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<h3>
Alexandre Mestiashvili pushed to branch master
at <a href="https://salsa.debian.org/med-team/subread">Debian Med / subread</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/subread/commit/17088b4b76b7b8d6514a0dfcd4e6be0adaddd3fd">17088b4b</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2019-01-30T18:54:39Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Don't install buggy detectionCall binary
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/subread/commit/d7f4e6bf0ddfd4cb9e387dd62a5f7cc88a730820">d7f4e6bf</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2019-01-30T19:03:54Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update d/README.Debian
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<li>
<strong><a href="https://salsa.debian.org/med-team/subread/commit/0c38a9c56ad2af07803b2fb1e02162ffd84471e2">0c38a9c5</a></strong>
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<span>by Alexandre Mestiashvili</span>
<i>at 2019-01-30T19:21:36Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update d/chaneglog
Gbp-Dch: Ignore
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
debian/README.Debian
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#6d3faf73fa0c7b80be9cc3c2d1b06a1be79b0425">
debian/subread.install
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<h4>Changes:</h4>
<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/subread/compare/21f35b1322a16a3a7753450c8cf3a1979b41caf9...0c38a9c56ad2af07803b2fb1e02162ffd84471e2#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,4 +12,9 @@ Subread User Guide can be found on the project's web site:</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">-- Alex Mestiashvili <alex@biotec.tu-dresden.de> Thu, 07 May 2015 15:24:57 +0200</span></pre>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Subread 1.6.3 changes:</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> detectionCall binary is excluded from 1.6.3+dfsg-1 package due to it's</span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> bugginess. The issue is submited to the upstream and hopefully will</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> be resolved in the next releases.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">-- Alex Mestiashvili <mestia@debian.org> Thu, 07 May 2015 15:24:57 +0200</span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/subread/compare/21f35b1322a16a3a7753450c8cf3a1979b41caf9...0c38a9c56ad2af07803b2fb1e02162ffd84471e2#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">subread (1.6.3+dfsg-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">subread (1.6.3+dfsg-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> [ Alexandre Mestiashvili ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * New upstream version 1.6.3+dfsg</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * DH_VERBOSE=1, check for nocheck in DEB_BUILD_OPTIONS</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Bump Policy to 4.3.0</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * Refresh patches</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> * New binary detectionCall segfaults,</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> remove dropped by upstream coverageCount</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> * TODO: waiting for answer from upstream regarding segfault on derectionCall</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Don't install buggy detectionCall binary</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Update d/README.Debian</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * debhelper 12</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> -- Alexandre Mestiashvili <mestia@debian.org> <span class="idiff left right">Thu, 11 Oct 2018 12:33:55 +00</span>00</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- Alexandre Mestiashvili <mestia@debian.org> <span class="idiff left right">Wed, 30 Jan 2019 20:19:47 +01</span>00</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">subread (1.6.2+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/subread/compare/21f35b1322a16a3a7753450c8cf3a1979b41caf9...0c38a9c56ad2af07803b2fb1e02162ffd84471e2#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -72,8 +72,8 @@ DNA-seq reads and RNA-seq reads (for the purpose of expression analysis)' \</td>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"># $(HELP2MAN) --name='counting the coverage of mapped reads at each location on the entire reference genome' \</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext"># $(utildir)/coverageCount | debian/filter.pl > $(mandir)/coverageCount.1;</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"> $(HELP2MAN) --name='detectionCall' \</span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"> $(utildir)/detectionCall | debian/filter.pl > $(mandir)/detectionCall.1;</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"><span class="idiff left right">#</span> $(HELP2MAN) --name='detectionCall' \</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"><span class="idiff left right">#</span> $(utildir)/detectionCall | debian/filter.pl > $(mandir)/detectionCall.1;</span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext"> $(HELP2MAN) --name='calculate the proportion of mapped reads/fragments' \</span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext"> $(utildir)/propmapped | debian/filter.pl > $(mandir)/propmapped.1;</span>
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<a href="https://salsa.debian.org/med-team/subread/compare/21f35b1322a16a3a7753450c8cf3a1979b41caf9...0c38a9c56ad2af07803b2fb1e02162ffd84471e2#6d3faf73fa0c7b80be9cc3c2d1b06a1be79b0425"><strong>debian/subread.install</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">@@ -5,7 +5,6 @@ bin/subjunc usr/bin</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">sublong</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">subread</span><span class="o" style="font-weight: 600;">-</span><span class="nx">align</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">subread</span><span class="o" style="font-weight: 600;">-</span><span class="nx">buildindex</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">utilities</span><span class="o" style="font-weight: 600;">/</span><span class="nx">detectionCall</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">subread</span></span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">utilities</span><span class="o" style="font-weight: 600;">/</span><span class="nx">propmapped</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">subread</span></span>
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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">utilities</span><span class="o" style="font-weight: 600;">/</span><span class="nx">qualityScores</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">subread</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">utilities</span><span class="o" style="font-weight: 600;">/</span><span class="nx">removeDup</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">subread</span></span>
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