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<h3>
Alexandre Mestiashvili pushed to branch master
at <a href="https://salsa.debian.org/med-team/bowtie2">Debian Med / bowtie2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/157dbc209f47672a9a7167d16e3a324803906000">157dbc20</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-08-14T09:16:33Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.3.4.2</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/c6c1606770ab53d3d23e1505de873da0a5ae75d4">c6c16067</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-08-14T09:17:08Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.3.4.2'
Update to upstream version '2.3.4.2'
with Debian dir c8219b584a3f214c8e384c1d1d64f3f8580722ec</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/25a7536767c99a29cc159fac09c1c3c417592871">25a75367</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-08-14T09:20:01Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump Standards-Version to 4.2.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/9a3ac321565cfc1adcb490d57db03986734f1c55">9a3ac321</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-08-14T09:48:24Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/6b58808a41ad2cd48f5f484a4baf0112ee5ccc14">6b58808a</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-08-14T11:03:58Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add patch fixing interpreter for bowite2 scripts
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/d7c4ead503a18eb9872cc71bd6bd30783fe4c8fe">d7c4ead5</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-08-14T11:27:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add patch removing reference to js lib for ie9...
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/dc419df9ec51dad7fb9c8b0db75de56d9b97b04c">dc419df9</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-08-14T11:31:44Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update uploader's email
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/d5e59a9ca4138dce566729d5b36c81f20dce4ff9">d5e59a9c</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-08-14T11:32:13Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog, upload to unstable
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
<span class="new-file">
+
CMakeLists.txt
</span>
</a>
</li>
<li class="file-stats">
<a href="#f11fb3bba37e7060bedcd5895812b7c511c52651">
MANUAL
</a>
</li>
<li class="file-stats">
<a href="#465370da702349b6dcb3f9f2026872cad6877efa">
MANUAL.markdown
</a>
</li>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
</a>
</li>
<li class="file-stats">
<a href="#9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8">
NEWS
</a>
</li>
<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
</a>
</li>
<li class="file-stats">
<a href="#057e0784d807c7b84958635ddeeb5003f2751ece">
aln_sink.cpp
</a>
</li>
<li class="file-stats">
<a href="#464ce98392db4e108605b7a12696e7c3434eaf56">
bowtie2-build
</a>
</li>
<li class="file-stats">
<a href="#622d3bcfba0df0e4ae8a0849416ed2d2cf987528">
bowtie2-inspect
</a>
</li>
<li class="file-stats">
<a href="#d1904db8401bf0137951f60c3d4a34a7cf8e2e84">
bt2_idx.h
</a>
</li>
<li class="file-stats">
<a href="#6026283a643bf7fb08c2ef0b797486df93cf0698">
bt2_search.cpp
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#72ea6b8af833c3baef496ab64176c6124c85b5d5">
<span class="new-file">
+
debian/patches/drop-not-needed-js-from-manual.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#76258ff6f1526200cf3fda90e9f37fd9ee4b4364">
debian/patches/reproducible.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#6815d1260ed0fdc6f0d97bc028700b124f2bf358">
debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch
</a>
</li>
<li class="file-stats">
<a href="#f79e82934d1623826dd9382e140be5b4fbfc695e">
<span class="new-file">
+
debian/patches/wrong-interpreter-path.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#ccc364c6c660e798a4f3c3b78119cbea257aee1e">
doc/manual.html
</a>
</li>
<li class="file-stats">
<a href="#a1ba375e8deab5b12b1347797835e927dca95425">
doc/website/manual.ssi
</a>
</li>
<li class="file-stats">
<a href="#9485aa1b2c39982f48264019fde0712132ed80f5">
doc/website/recent_news.ssi
</a>
</li>
<li class="file-stats">
<a href="#59bf596910fb7006481a4d8a45de81ff2bd75a4d">
doc/website/rhsidebar.ssi
</a>
</li>
<li class="file-stats">
<a href="#f33859afffab10e65cd96fbe0811935a2f3508a1">
<span class="new-file">
+
example/reads/combined_reads.bam
</span>
</a>
</li>
<li class="file-stats">
<a href="#ca0679d32b003b8024f4d51789e4d6e5b06db9c9">
formats.h
</a>
</li>
<li class="file-stats">
<a href="#50b0e95b63ccb2c46e008fda8904d780b714df41">
opts.h
</a>
</li>
<li class="file-stats">
<a href="#7c4ae52e4a13c990d16c9530fb874ed79064a5cd">
pat.cpp
</a>
</li>
<li class="file-stats">
<a href="#6c8922e214bc665a49b5acea11b505cbd36446c5">
pat.h
</a>
</li>
<li class="file-stats">
<a href="#9fc1681b02d842aa2b7bb9db116eff864b181fdf">
presets.cpp
</a>
</li>
<li class="file-stats">
<a href="#c297ba4595a07ed6c1a79135075b7b1f5e55a14c">
read.h
</a>
</li>
<li class="file-stats">
<a href="#66965a83f981ce6b0882f308dd88614650b6582c">
ref_read.cpp
</a>
</li>
</ul>
<h5>The diff was not included because it is too large.</h5>
</div>
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