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<h3>
Andreas Tille 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/2da2948bfbdc6849e8412423a1ad0db4916faad3">2da2948b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-27T10:19:05Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">After running dh-maven helper
</pre>
</li>
</ul>
<h4>12 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#cf9802e192b48f765b1b5c8268d550d89c933053">
<span class="new-file">
+
debian/README.source
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#c0e6ac783af8451faa5e88ff2426dbbaa309df8b">
<span class="new-file">
+
debian/libsnpeff-java-doc.doc-base.api
</span>
</a>
</li>
<li class="file-stats">
<a href="#f059acb09953e85f3950991e4b07da0722943516">
<span class="new-file">
+
debian/libsnpeff-java-doc.install
</span>
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<li class="file-stats">
<a href="#8f26a3ee4710acd4172b137f1a6174dcf0808341">
<span class="new-file">
+
debian/libsnpeff-java.poms
</span>
</a>
</li>
<li class="file-stats">
<a href="#5f7c96eb17e78b0de55008d54b51e8dee2f412bc">
<span class="new-file">
+
debian/maven.cleanIgnoreRules
</span>
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</li>
<li class="file-stats">
<a href="#26121dc92cd4cd9822d2e9e2b619b799bf9a51f4">
<span class="new-file">
+
debian/maven.ignoreRules
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<li class="file-stats">
<a href="#d006b76813d91cccc2a85e222d10982eb5d52728">
<span class="new-file">
+
debian/maven.properties
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<li class="file-stats">
<a href="#24b90c28b48ee27d2ecad460d66ac6959df5c033">
<span class="new-file">
+
debian/maven.publishedRules
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<li class="file-stats">
<a href="#58530b38acb0fa3a65612c676abaea46c4a3f2f3">
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+
debian/maven.rules
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<li class="file-stats">
<a href="#f6c6956cf73acf73842e03af1a6088b689674ca7">
<span class="new-file">
+
debian/snpeff.poms
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="cf9802e192b48f765b1b5c8268d550d89c933053">
<a href="https://salsa.debian.org/med-team/snpeff/commit/2da2948bfbdc6849e8412423a1ad0db4916faad3#cf9802e192b48f765b1b5c8268d550d89c933053"><strong>debian/README.source</strong></a>
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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">
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Information about snpeff</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">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">------------------------</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">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">This package was debianized using the mh_make command</span>
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<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">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">from the maven-debian-helper package.</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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">The build system uses Maven but prevents it from downloading</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="plaintext">anything from the Internet, making the build compliant with</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">the Debian policy.</span></pre>
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<br>
</li>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/snpeff/commit/2da2948bfbdc6849e8412423a1ad0db4916faad3#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,10 +6,11 @@ Priority: optional</td>
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6
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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7
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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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> javahelper,</span>
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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="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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> default-jdk,</span>
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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="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> default-jdk-doc,</span>
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<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
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<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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> maven-debian-helper,</span>
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<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
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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 noteable_line" 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>
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<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
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<td class="diff-line-num new_line" data-linenumber="12" 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">
12
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libtrove-java,</span>
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<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
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<td class="diff-line-num new_line old" data-linenumber="13" 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="LC12" class="line" lang="plaintext"> liblog4j2-java,</span>
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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">
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> liblog4j<span class="idiff left right">1.</span>2-java,</span>
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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
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<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
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libhtsjdk-java,</span>
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<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
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<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
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> libbiojava4-java,</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> junit4,</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,14 +19,22 @@ Build-Depends: debhelper (>= 11~),</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> libcommons-cli-java,</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> libcommons-math3-java,</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> libcommons-cli-java-doc,</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> libfreemarker-java</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> libfreemarker-java,</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> libmaven-javadoc-plugin-java,</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> junit4-doc,</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> libcommons-codec-java-doc,</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> libcommons-io-java-doc,</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> libcommons-math3-java-doc,</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> libfreemarker-java-doc,</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> liblog4j1.2-java-doc,</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> libtrove-java-doc</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">Standards-Version: 4.1.4</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/snpeff</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/snpeff.git</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">Homepage: http://snpeff.sourceforge.net/</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">Package: snpeff</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">Architecture: a<span class="idiff left right">ny</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">Architecture: a<span class="idiff left right">ll</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">Description: genetic variant annotation and effect prediction toolbox</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -41,3 +50,21 @@ Description: genetic variant annotation and effect prediction toolbox</td>
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<pre style="margin: 0;"> <span id="LC50" 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="LC51" class="line" lang="plaintext"> changes). A list of effects and annotations that SnpEff can calculate</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> can be found here. </span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">Package: libsnpeff-java</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">Depends: ${misc:Depends}, ${maven:Depends}</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">Suggests: ${maven:OptionalDepends}, libsnpeff-java-doc</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">Description: Snp Effect</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> Variant annotation and effect prediction package.</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">Package: libsnpeff-java-doc</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">Section: doc</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">Recommends: ${maven:DocDepends}, ${maven:DocOptionalDepends}</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">Suggests: libsnpeff-java</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">Description: Documentation for Snp Effect</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> Variant annotation and effect prediction package.</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> This package contains the API documentation of libsnpeff-java.</span></pre>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/snpeff/commit/2da2948bfbdc6849e8412423a1ad0db4916faad3#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -9,16 +9,16 @@ Files-Excluded: */config/OLD</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Files: *</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Copyright: © 2008-2016, Pablo Cingolani <pcingola@users.sourceforge.net></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">License: <span class="idiff left right">LGPL-3+</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">License: <span class="idiff left right">Apache-2.0 or BSD or LGPL-2 or LGPL-2.1</span></span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Files: debian/*</span>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Copyright: © 2012 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">License: <span class="idiff left right">LGPL-3+</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">License: <span class="idiff left right">Apache-2.0</span></span>
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17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">License: LGPL-<span class="idiff left right">3+</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">License: LGPL-<span class="idiff left right">2.1</span></span>
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<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
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> This program is free software: you can redistribute it and/or modify</span>
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20
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> it under the terms of the GNU Lesser General Public License as published by</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> the Free Software Foundation, either version <span class="idiff left right">3</span> of the License, or</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> the Free Software Foundation, either version <span class="idiff left right">2.1</span> of the License, or</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> (at your option) any later version.</span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> This program is distributed in the hope that it will be useful,</span>
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<td class="diff-line-num unfold js-unfold old_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>
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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">@@ -26,8 +26,16 @@ License: LGPL-3+</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> GNU General Public License for more details.</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> .</span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> You should have received a copy of the GNU Lesser General Public License</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> along with this program. If not, see <http://www.gnu.org/licenses/>.</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> On a Debian GNU/Linux system, the GNU Lesser GPL license version 3 is included</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> in the file ‘/usr/share/common-licenses/LGPL-3’.</span></pre>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> in the file ‘/usr/share/common-licenses/LGPL-2.1’.</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">License: Apache-2.0</span>
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<td class="diff-line-num new old_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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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> On Debian systems, the full text of the Apache-2.0 license</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> can be found in the file '/usr/share/common-licenses/Apache-2.0'</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">License: BSD</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> FIXME: include the full text of the license here</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">License: LGPL-2</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> On Debian systems, the full text of the LGPL-2 license</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> can be found in the file '/usr/share/common-licenses/LGPL-2'</span></pre>
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<li id="c0e6ac783af8451faa5e88ff2426dbbaa309df8b">
<a href="https://salsa.debian.org/med-team/snpeff/commit/2da2948bfbdc6849e8412423a1ad0db4916faad3#c0e6ac783af8451faa5e88ff2426dbbaa309df8b"><strong>debian/libsnpeff-java-doc.doc-base.api</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Document: libsnpeff-java</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Title: API Javadoc for Snp Effect</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Author: Snp Effect developers</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Abstract: This is the API Javadoc provided for the</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> libsnpeff-java library.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Section: Programming</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Format: HTML</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Index: /usr/share/doc/libsnpeff-java/api/index.html</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Files: /usr/share/doc/libsnpeff-java/api/*</span></pre>
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<li id="f059acb09953e85f3950991e4b07da0722943516">
<a href="https://salsa.debian.org/med-team/snpeff/commit/2da2948bfbdc6849e8412423a1ad0db4916faad3#f059acb09953e85f3950991e4b07da0722943516"><strong>debian/libsnpeff-java-doc.install</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">target</span><span class="o" style="font-weight: 600;">/</span><span class="nx">apidocs</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">libsnpeff</span><span class="o" style="font-weight: 600;">-</span><span class="nx">java</span><span class="o" style="font-weight: 600;">/</span><span class="nx">api</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"></span></pre>
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<a href="https://salsa.debian.org/med-team/snpeff/commit/2da2948bfbdc6849e8412423a1ad0db4916faad3#8f26a3ee4710acd4172b137f1a6174dcf0808341"><strong>debian/libsnpeff-java.poms</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># List of POM files for the package</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"># Format of this file is:</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># <path to pom file> [option]*</span>
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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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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"># Empty by default. [mh_install]</span>
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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 --has-package-version</span></pre>
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<a href="https://salsa.debian.org/med-team/snpeff/commit/2da2948bfbdc6849e8412423a1ad0db4916faad3#5f7c96eb17e78b0de55008d54b51e8dee2f412bc"><strong>debian/maven.cleanIgnoreRules</strong></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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<a href="https://salsa.debian.org/med-team/snpeff/commit/2da2948bfbdc6849e8412423a1ad0db4916faad3#26121dc92cd4cd9822d2e9e2b619b799bf9a51f4"><strong>debian/maven.ignoreRules</strong></a>
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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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2
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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="LC3" class="line" lang="plaintext">com.typesafe.akka akka-actor * * * *</span>
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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>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">org.apache.maven.plugins maven-javadoc-plugin * * * *</span>
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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>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">org.biojava biojava3-structure * * * *</span>
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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/commit/2da2948bfbdc6849e8412423a1ad0db4916faad3#d006b76813d91cccc2a85e222d10982eb5d52728"><strong>debian/maven.properties</strong></a>
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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>
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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>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;"># maven.test.skip=true</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;"># project.build.sourceEncoding=UTF-8</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="properties"></span></pre>
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<li id="24b90c28b48ee27d2ecad460d66ac6959df5c033">
<a href="https://salsa.debian.org/med-team/snpeff/commit/2da2948bfbdc6849e8412423a1ad0db4916faad3#24b90c28b48ee27d2ecad460d66ac6959df5c033"><strong>debian/maven.publishedRules</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">org.snpeff SnpEff jar s/.*/debian/ * *</span></pre>
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<li id="58530b38acb0fa3a65612c676abaea46c4a3f2f3">
<a href="https://salsa.debian.org/med-team/snpeff/commit/2da2948bfbdc6849e8412423a1ad0db4916faad3#58530b38acb0fa3a65612c676abaea46c4a3f2f3"><strong>debian/maven.rules</strong></a>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">junit junit jar s/4\..*/4.x/ * *</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">org.snpeff SnpEff jar * * *</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">org.snpeff SnpEff jar s/.*/debian/ * *</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">log4j log4j * s/1\.2\..*/1.2.x/ * *</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">net.sf.trove4j trove4j * s/.*/2.x/ * *</span></pre>
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<a href="https://salsa.debian.org/med-team/snpeff/commit/2da2948bfbdc6849e8412423a1ad0db4916faad3#f6c6956cf73acf73842e03af1a6088b689674ca7"><strong>debian/snpeff.poms</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># List of POM files for the package</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"># Format of this file is:</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># <path to pom file> [option]*</span>
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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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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"># Empty by default. [mh_install]</span>
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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></pre>
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