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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/lofreq">Debian Med / lofreq</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/lofreq/commit/4c4b1cb35b28ca460002eb6b742cf08914e529cd">4c4b1cb3</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-04-30T23:06:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">No long lines in yaml file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/lofreq/commit/24557efd2d3a198bbf404cbe50287a473f7dbd72">24557efd</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-04-30T23:11:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added d/watch file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/lofreq/commit/6d9659ab3c552fb6db53e1b0f7f1b0077fd6e4e3">6d9659ab</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-04-30T23:18:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">uthash still ref'ed in configure.ac
</pre>
</li>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#d886176b28119a37c5a8a1810229202bd7744dd6">
debian/patches/external-htslib.patch
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
<span class="new-file">
+
debian/watch
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="d886176b28119a37c5a8a1810229202bd7744dd6">
<a href="https://salsa.debian.org/med-team/lofreq/compare/abed31bab5ce3bcaedb611e67bfe106f8e0c9af8...6d9659ab3c552fb6db53e1b0f7f1b0077fd6e4e3#d886176b28119a37c5a8a1810229202bd7744dd6"><strong>debian/patches/external-htslib.patch</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">@@ -6,11 +6,42 @@ Description: Allow linking to external htslib</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="LC6" class="line" lang="diff">Author: Afif Elghraoui <afif@ghraoui.name></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff">Forwarded: no</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff">Last-Update: 2015-12-24</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lofreq.orig/src/lofreq/Makefile.am</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lofreq/src/lofreq/Makefile.am</span></span>
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<td class="diff-line-num old old_line" data-linenumber="11" 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="LC11" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -29,4 +29,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gh" style="color: #999;">Index: lofreq-2.1.3.1/src/lofreq/Makefile.am</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lofreq-2.1.3.1.orig/src/lofreq/Makefile.am</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lofreq-2.1.3.1/src/lofreq/Makefile.am</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -29,4 +29,4 @@ viterbi.c viterbi.h</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> </span>
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<td class="diff-line-num new_line" data-linenumber="15" 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="LC15" class="line" lang="diff"> # note: order matters</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> #lofreq_LDADD = @htslib_dir@/libhts.a @samtools_dir@/libbam.a</span>
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-lofreq_LDADD = @HTSLIB@/libhts.a @SAMTOOLS@/libbam.a ../cdflib90/libcdf.a</span></span>
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+lofreq_LDADD = -L@HTSLIB@ -lhts @SAMTOOLS@/libbam.a ../cdflib90/libcdf.a</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gh" style="color: #999;">Index: lofreq-2.1.3.1/Makefile.am</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lofreq-2.1.3.1.orig/Makefile.am</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lofreq-2.1.3.1/Makefile.am</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9,10 +9,10 @@ if ENABLE_TOOLS</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> TOOLS = src/tools</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-LICENSES = LICENSE src/cdflib90.README src/uthash/LICENSE</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+LICENSES = LICENSE src/cdflib90.README</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> EXTRA_DIST = binary_installer.sh $(LICENSES)</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-SUBDIRS = src/cdflib90 src/uthash src/lofreq src/scripts $(TOOLS) </span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SUBDIRS = src/cdflib90 src/lofreq src/scripts $(TOOLS)</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> bug-tests: all</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> cd tests && $(SHELL) run_all.sh;</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gh" style="color: #999;">Index: lofreq-2.1.3.1/configure.ac</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lofreq-2.1.3.1.orig/configure.ac</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lofreq-2.1.3.1/configure.ac</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -215,7 +215,6 @@ AC_DEFINE([_USE_KNETFILE], [1], [KNETFIL</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> AC_CONFIG_FILES(Makefile</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> src/cdflib90/Makefile </span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- src/uthash/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> src/lofreq/Makefile</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> src/scripts/Makefile </span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> src/tools/setup_conf.py </span></pre>
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<a href="https://salsa.debian.org/med-team/lofreq/compare/abed31bab5ce3bcaedb611e67bfe106f8e0c9af8...6d9659ab3c552fb6db53e1b0f7f1b0077fd6e4e3#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> Author: Andreas Wilm and Pauline Poh Kim Aw and Denis Bertrand and Grace Hui Ting Yeo and Swee Hoe Ong and Chang Hua Wong and Chiea Chuen Khor and Rosemary Petric and Martin Lloyd Hibberd and Niranjan Nagarajan</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> Title: "LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Author: ></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Andreas Wilm and Pauline Poh Kim Aw and Denis Bertrand and Grace Hui</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Ting Yeo and Swee Hoe Ong and Chang Hua Wong and Chiea Chuen Khor</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> and Rosemary Petric and Martin Lloyd Hibberd and Niranjan Nagarajan</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Title: ></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> LoFreq: a sequence-quality aware, ultra-sensitive variant caller</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> for uncovering cell-population heterogeneity from high-throughput</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> sequencing datasets</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> Journal: Nucleic Acids Research</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> Year: 2012</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> Volume: 40</span>
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<a href="https://salsa.debian.org/med-team/lofreq/compare/abed31bab5ce3bcaedb611e67bfe106f8e0c9af8...6d9659ab3c552fb6db53e1b0f7f1b0077fd6e4e3#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">version=4</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%lofreq-$1.tar.gz%" \</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> https://github.com/CSB5/lofreq/tags \</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> (?:.*?/)?v?(\d[\d.]*)\.tar\.gz debian uupdate</span></pre>
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