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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/d8902ed2a6b6f74f65053aed76549b4a51587b75">d8902ed2</a></strong>
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<span>by Steffen Möller</span>
<i>at 2019-04-18T15:46:53Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updates to bcbio's TODO list
</pre>
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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/d8902ed2a6b6f74f65053aed76549b4a51587b75#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba"><strong>debian/TODO</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,6 +30,7 @@ Now at https://github.com/AdamaJava/adamajava</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC31" 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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32
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<td class="diff-line-num new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC32" 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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<pre style="margin: 0;">+<span id="LC33" 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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34
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<pre style="margin: 0;"> <span id="LC34" 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;">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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35
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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;">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 unfold js-unfold old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,8 +38,7 @@ Package MutliQC - in salsa</td>
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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;">sailfish</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;">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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<pre style="margin: 0;"> <span id="LC40" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">kallisto</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="mosel"> <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>
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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;">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="LC42" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC43" 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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<pre style="margin: 0;"> <span id="LC44" 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;">COMBINE</span><span class="p">-</span><span class="n" style="color: #333;">lab</span><span class="p">/</span><span class="n" style="color: #333;">wasabi</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -67,6 +67,11 @@ https://github.com/fulcrumgenomics/fgbio</td>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC68" 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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69
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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;">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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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="mosel"> <span class="p">-</span> <span class="n" style="color: #333;">Steffen</span> <span class="n" style="color: #333;">works</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>
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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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72
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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;">strelka</span></span>
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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;">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 new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="mosel"> <span class="p">-</span> <span class="n" style="color: #333;">Steffen</span> <span class="n" style="color: #333;">works</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>
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70
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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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71
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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;">lumpy</span></span>
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72
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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;">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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="76" 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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -76,7 +81,7 @@ http://research.cs.wisc.edu/wham/</td>
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="mosel"></span>
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82
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<pre style="margin: 0;"> <span id="LC82" 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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78
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83
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<pre style="margin: 0;"> <span id="LC83" 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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79
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<pre style="margin: 0;">-<span id="LC79" 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>
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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="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="idiff left"> </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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80
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="mosel"></span>
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81
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<pre style="margin: 0;"> <span id="LC86" 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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82
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87
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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;">qualimap</span></span>
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