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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/bcbio">Debian Med / bcbio</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/3975d052b2f40110b87c667bbc0fef2bf147d43b">3975d052</a></strong>
<div>
<span>by Steffen Möller</span>
<i>at 2019-06-08T18:30:17Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reordering for importance
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<h4>1 changed file:</h4>
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<a href="#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
debian/TODO
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<h4>Changes:</h4>
<li id="d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
<a href="https://salsa.debian.org/med-team/bcbio/commit/3975d052b2f40110b87c667bbc0fef2bf147d43b#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba"><strong>debian/TODO</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="mosel"><span class="k" style="font-weight: 600;"><span class="idiff left">package</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bamtofastq</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">from</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">biobambam2</span></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="mosel"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">https</span></span><span class="p"><span class="idiff">://</span></span><span class="n" style="color: #333;"><span class="idiff">salsa</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">debian</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">org</span></span><span class="p"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">med</span></span><span class="p"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">team</span></span><span class="p"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">biobambam2</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">queue</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;"><span class="idiff left">TODO</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bcbio</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">with</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">Debian</span></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="mosel"><span class="p"><span class="idiff left right">==========================</span></span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">snpEff</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="mosel"> <span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;">snpeff</span><span class="p">.</span><span class="n" style="color: #333;">sourceforge</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">snpeff</span><span class="p">/</span><span class="n" style="color: #333;">blob</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">debian</span><span class="p">/</span><span class="n" style="color: #333;">changelog</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="mosel"> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">packaging</span> <span class="n" style="color: #333;">needs</span> <span class="n" style="color: #333;">help</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">its</span> <span class="n" style="color: #333;">dependencies</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="mosel"> <span class="n" style="color: #333;">apfloat</span> <span class="m" style="color: #099;">1.6.3</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">mtommila</span><span class="p">/</span><span class="n" style="color: #333;">apfloat</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="mosel"> <span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;">www</span><span class="p">.</span><span class="n" style="color: #333;">apfloat</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">apfloat_java</span><span class="p">/</span><span class="n" style="color: #333;">maven</span><span class="p">.</span><span class="n" style="color: #333;">html</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="mosel"> <span class="n" style="color: #333;">charts4j</span> <span class="m" style="color: #099;">1.3</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">mvnrepository</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">artifact</span><span class="p">/</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">googlecode</span><span class="p">.</span><span class="n" style="color: #333;">charts4j</span><span class="p">/</span><span class="n" style="color: #333;">charts4j</span><span class="p">/</span><span class="m" style="color: #099;">1.3</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="mosel"> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">typesafe</span><span class="p">.</span><span class="n" style="color: #333;">akka</span><span class="p">:</span><span class="n" style="color: #333;">akka</span><span class="p">-</span><span class="n" style="color: #333;">actor</span> <span class="m" style="color: #099;">2.0.1</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="mosel"> <span class="n" style="color: #333;">distlib</span> <span class="m" style="color: #099;">0.9.1</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">sourceforge</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">projects</span><span class="p">/</span><span class="n" style="color: #333;">statdistlib</span><span class="p">/?</span><span class="n" style="color: #333;">source</span><span class="p">=</span><span class="n" style="color: #333;">navbar</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">following</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">list</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">packages</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">used</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">least</span> <span class="n" style="color: #333;">one</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">workflows</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">aggregates</span><span class="p">.</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">complete</span> <span class="n" style="color: #333;">coverage</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">Debian</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">these</span> <span class="n" style="color: #333;">tools</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"><span class="n" style="color: #333;">seems</span> <span class="n" style="color: #333;">increasingly</span> <span class="n" style="color: #333;">unlikely</span> <span class="p">-</span> <span class="n" style="color: #333;">their</span> <span class="n" style="color: #333;">packaging</span> <span class="n" style="color: #333;">would</span> <span class="n" style="color: #333;">take</span> <span class="n" style="color: #333;">longer</span> <span class="n" style="color: #333;">than</span> <span class="n" style="color: #333;">the</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"><span class="n" style="color: #333;">tools</span> <span class="n" style="color: #333;">scientific</span> <span class="n" style="color: #333;">lifespan</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">e</span><span class="p">.</span> <span class="n" style="color: #333;">there</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">generation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">problem</span> <span class="n" style="color: #333;">solving</span></span>
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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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"><span class="n" style="color: #333;">emerging</span> <span class="k" style="font-weight: 600;">and</span><span class="p">/</span><span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">workflow</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">whole</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">mutated</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">meantime</span><span class="p">.</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"><span class="n" style="color: #333;">Packages</span> <span class="n" style="color: #333;">already</span> <span class="n" style="color: #333;">accepted</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="mosel"><span class="p">------------------------</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="mosel"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="mosel"><span class="n" style="color: #333;">Are</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">longer</span> <span class="n" style="color: #333;">shown</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">this</span> <span class="k" style="font-weight: 600;">list</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">added</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">dependencies</span> <span class="k" style="font-weight: 600;">of</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="mosel"><span class="n" style="color: #333;">bcbio</span><span class="p">.</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="mosel"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="mosel"><span class="n" style="color: #333;">Packages</span> <span class="n" style="color: #333;">already</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">New</span> <span class="n" style="color: #333;">Queue</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="mosel"><span class="p">---------------------------------</span></span>
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16
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="mosel"></span>
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17
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">atropos</span></span>
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18
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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;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">atropos</span> <span class="p">(</span><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">queue</span><span class="p">)</span></span>
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19
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="mosel"></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">mosdepth</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">mosdepth</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="mosel"> <span class="n" style="color: #333;">several</span> <span class="n" style="color: #333;">nim</span> <span class="n" style="color: #333;">libraries</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">needed</span><span class="p">.</span> <span class="n" style="color: #333;">These</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">been</span> <span class="n" style="color: #333;">addressed</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">nim</span><span class="p">-</span><span class="n" style="color: #333;">team</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">already</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">queue</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">bamtofastq</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">biobambam2</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">biobambam2</span> <span class="p">(</span><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">queue</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">hts_nim_tools</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">brentp</span><span class="p">/</span><span class="n" style="color: #333;">hts</span><span class="p">-</span><span class="n" style="color: #333;">nim</span><span class="p">-</span><span class="n" style="color: #333;">tools</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="mosel"> <span class="n" style="color: #333;">Likely</span> <span class="n" style="color: #333;">addressed</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">efforts</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">nim</span> <span class="n" style="color: #333;">behind</span> <span class="n" style="color: #333;">mosdepth</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">kallisto</span> <span class="p">(</span><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">queue</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">qsignature</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">sourceforge</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">p</span><span class="p">/</span><span class="n" style="color: #333;">adamajava</span><span class="p">/</span><span class="n" style="color: #333;">wiki</span><span class="p">/</span><span class="n" style="color: #333;">Home</span><span class="p">/</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">sourceforge</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">p</span><span class="p">/</span><span class="n" style="color: #333;">adamajava</span><span class="p">/</span><span class="n" style="color: #333;">wiki</span><span class="p">/</span><span class="n" style="color: #333;">qSignature</span><span class="p">/</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="mosel"> <span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;">sourceforge</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">projects</span><span class="p">/</span><span class="n" style="color: #333;">adamajava</span><span class="p">/</span><span class="n" style="color: #333;">files</span><span class="p">/</span><span class="n" style="color: #333;">qsignature</span><span class="p">.</span><span class="n" style="color: #333;">tar</span><span class="p">.</span><span class="n" style="color: #333;">bz2</span><span class="p">/</span><span class="n" style="color: #333;">download</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">sourceforge</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">p</span><span class="p">/</span><span class="n" style="color: #333;">adamajava</span><span class="p">/</span><span class="n" style="color: #333;">code</span><span class="p">/</span><span class="n" style="color: #333;">HEAD</span><span class="p">/</span><span class="n" style="color: #333;">tree</span><span class="p">/</span><span class="n" style="color: #333;">trunk</span><span class="p">/</span><span class="n" style="color: #333;">adamajava</span><span class="p">/</span><span class="n" style="color: #333;">qsignature</span><span class="p">/</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">Python</span> <span class="n" style="color: #333;">module</span> <span class="n" style="color: #333;">geneimpacts</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">pypi</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">project</span><span class="p">/</span><span class="n" style="color: #333;">geneimpacts</span><span class="p">/</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">brentp</span><span class="p">/</span><span class="n" style="color: #333;">geneimpacts</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">geneimpacts</span> <span class="p">(</span><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">queue</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">pizzly</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">pmelsted</span><span class="p">/</span><span class="n" style="color: #333;">pizzly</span> <span class="p">(</span><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">queue</span><span class="p">)</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="mosel"></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">wasabi</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">pkg</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">other</span><span class="p">-</span><span class="n" style="color: #333;">wasabi</span> <span class="p">(</span><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">queue</span><span class="p">)</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">tophat</span><span class="p">-</span><span class="n" style="color: #333;">recondition</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">cbrueffer</span><span class="p">/</span><span class="n" style="color: #333;">tophat</span><span class="p">-</span><span class="n" style="color: #333;">recondition</span> <span class="p">(</span><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">queue</span><span class="p">)</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">wham</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="mosel"> <span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;">research</span><span class="p">.</span><span class="n" style="color: #333;">cs</span><span class="p">.</span><span class="n" style="color: #333;">wisc</span><span class="p">.</span><span class="n" style="color: #333;">edu</span><span class="p">/</span><span class="n" style="color: #333;">wham</span><span class="p">/</span> <span class="p">(</span><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">queue</span><span class="p">)</span></span>
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34
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">optitype</span></span>
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36
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<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">
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">optitype</span> <span class="p">(</span><span class="n" style="color: #333;">rudimentary</span><span class="p">)</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="mosel"></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="mosel"><span class="n" style="color: #333;">Packages</span> <span class="n" style="color: #333;">just</span> <span class="n" style="color: #333;">waiting</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">someone</span> <span class="n" style="color: #333;">addressing</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">last</span> <span class="n" style="color: #333;">mile</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">upload</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="mosel"><span class="p">-------------------------------------------------------------------------</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="mosel"></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">gffread</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">gffread</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">pyomo</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">Pyomo</span><span class="p">/</span><span class="n" style="color: #333;">pyomo</span></span>
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<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">@@ -45,57 +58,88 @@ package pyutilib</td>
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">modules</span><span class="p">/</span><span class="n" style="color: #333;">pyutilib</span> <span class="p">-</span> <span class="n" style="color: #333;">builds</span><span class="p">,</span> <span class="n" style="color: #333;">tests</span> <span class="n" style="color: #333;">fail</span></span>
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46
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<td class="diff-line-num new_line" data-linenumber="59" 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="LC59" class="line" lang="mosel"> <span class="n" style="color: #333;">needed</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">pyomo</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">testing</span></span>
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47
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">seqcluster</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">lpantano</span><span class="p">/</span><span class="n" style="color: #333;">seqcluster</span><span class="p">/</span><span class="n" style="color: #333;">archive</span><span class="p">/</span><span class="m" style="color: #099;">1824</span><span class="n" style="color: #333;">d37</span><span class="p">.</span><span class="n" style="color: #333;">tar</span><span class="p">.</span><span class="n" style="color: #333;">gz</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">seqcluster</span></span>
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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">
64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="mosel"> <span class="n" style="color: #333;">Some</span> <span class="n" style="color: #333;">nitty</span><span class="p">-</span><span class="n" style="color: #333;">gritty</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">going</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">there</span> <span class="n" style="color: #333;">wrt</span> <span class="n" style="color: #333;">Python3</span> <span class="n" style="color: #333;">transition</span></span>
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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">
65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">upcoming</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">release</span><span class="p">.</span> <span class="n" style="color: #333;">Needs</span> <span class="n" style="color: #333;">another</span> <span class="n" style="color: #333;">review</span> <span class="k" style="font-weight: 600;">and</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="mosel"> <span class="n" style="color: #333;">likely</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">communication</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">upstream</span><span class="p">.</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="mosel"></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="mosel"></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="mosel"><span class="n" style="color: #333;">Packages</span> <span class="n" style="color: #333;">presumed</span> <span class="n" style="color: #333;">easy</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">package</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="mosel"><span class="p">---------------------------------</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="mosel"></span>
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48
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">gjh_asl_json</span></span>
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49
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">ghackebeil</span><span class="p">/</span><span class="n" style="color: #333;">gjh_asl_json</span></span>
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50
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="mosel"> <span class="n" style="color: #333;">needed</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">pyomo</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">testing</span></span>
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51
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="mosel"></span>
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<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="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">hts_nim_tools</span></span>
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<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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<pre style="margin: 0;">+<span id="LC77" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">brentp</span><span class="p">/</span><span class="n" style="color: #333;">hts</span><span class="p">-</span><span class="n" style="color: #333;">nim</span><span class="p">-</span><span class="n" style="color: #333;">tools</span></span>
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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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="mosel"> <span class="n" style="color: #333;">Likely</span> <span class="n" style="color: #333;">addressed</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">efforts</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">nim</span> <span class="n" style="color: #333;">behind</span> <span class="n" style="color: #333;">mosdepth</span></span>
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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">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="mosel"></span>
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52
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<td class="diff-line-num new_line" data-linenumber="80" 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">
80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="s2" style="color: #d14;">"asl solver"</span></span>
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53
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<td class="diff-line-num new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="mosel"> <span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;">www</span><span class="p">.</span><span class="n" style="color: #333;">ampl</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">netlib</span><span class="p">/</span><span class="n" style="color: #333;">ampl</span><span class="p">/</span><span class="n" style="color: #333;">solvers</span><span class="p">.</span><span class="n" style="color: #333;">tgz</span></span>
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54
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<td class="diff-line-num new_line" data-linenumber="82" 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">
82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="mosel"> <span class="n" style="color: #333;">needed</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">gjh_asl_json</span></span>
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55
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="mosel"></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Package</span> <span class="n" style="color: #333;">MutliQC</span> <span class="p">-</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">salsa</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">multiqc</span></span>
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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">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="mosel"> <span class="n" style="color: #333;">Steffen</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">address</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">one</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="mosel"></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="mosel"></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="mosel"></span>
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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="mosel"><span class="n" style="color: #333;">Packages</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">importance</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">basic</span> <span class="n" style="color: #333;">NGS</span> <span class="n" style="color: #333;">workflow</span> <span class="n" style="color: #333;">well</span> <span class="n" style="color: #333;">beyond</span> <span class="n" style="color: #333;">bcbio</span></span>
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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="mosel"><span class="p">---------------------------------------------------------------</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="mosel"></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">mosdepth</span></span>
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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">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">mosdepth</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="mosel"> <span class="n" style="color: #333;">several</span> <span class="n" style="color: #333;">nim</span> <span class="n" style="color: #333;">libraries</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">needed</span><span class="p">.</span> <span class="n" style="color: #333;">These</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">been</span> <span class="n" style="color: #333;">addressed</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">nim</span><span class="p">-</span><span class="n" style="color: #333;">team</span></span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">already</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">queue</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="mosel"></span>
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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">oncofuse</span></span>
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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">oncofuse</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="mosel"></span>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">optitype</span></span>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">optitype</span> <span class="p">(</span><span class="n" style="color: #333;">rudimentary</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="mosel"></span>
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56
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<td class="diff-line-num new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">vcfanno</span></span>
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57
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<td class="diff-line-num new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">vcfanno</span></span>
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58
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<td class="diff-line-num new_line" data-linenumber="106" 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">
106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">Not</span> <span class="n" style="color: #333;">fun</span> <span class="n" style="color: #333;">because</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">many</span> <span class="n" style="color: #333;">GO</span> <span class="n" style="color: #333;">packages</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">still</span> <span class="n" style="color: #333;">missing</span><span class="p">,</span></span>
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59
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<td class="diff-line-num new_line" data-linenumber="107" 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">
107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="mosel"> <span class="s2" style="color: #d14;">"biogo"</span> <span class="n" style="color: #333;">being</span> <span class="n" style="color: #333;">one</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">them</span><span class="p">.</span></span>
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60
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="mosel"></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="mosel"></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="mosel"></span>
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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="mosel"><span class="n" style="color: #333;">Difficult</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">package</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">degree</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">one</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">tempted</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">conda</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">meantime</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="mosel"><span class="p">------------------------------------------------------------------------------------</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="mosel"></span>
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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">snpEff</span></span>
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<td class="diff-line-num new new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="mosel"> <span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;">snpeff</span><span class="p">.</span><span class="n" style="color: #333;">sourceforge</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">snpeff</span><span class="p">/</span><span class="n" style="color: #333;">blob</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">debian</span><span class="p">/</span><span class="n" style="color: #333;">changelog</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="mosel"> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">packaging</span> <span class="n" style="color: #333;">needs</span> <span class="n" style="color: #333;">help</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">its</span> <span class="n" style="color: #333;">dependencies</span><span class="p">:</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="mosel"> <span class="n" style="color: #333;">apfloat</span> <span class="m" style="color: #099;">1.6.3</span><span class="p">:</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">mtommila</span><span class="p">/</span><span class="n" style="color: #333;">apfloat</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="mosel"> <span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;">www</span><span class="p">.</span><span class="n" style="color: #333;">apfloat</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">apfloat_java</span><span class="p">/</span><span class="n" style="color: #333;">maven</span><span class="p">.</span><span class="n" style="color: #333;">html</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="mosel"> <span class="n" style="color: #333;">charts4j</span> <span class="m" style="color: #099;">1.3</span><span class="p">:</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">mvnrepository</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">artifact</span><span class="p">/</span><span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">googlecode</span><span class="p">.</span><span class="n" style="color: #333;">charts4j</span><span class="p">/</span><span class="n" style="color: #333;">charts4j</span><span class="p">/</span><span class="m" style="color: #099;">1.3</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="mosel"> <span class="n" style="color: #333;">com</span><span class="p">.</span><span class="n" style="color: #333;">typesafe</span><span class="p">.</span><span class="n" style="color: #333;">akka</span><span class="p">:</span><span class="n" style="color: #333;">akka</span><span class="p">-</span><span class="n" style="color: #333;">actor</span> <span class="m" style="color: #099;">2.0.1</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="mosel"> <span class="n" style="color: #333;">distlib</span> <span class="m" style="color: #099;">0.9.1</span><span class="p">:</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">sourceforge</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">projects</span><span class="p">/</span><span class="n" style="color: #333;">statdistlib</span><span class="p">/?</span><span class="n" style="color: #333;">source</span><span class="p">=</span><span class="n" style="color: #333;">navbar</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="mosel"></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">qsignature</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">sourceforge</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">p</span><span class="p">/</span><span class="n" style="color: #333;">adamajava</span><span class="p">/</span><span class="n" style="color: #333;">wiki</span><span class="p">/</span><span class="n" style="color: #333;">Home</span><span class="p">/</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">sourceforge</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">p</span><span class="p">/</span><span class="n" style="color: #333;">adamajava</span><span class="p">/</span><span class="n" style="color: #333;">wiki</span><span class="p">/</span><span class="n" style="color: #333;">qSignature</span><span class="p">/</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="mosel"> <span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;">sourceforge</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">projects</span><span class="p">/</span><span class="n" style="color: #333;">adamajava</span><span class="p">/</span><span class="n" style="color: #333;">files</span><span class="p">/</span><span class="n" style="color: #333;">qsignature</span><span class="p">.</span><span class="n" style="color: #333;">tar</span><span class="p">.</span><span class="n" style="color: #333;">bz2</span><span class="p">/</span><span class="n" style="color: #333;">download</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">sourceforge</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">p</span><span class="p">/</span><span class="n" style="color: #333;">adamajava</span><span class="p">/</span><span class="n" style="color: #333;">code</span><span class="p">/</span><span class="n" style="color: #333;">HEAD</span><span class="p">/</span><span class="n" style="color: #333;">tree</span><span class="p">/</span><span class="n" style="color: #333;">trunk</span><span class="p">/</span><span class="n" style="color: #333;">adamajava</span><span class="p">/</span><span class="n" style="color: #333;">qsignature</span><span class="p">/</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="mosel"></span>
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61
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="mosel"><span class="n" style="color: #333;">Now</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">AdamaJava</span><span class="p">/</span><span class="n" style="color: #333;">adamajava</span></span>
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62
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="mosel"></span>
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63
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<td class="diff-line-num new_line" data-linenumber="135" 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">
135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="mosel"><span class="n" style="color: #333;">add</span> <span class="n" style="color: #333;">hisat2_extract_splice_sites</span><span class="p">.</span><span class="n" style="color: #333;">py</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">hisat2</span> <span class="k" style="font-weight: 600;">package</span></span>
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64
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<td class="diff-line-num new_line" data-linenumber="136" 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">
136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="mosel"> <span class="p">-></span> <span class="n" style="color: #333;">Done</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Git</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">preparation</span> <span class="n" style="color: #333;">for</span> <span class="m" style="color: #099;">2.1.0</span><span class="p">-</span><span class="m" style="color: #099;">3</span></span>
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65
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<td class="diff-line-num new_line" data-linenumber="137" 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">
137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="mosel"> <span class="p">-></span> <span class="n" style="color: #333;">Added</span> <span class="n" style="color: #333;">arch</span><span class="p">-</span><span class="n" style="color: #333;">indep</span> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">hisat2</span> <span class="k" style="font-weight: 600;">package</span></span>
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66
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<td class="diff-line-num new_line" data-linenumber="138" 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">
138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="mosel"></span>
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67
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<td class="diff-line-num new_line old" data-linenumber="139" 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="LC67" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Package</span> <span class="n" style="color: #333;">MutliQC</span> <span class="p">-</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">salsa</span></span>
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68
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<td class="diff-line-num new_line old" data-linenumber="139" 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="LC68" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">multiqc</span></span>
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69
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<td class="diff-line-num new_line old" data-linenumber="139" 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="LC69" class="line" lang="mosel"> <span class="n" style="color: #333;">Nobody</span> <span class="n" style="color: #333;">active</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">one</span> <span class="p">-</span> <span class="n" style="color: #333;">needs</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">peer</span> <span class="n" style="color: #333;">review</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">upload</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="mosel"></span>
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71
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<td class="diff-line-num new_line" data-linenumber="139" 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">
139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">sailfish</span></span>
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72
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<td class="diff-line-num new_line" data-linenumber="140" 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">
140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">sailfish</span></span>
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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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<td class="diff-line-num new_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="mosel"> <span class="n" style="color: #333;">FTBFS</span></span>
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74
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<td class="diff-line-num new_line" data-linenumber="142" 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">
142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="mosel"></span>
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75
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<td class="diff-line-num new_line old" 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="LC75" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">kallisto</span> <span class="p">(</span><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">queue</span><span class="p">)</span></span>
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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="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="LC76" class="line" lang="mosel"></span>
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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="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="LC77" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">wasabi</span></span>
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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="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="LC78" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">pkg</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">other</span><span class="p">-</span><span class="n" style="color: #333;">wasabi</span> <span class="p">(</span><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">queue</span><span class="p">)</span></span>
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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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<td class="diff-line-num new_line old" 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="LC79" class="line" lang="mosel"></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">oncofuse</span></span>
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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">
81
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<td class="diff-line-num new_line old" 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="LC81" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">oncofuse</span></span>
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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="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="LC82" class="line" lang="mosel"> <span class="n" style="color: #333;">Nobody</span> <span class="n" style="color: #333;">active</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">one</span> <span class="p">-</span> <span class="n" style="color: #333;">needs</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">peer</span> <span class="n" style="color: #333;">review</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">upload</span></span>
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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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<pre style="margin: 0;">-<span id="LC83" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">Python</span> <span class="n" style="color: #333;">module</span> <span class="n" style="color: #333;">geneimpacts</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">pypi</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">project</span><span class="p">/</span><span class="n" style="color: #333;">geneimpacts</span><span class="p">/</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">brentp</span><span class="p">/</span><span class="n" style="color: #333;">geneimpacts</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">geneimpacts</span> <span class="p">(</span><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">queue</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">seqcluster</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">lpantano</span><span class="p">/</span><span class="n" style="color: #333;">seqcluster</span><span class="p">/</span><span class="n" style="color: #333;">archive</span><span class="p">/</span><span class="m" style="color: #099;">1824</span><span class="n" style="color: #333;">d37</span><span class="p">.</span><span class="n" style="color: #333;">tar</span><span class="p">.</span><span class="n" style="color: #333;">gz</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">seqcluster</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="mosel"> <span class="n" style="color: #333;">Some</span> <span class="n" style="color: #333;">nitty</span><span class="p">-</span><span class="n" style="color: #333;">gritty</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">going</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">there</span> <span class="n" style="color: #333;">wrt</span> <span class="n" style="color: #333;">Python3</span> <span class="n" style="color: #333;">transition</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">upcoming</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">release</span><span class="p">.</span> <span class="n" style="color: #333;">Needs</span> <span class="n" style="color: #333;">another</span> <span class="n" style="color: #333;">review</span> <span class="k" style="font-weight: 600;">and</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="mosel"> <span class="n" style="color: #333;">likely</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">communication</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">upstream</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="mosel"></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="mosel"></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">pizzly</span></span>
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<td class="diff-line-num old old_line" data-linenumber="98" 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">
98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">pmelsted</span><span class="p">/</span><span class="n" style="color: #333;">pizzly</span> <span class="p">(</span><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">queue</span><span class="p">)</span></span>
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">vt</span></span>
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101
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">atks</span><span class="p">/</span><span class="n" style="color: #333;">vt</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="111" 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="155" 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">@@ -111,7 +155,6 @@ package fgbio</td>
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">manta</span></span>
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112
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="mosel"><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">Illumina</span><span class="p">/</span><span class="n" style="color: #333;">manta</span><span class="p">/</span></span>
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113
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<td class="diff-line-num new_line" data-linenumber="157" 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">
157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">manta</span></span>
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114
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<td class="diff-line-num new_line old" 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="LC114" class="line" lang="mosel"> <span class="p">@</span><span class="n" style="color: #333;">Andreas</span> <span class="p">-</span> <span class="n" style="color: #333;">where</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">we</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">one</span><span class="p">?</span></span>
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115
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="mosel"></span>
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116
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<td class="diff-line-num new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">strelka</span></span>
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<td class="diff-line-num old_line" data-linenumber="117" 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">
117
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<td class="diff-line-num new_line" data-linenumber="160" 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">
160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="mosel"><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">Illumina</span><span class="p">/</span><span class="n" style="color: #333;">strelka</span><span class="p">/</span><span class="n" style="color: #333;">releases</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="121" 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="164" 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">@@ -121,21 +164,16 @@ https://github.com/Illumina/strelka/releases</td>
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<td class="diff-line-num old_line" data-linenumber="121" 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">
121
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<td class="diff-line-num new_line" data-linenumber="164" 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">
164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="mosel"> <span class="p">#</span><span class="k" style="font-weight: 600;">set</span><span class="p">(</span><span class="n" style="color: #333;">HTSLIB_CFLAGS</span> <span class="s1" style="color: #d14;">'-O0 -g -fsanitize=address -fno-omit-frame-pointer -fno-optimize-sibling-calls'</span><span class="p">)</span></span>
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122
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="mosel"></span>
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123
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<td class="diff-line-num new_line" data-linenumber="166" 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">
166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="mosel"></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">lumpy</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="mosel"><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">arq5x</span><span class="p">/</span><span class="n" style="color: #333;">lumpy</span><span class="p">-</span><span class="n" style="color: #333;">sv</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="127" 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">
127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">wham</span></span>
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<td class="diff-line-num old old_line" data-linenumber="128" 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">
128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="mosel"> <span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;">research</span><span class="p">.</span><span class="n" style="color: #333;">cs</span><span class="p">.</span><span class="n" style="color: #333;">wisc</span><span class="p">.</span><span class="n" style="color: #333;">edu</span><span class="p">/</span><span class="n" style="color: #333;">wham</span><span class="p">/</span> <span class="p">(</span><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">queue</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="129" 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">
129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="mosel"></span>
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130
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<td class="diff-line-num new_line" data-linenumber="167" 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">
167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="mosel"><span class="p">#</span> <span class="n" style="color: #333;">An</span> <span class="n" style="color: #333;">easy</span> <span class="n" style="color: #333;">one</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="131" 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">
131
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<td class="diff-line-num new_line old" data-linenumber="168" 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="LC131" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">tophat</span><span class="p">-</span><span class="n" style="color: #333;">recondition</span></span>
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<td class="diff-line-num old old_line" data-linenumber="132" 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">
132
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<td class="diff-line-num new_line old" data-linenumber="168" 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="LC132" class="line" lang="mosel"><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">cbrueffer</span><span class="p">/</span><span class="n" style="color: #333;">tophat</span><span class="p">-</span><span class="n" style="color: #333;">recondition</span> <span class="p">(</span><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">queue</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="133" 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">
133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="mosel"></span>
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134
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">qualimap</span></span>
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<td class="diff-line-num old_line" data-linenumber="135" 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">
135
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<td class="diff-line-num new_line" data-linenumber="169" 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">
169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">qualimap</span></span>
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136
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="mosel"> <span class="n" style="color: #333;">Unfortunately</span> <span class="n" style="color: #333;">some</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Java</span> <span class="n" style="color: #333;">code</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">needed</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">predepenceny</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">simply</span> <span class="n" style="color: #333;">lost</span> <span class="n" style="color: #333;">see</span></span>
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137
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">alioth</span><span class="p">-</span><span class="n" style="color: #333;">lists</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">pipermail</span><span class="p">/</span><span class="n" style="color: #333;">debian</span><span class="p">-</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">packaging</span><span class="p">/</span><span class="m" style="color: #099;">2016</span><span class="p">-</span><span class="n" style="color: #333;">January</span><span class="p">/</span><span class="m" style="color: #099;">038322.</span><span class="n" style="color: #333;">html</span></span>
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138
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="mosel"></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">gffread</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">gffread</span></span>
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<td class="diff-line-num old old_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="mosel"> <span class="p">@</span><span class="n" style="color: #333;">andreas</span> <span class="p">-</span> <span class="n" style="color: #333;">What</span> <span class="n" style="color: #333;">happened</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">one</span><span class="p">?</span></span></pre>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="mosel"></span>
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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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="mosel"><span class="n" style="color: #333;">Packages</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">longer</span> <span class="n" style="color: #333;">used</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">bcbio</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="mosel"><span class="p">--------------------------------</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="mosel"></span>
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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">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">lumpy</span></span>
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<td class="diff-line-num new old_line" data-linenumber="142" style="width: 35px; color: rgba(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="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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="mosel"><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">arq5x</span><span class="p">/</span><span class="n" style="color: #333;">lumpy</span><span class="p">-</span><span class="n" style="color: #333;">sv</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="mosel"></span></pre>
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