public MasterVcf(Props props, int numWorkers) {</span></span>

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        public MasterVcf(ConcurrentProperties props, int numWorkers) {</span></span>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff">                 super(props, numWorkers);</span>

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff">         }</span>

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="p">@@ -70,7 +70,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff">                         }</span>

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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff">                 } catch (Throwable t) {</span>

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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff">                         t.printStackTrace();</span>

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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        shutdown();</span></span>

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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        pool.shutdown();</span></span>

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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff">                 }</span>

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff">         }</span>

</pre>

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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"> }</span>

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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/akka/vcf/VcfWorkQueue.java</span></span>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/akka/vcf/VcfWorkQueue.java</span></span>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"><span class="p">@@ -2,10 +2,8 @@</span></span>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"> import org.snpeff.snpEffect.Config;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import akka.actor.Actor;</span></span>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import akka.actor.ActorRef;</span></span>

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import akka.actor.ActorSystem;</span></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;">-import akka.actor.Props;</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;">+import org.snpeff.akka.Master;</span></span>

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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.snpeff.akka.ConcurrentProperties;</span></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"> /**</span>

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff">  * A work queue that processes a VCF file</span>

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"><span class="p">@@ -18,11 +16,10 @@</span></span>

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff">         String fileName;</span>

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff">         int batchSize, showEvery;</span>

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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        Class<? extends Actor> masterClazz;</span></span>

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        Props masterProps;</span></span>

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        ConcurrentProperties masterProps;</span></span>

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff">         Config config;</span>

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        public VcfWorkQueue(String fileName, Config config, int batchSize, int showEvery, Props masterProps) {</span></span>

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        public VcfWorkQueue(String fileName, Config config, int batchSize, int showEvery, ConcurrentProperties masterProps) {</span></span>

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff">                 this.fileName = fileName;</span>

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff">                 this.batchSize = batchSize;</span>

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff">                 this.showEvery = showEvery;</span>

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="p">@@ -30,19 +27,12 @@</span></span>

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff">                 this.config = config;</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"><span class="gi" style="color: #000; background-color: #dfd;">+        //Argument wait is now unused.</span></span>

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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff">         public void run(boolean wait) {</span>

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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                // Create an Akka system</span></span>

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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                ActorSystem workQueue = ActorSystem.create("vcfWorkQueue");</span></span>

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff">                 // Create the master</span>

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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                ActorRef master;</span></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;">-                if (masterClazz != null) master = workQueue.actorOf(new Props(masterClazz), "masterVcf");</span></span>

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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                else master = workQueue.actorOf(masterProps, "masterVcf");</span></span>

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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                Master master = (Master)(masterProps.getFactory().create());</span></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">                 // Start processing</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;">-                master.tell(new StartMasterVcf(fileName, config, batchSize, showEvery));</span></span>

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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                // Wait until completion</span></span>

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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                if (wait) workQueue.awaitTermination();</span></span>

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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                master.get(new StartMasterVcf(fileName, config, batchSize, showEvery));</span></span>

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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff">         }</span>

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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"> }</span>

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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/akka/vcfStr/MasterVcfStr.java</span></span>

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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/akka/vcfStr/MasterVcfStr.java</span></span>

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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"><span class="p">@@ -2,7 +2,9 @@</span></span>

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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"> import org.snpeff.akka.vcf.MasterVcf;</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 class="gd" style="color: #000; background-color: #fdd;">-import akka.actor.Props;</span></span>

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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.snpeff.akka.ConcurrentActor;</span></span>

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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.snpeff.akka.ConcurrentFactory;</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;">+import org.snpeff.akka.ConcurrentProperties;</span></span>

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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"> /**</span>

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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff">  * A simple demo of a master process</span>

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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"><span class="p">@@ -12,7 +14,13 @@</span></span>

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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"> public class MasterVcfStr extends MasterVcf<String> {</span>

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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff">         public MasterVcfStr(int numWorkers) {</span>

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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                super(new Props(WorkerVcfStr.class), numWorkers);</span></span>

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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                super(new ConcurrentProperties(</span></span>

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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        new ConcurrentFactory() {</span></span>

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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                @Override</span></span>

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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                public ConcurrentActor create() {</span></span>

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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                return new WorkerVcfStr();</span></span>

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<pre style="margin: 0;">+<span id="LC368" 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="LC369" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        }), numWorkers);</span></span>

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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff">         }</span>

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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"> }</span>

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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdEff.java</span></span>

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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdEff.java</span></span>

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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"><span class="p">@@ -47,9 +47,10 @@</span></span>

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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"> import org.snpeff.vcf.VcfEntry;</span>

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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"> import org.snpeff.vcf.VcfGenotype;</span>

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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import akka.actor.Actor;</span></span>

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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import akka.actor.Props;</span></span>

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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import akka.actor.UntypedActorFactory;</span></span>

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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.snpeff.akka.ConcurrentFactory;</span></span>

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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.snpeff.akka.ConcurrentActor;</span></span>

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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.snpeff.akka.ConcurrentProperties;</span></span>

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<pre style="margin: 0;">+<span id="LC385" 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="LC386" class="line" lang="diff"> import freemarker.template.Configuration;</span>

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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"> import freemarker.template.DefaultObjectWrapper;</span>

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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"> import freemarker.template.Template;</span>

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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"><span class="p">@@ -496,12 +497,12 @@</span></span>

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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff">                 VcfFileIterator vcf = new VcfFileIterator(inputFile, config.getGenome());</span>

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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff">                 // Master factory</span>

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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                Props props = new Props(new UntypedActorFactory() {</span></span>

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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                ConcurrentProperties props = new ConcurrentProperties(new ConcurrentFactory() {</span></span>

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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff">                         private static final long serialVersionUID = 1L;</span>

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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff">                         @Override</span>

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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        public Actor create() {</span></span>

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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        public ConcurrentActor create() {</span></span>

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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff">                                 MasterEff master = new MasterEff(numWorkers, snpEffCmdEff, snpEffectPredictor, outputFormatter, filterIntervals);</span>

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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff">                                 master.setAddHeader(vcfOutForm.getNewHeaderLines().toArray(new String[0]));</span>

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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff">                                 return master;</span>

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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/commandLine/eff/MasterEff.java</span></span>

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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/commandLine/eff/MasterEff.java</span></span>

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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"><span class="p">@@ -6,9 +6,9 @@</span></span>

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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"> import org.snpeff.snpEffect.SnpEffectPredictor;</span>

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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"> import org.snpeff.snpEffect.commandLine.SnpEffCmdEff;</span>

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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import akka.actor.Actor;</span></span>

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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import akka.actor.Props;</span></span>

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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import akka.actor.UntypedActorFactory;</span></span>

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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.snpeff.akka.ConcurrentFactory;</span></span>

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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.snpeff.akka.ConcurrentActor;</span></span>

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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.snpeff.akka.ConcurrentProperties;</span></span>

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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"> /**</span>

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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff">  * Master agent for SnpEff 'eff' command</span>

</pre>

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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"><span class="p">@@ -18,14 +18,14 @@</span></span>

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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"> public class MasterEff extends MasterVcf<String> {</span>

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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff">         public MasterEff(int numWorkers, final SnpEffCmdEff snpEffCmdEff, final SnpEffectPredictor snpEffectPredictor, final OutputFormatter outputFormatter, final IntervalForest filterIntervals) {</span>

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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                super(new Props( //</span></span>

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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                super(new ConcurrentProperties( //</span></span>

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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff">                                 // Create a factory</span>

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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                new UntypedActorFactory() {</span></span>

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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                new ConcurrentFactory() {</span></span>

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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff">                                         private static final long serialVersionUID = 1L;</span>

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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff">                                         @Override</span>

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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                        public Actor create() {</span></span>

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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                        public ConcurrentActor create() {</span></span>

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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff">                                                 return new WorkerEff(snpEffCmdEff, snpEffectPredictor, outputFormatter.clone(), filterIntervals);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff">                                         }</span>

</pre>

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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"> </span></pre>

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<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/snpeff/-/compare/ddb09726588ba978ba10bc1b27e077b785cb86ee...0772e188d7e0fad41547fc151ff3be89ba8e9a16#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">pom_xml.patch</span></pre>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">replacing_akka_with_java_util_concurrent.patch</span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">depending_on_biojava4.patch</span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">adapting_to_htsjdk.patch</span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">adding_scala_in_pom.patch</span>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">fix_tests.patch</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">prepare_to_put_package_version_in_pom.xml</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/snpeff/-/compare/ddb09726588ba978ba10bc1b27e077b785cb86ee...0772e188d7e0fad41547fc151ff3be89ba8e9a16#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,36 @@</td>

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2

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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"># DH_VERBOSE := 1</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">export JAVA_HOME=/usr/lib/jvm/default-java</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">export LC_ALL=C.UTF-8</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

</td>

<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

</td>

<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">%:</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">     dh $@ --with javahelper</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">override_dh_auto_clean:</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">     dh_auto_clean</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">     # Removing the unit tests we copied into a subdirectory of src/test.</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">     if [ -e src/test/java/org ]; then \</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">             $(RM) -rf src/test/java/org; \</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">     fi</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">     # Replacing our pom with the true version number by the original one.</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">     if [ -e pom.xml.old ]; then \</span>

</pre>

</td>

</tr>

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</td>

<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">             mv pom.xml.old pom.xml; \</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">     fi</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">override_dh_auto_configure:</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

25

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">     # Upstream provides pom.xml with an incomplete version number. We do a trick</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">     # with a patch in debian/patches and with the next lines to put the right one.</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

27

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">     cp pom.xml pom.xml.old</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">     sed 's/@VERSION@/$(DEB_VERSION_UPSTREAM)/ ; s/\+dfsg[[:digit:]]*//' pom.xml.old > pom.xml</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

29

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">     dh_auto_configure</span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

30

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

31

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">override_dh_auto_test:</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

32

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

33

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">     # Moving the unit tests into a subdir of src/test so that Maven sees them.</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

34

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">     mkdir -p src/test/java/org/snpeff/snpEffect/testCases/unity</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

35

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">     cp -a src/main/java/org/snpeff/snpEffect/testCases/unity src/test/java/org/snpeff/snpEffect/testCases</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

36

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">     dh_auto_test</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

37

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">endif</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="f6c6956cf73acf73842e03af1a6088b689674ca7">

<a href="https://salsa.debian.org/med-team/snpeff/-/compare/ddb09726588ba978ba10bc1b27e077b785cb86ee...0772e188d7e0fad41547fc151ff3be89ba8e9a16#f6c6956cf73acf73842e03af1a6088b689674ca7"><strong>debian/snpeff.poms</strong>

deleted

</a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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1

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"># List of POM files for the package</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"># Format of this file is:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"># <path to pom file> [option]*</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"># where option can be:</span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">#   --ignore: ignore this POM and its artifact if any</span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">#   --ignore-pom: don't install the POM. To use on POM files that are created</span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">#     temporarily for certain artifacts such as Javadoc jars. [mh_install, mh_installpoms]</span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">#   --no-parent: remove the <parent> tag from the POM</span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">#   --package=<package>: an alternative package to use when installing this POM</span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">#      and its artifact</span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">#   --has-package-version: to indicate that the original version of the POM is the same as the upstream part</span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">#      of the version for the package.</span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">#   --keep-elements=<elem1,elem2>: a list of XML elements to keep in the POM</span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">#      during a clean operation with mh_cleanpom or mh_installpom</span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">#   --artifact=<path>: path to the build artifact associated with this POM,</span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">#      it will be installed when using the command mh_install. [mh_install]</span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">#   --java-lib: install the jar into /usr/share/java to comply with Debian</span>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">#      packaging guidelines</span>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">#   --usj-name=<name>: name to use when installing the library in /usr/share/java</span>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">#   --usj-version=<version>: version to use when installing the library in /usr/share/java</span>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">#   --no-usj-versionless: don't install the versionless link in /usr/share/java</span>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">#   --dest-jar=<path>: the destination for the real jar.</span>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">#     It will be installed with mh_install. [mh_install]</span>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">#   --classifier=<classifier>: Optional, the classifier for the jar. Empty by default.</span>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">#   --site-xml=<location>: Optional, the location for site.xml if it needs to be installed.</span>

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26

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">#     Empty by default. [mh_install]</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

27

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">#</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

28

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">pom.xml</span></pre>

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