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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/bbmap">Debian Med / bbmap</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bbmap/commit/d76deac3e0a39cd5476cc84b6d195ef405ddf47b">d76deac3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-28T05:34:11Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Delete precompiled jni *.so file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bbmap/commit/41c2d0b59e798367784d0b658eba11f14e407e81">41c2d0b5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-28T05:34:41Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 38.26+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bbmap/commit/e68cc2e7ace6e9024b37e2501f6f0c86d78bd88e">e68cc2e7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-28T05:34:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/38.26+dfsg'
Update to upstream version '38.26+dfsg'
with Debian dir 787869ed4805220f074157bbea2dbf6a6edd45c1</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bbmap/commit/cbfec0772d56a8356dd9f4e0823dfbb1377ce797">cbfec077</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-28T05:37:44Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Recreate JNI *.so
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bbmap/commit/b234f838f90dc900fac03c17ff8822a7fcea09d8">b234f838</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-28T05:39:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">install JNI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bbmap/commit/3df97c7541329d17dd1a845cb718c83d171939f4">3df97c75</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-28T05:41:29Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix permissions
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bbmap/commit/e2b14b26588718b781d0003ad6707cd922a21a6d">e2b14b26</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-28T05:50:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix installation of JNI file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bbmap/commit/b7a06c51564e0f92e47a792783c22e89857a8025">b7a06c51</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-28T05:51:41Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix synopsis
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bbmap/commit/b092c71e542984a7505db404c5f9f21c1c9976af">b092c71e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-28T07:48:55Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Separate package for JNI lib
</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#fb5edd926911823aec2e1408eb217a92497a0a68">
<span class="new-file">
+
debian/bbmap-jni.install
</span>
</a>
</li>
<li class="file-stats">
<a href="#903ef527721688d274ade925c54900120485ec31">
<span class="new-file">
+
debian/bbmap.install
</span>
</a>
</li>
<li class="file-stats">
<a href="#fe8195ad2fa2d6648bfa965bf0ee6cb1e8faa46e">
debian/manifest
→
debian/bbmap.manifest
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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</li>
<li class="file-stats">
<a href="#68d8c5c6babbf5cf109b2584c454449dbff75772">
<span class="deleted-file">
−
debian/install
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#62e0ac46aff221ec43b47b6917ef10cf42ae27f9">
<span class="deleted-file">
−
jni/libbbtoolsjni.so
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</a>
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<h4>Changes:</h4>
<li id="fb5edd926911823aec2e1408eb217a92497a0a68">
<a href="https://salsa.debian.org/med-team/bbmap/compare/d366ef0443cfc57f90723c13e5df27b463ef9e10...b092c71e542984a7505db404c5f9f21c1c9976af#fb5edd926911823aec2e1408eb217a92497a0a68"><strong>debian/bbmap-jni.install</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">
1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">jni</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">so</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">jni</span></span></pre>
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<br>
</li>
<li id="903ef527721688d274ade925c54900120485ec31">
<a href="https://salsa.debian.org/med-team/bbmap/compare/d366ef0443cfc57f90723c13e5df27b463ef9e10...b092c71e542984a7505db404c5f9f21c1c9976af#903ef527721688d274ade925c54900120485ec31"><strong>debian/bbmap.install</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">
1
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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="LC1" class="line" lang="php"><span class="o" style="font-weight: 600;">*.</span><span class="nx">jar</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">java</span></span></pre>
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</li>
<li id="fe8195ad2fa2d6648bfa965bf0ee6cb1e8faa46e">
<a href="https://salsa.debian.org/med-team/bbmap/compare/d366ef0443cfc57f90723c13e5df27b463ef9e10...b092c71e542984a7505db404c5f9f21c1c9976af#fe8195ad2fa2d6648bfa965bf0ee6cb1e8faa46e"><strong>debian/manifest</strong>
→
<strong>debian/bbmap.manifest</strong>
</a>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/bbmap/compare/d366ef0443cfc57f90723c13e5df27b463ef9e10...b092c71e542984a7505db404c5f9f21c1c9976af#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" 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="16" 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">@@ -16,7 +16,7 @@ Package: bbmap</td>
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<td class="diff-line-num old_line" data-linenumber="16" 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">
16
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<td class="diff-line-num new_line" data-linenumber="16" 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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC16" class="line" lang="mosel"><span class="n" style="color: #333;">Architecture</span><span class="p">:</span> <span class="n" style="color: #333;">all</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="17" 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">
17
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<td class="diff-line-num new_line" data-linenumber="17" 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">
17
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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="LC17" class="line" lang="mosel"><span class="n" style="color: #333;">Depends</span><span class="p">:</span> <span class="p">${</span><span class="n" style="color: #333;">java</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">},</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
18
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="mosel"> <span class="p">${</span><span class="n" style="color: #333;">misc</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">}</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="19" 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">
19
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<td class="diff-line-num new_line old" data-linenumber="19" 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="LC19" class="line" lang="mosel"><span class="n" style="color: #333;">Description</span><span class="p">:</span> <span class="n" style="color: #333;">short</span> <span class="nb" style="color: #0086b3;">read</span> <span class="n" style="color: #333;">aligner</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">other</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bioinformatic</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">tools</span></span><span class="p"><span class="idiff right">.</span></span></span>
</pre>
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<td class="diff-line-num new old_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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<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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<pre style="margin: 0;">+<span id="LC19" class="line" lang="mosel"><span class="n" style="color: #333;">Description</span><span class="p">:</span> <span class="n" style="color: #333;">short</span> <span class="nb" style="color: #0086b3;">read</span> <span class="n" style="color: #333;">aligner</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">other</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bioinformatic</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tools</span></span></span>
</pre>
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<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
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<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">
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="mosel"> <span class="n" style="color: #333;">BBMap</span><span class="p">:</span> <span class="n" style="color: #333;">Short</span> <span class="nb" style="color: #0086b3;">read</span> <span class="n" style="color: #333;">aligner</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">DNA</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">RNA</span><span class="p">-</span><span class="n" style="color: #333;">seq</span> <span class="n" style="color: #333;">data</span><span class="p">.</span> <span class="n" style="color: #333;">Capable</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">handling</span></span>
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<td class="diff-line-num old_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
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<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">
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="mosel"> <span class="n" style="color: #333;">arbitrarily</span> <span class="n" style="color: #333;">large</span> <span class="n" style="color: #333;">genomes</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">millions</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">scaffolds</span><span class="p">.</span> <span class="n" style="color: #333;">Handles</span> <span class="n" style="color: #333;">Illumina</span><span class="p">,</span></span>
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<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
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<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">
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="mosel"> <span class="n" style="color: #333;">PacBio</span><span class="p">,</span> <span class="m" style="color: #099;">454</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">reads</span><span class="p">;</span> <span class="n" style="color: #333;">very</span> <span class="n" style="color: #333;">high</span> <span class="n" style="color: #333;">sensitivity</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">tolerant</span> <span class="k" style="font-weight: 600;">of</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,3 +35,16 @@ Description: short read aligner, and other bioinformatic tools.</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="mosel"> <span class="p">.</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="mosel"> <span class="n" style="color: #333;">BBDuk</span><span class="p">:</span> <span class="n" style="color: #333;">Filters</span><span class="p">,</span> <span class="n" style="color: #333;">trims</span><span class="p">,</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">masks</span> <span class="n" style="color: #333;">reads</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">kmer</span> <span class="n" style="color: #333;">matches</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">an</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="mosel"> <span class="n" style="color: #333;">artifact</span><span class="p">/</span><span class="n" style="color: #333;">contaminant</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Package</span><span class="p">:</span> <span class="n" style="color: #333;">bbmap</span><span class="p">-</span><span class="n" style="color: #333;">jni</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="mosel"><span class="n" style="color: #333;">Architecture</span><span class="p">:</span> <span class="n" style="color: #333;">any</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="mosel"><span class="n" style="color: #333;">Depends</span><span class="p">:</span> <span class="p">${</span><span class="n" style="color: #333;">shlibs</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="mosel"> <span class="p">${</span><span class="n" style="color: #333;">misc</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="mosel"><span class="n" style="color: #333;">Description</span><span class="p">:</span> <span class="n" style="color: #333;">short</span> <span class="nb" style="color: #0086b3;">read</span> <span class="n" style="color: #333;">aligner</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">bioinformatic</span> <span class="n" style="color: #333;">tools</span> <span class="p">-</span> <span class="n" style="color: #333;">JNI</span> <span class="n" style="color: #333;">library</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="mosel"> <span class="n" style="color: #333;">BBMap</span><span class="p">:</span> <span class="n" style="color: #333;">Short</span> <span class="nb" style="color: #0086b3;">read</span> <span class="n" style="color: #333;">aligner</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">DNA</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">RNA</span><span class="p">-</span><span class="n" style="color: #333;">seq</span> <span class="n" style="color: #333;">data</span><span class="p">.</span> <span class="n" style="color: #333;">Capable</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">handling</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="mosel"> <span class="n" style="color: #333;">arbitrarily</span> <span class="n" style="color: #333;">large</span> <span class="n" style="color: #333;">genomes</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">millions</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">scaffolds</span><span class="p">.</span> <span class="n" style="color: #333;">Handles</span> <span class="n" style="color: #333;">Illumina</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="mosel"> <span class="n" style="color: #333;">PacBio</span><span class="p">,</span> <span class="m" style="color: #099;">454</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">reads</span><span class="p">;</span> <span class="n" style="color: #333;">very</span> <span class="n" style="color: #333;">high</span> <span class="n" style="color: #333;">sensitivity</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">tolerant</span> <span class="k" style="font-weight: 600;">of</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="mosel"> <span class="n" style="color: #333;">errors</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">numerous</span> <span class="n" style="color: #333;">large</span> <span class="n" style="color: #333;">indels</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="mosel"> <span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="mosel"> <span class="n" style="color: #333;">This</span> <span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">contains</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">architecture</span> <span class="n" style="color: #333;">dependant</span> <span class="n" style="color: #333;">library</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">bbmap</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="mosel"> <span class="n" style="color: #333;">tools</span><span class="p">.</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bbmap/compare/d366ef0443cfc57f90723c13e5df27b463ef9e10...b092c71e542984a7505db404c5f9f21c1c9976af#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">@@ -2,6 +2,7 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Upstream-Name: BBmap</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Source: https://sourceforge.net/projects/bbmap/</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Files-Excluded: *.class</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> *.so</span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Files: *</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Copyright: 2008-2015 Brian Bushnell, Jon Rood</span>
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<a href="https://salsa.debian.org/med-team/bbmap/compare/d366ef0443cfc57f90723c13e5df27b463ef9e10...b092c71e542984a7505db404c5f9f21c1c9976af#68d8c5c6babbf5cf109b2584c454449dbff75772"><strong>debian/install</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">*.jar usr/share/java</span></pre>
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<a href="https://salsa.debian.org/med-team/bbmap/compare/d366ef0443cfc57f90723c13e5df27b463ef9e10...b092c71e542984a7505db404c5f9f21c1c9976af#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -19,8 +19,10 @@ override_dh_auto_clean:</td>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">override_dh_clean:</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> dh_clean</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> find . -name "*.class" -delete</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> find . -name "*.so" -delete</span>
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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">override_dh_auto_build:</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> cd jni && make -f makefile.linux</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> jh_build $(DEB_SOURCE).jar current</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">override_dh_install:</span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,3 +37,7 @@ override_dh_install:</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> $${scr} > $(PKGBINDIR)/`basename $${scr} .sh` ; \</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> fi ; \</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> done</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">override_dh_fixperms:</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> dh_fixperms</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> chmod -x $(PKGBINDIR)/*</span></pre>
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