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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>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/8949f2be90a5bacef52ea999e0e82a4b4ffe64fa">8949f2be</a></strong>
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<span>by Steffen Möller</span>
<i>at 2019-07-11T04:51:39Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">wham accepted as wham-align in main
</pre>
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<h4>2 changed files:</h4>
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<li class="file-stats">
<a href="#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
debian/TODO
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<h4>Changes:</h4>
<li id="d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
<a href="https://salsa.debian.org/med-team/bcbio/commit/8949f2be90a5bacef52ea999e0e82a4b4ffe64fa#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba"><strong>debian/TODO</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="42" 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">@@ -42,9 +42,6 @@ package r-wasabi</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="mosel"><span class="s1" style="color: #d14;">package tophat-recondition</span></span>
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<td class="diff-line-num new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/cbrueffer/tophat-recondition (in new queue)</span></span>
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<td class="diff-line-num old_line" data-linenumber="44" 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="LC44" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="mosel"><span class="s1" style="color: #d14;">package wham</span></span>
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<td class="diff-line-num old old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="mosel"><span class="s1" style="color: #d14;"> http://research.cs.wisc.edu/wham/ (in new queue)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="mosel"><span class="s1" style="color: #d14;">package gffread</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC46" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/gffread (in new queue)</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="mosel"></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/bcbio/commit/8949f2be90a5bacef52ea999e0e82a4b4ffe64fa#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="45" 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">@@ -45,6 +45,7 @@ Build-Depends: debhelper (>= 10),</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> seqtk,</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> tabix,</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> tophat,</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> wham-align,</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> xonsh,</span>
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49
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"># documentation</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> python3-sphinx</span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -104,7 +105,8 @@ Recommends: bcftools,</td>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext"> tabix,</span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext"> umis,</span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext"> varscan,</span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="plaintext"> wget</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> wget,</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> wham-align</span>
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108
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="plaintext">Suggests: toil,</span>
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109
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="plaintext"> cwltool,</span>
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110
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="plaintext"> kallisto,</span>
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