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<h3>
Dylan Aïssi pushed to branch master
at <a href="https://salsa.debian.org/med-team/beagle">Debian Med / beagle</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/beagle/commit/62500e0bf845f8c4b61307cf5bfda5e4c93f816a">62500e0b</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2019-09-09T20:06:11Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelogs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/beagle/commit/9ea91de8884359f05f558faf0e8795e35f8cd66b">9ea91de8</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2019-09-09T20:06:42Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.1-190824+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/beagle/commit/3813c4d3083a253af51ba006fe0533ee6be2c26c">3813c4d3</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2019-09-09T20:06:43Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/5.1-190824+dfsg'
Update to upstream version '5.1-190824+dfsg'
with Debian dir c9262ec484b358ca77507e11f85003f3f04a9b0f</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/beagle/commit/0e95f1cc0efd492a75c8a6909c9848aa0e52985f">0e95f1cc</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2019-09-09T20:07:43Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update d/s/include-binaries
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/beagle/commit/6b5341ef2d6f9477d7d8f41efb479e415e7430b1">6b5341ef</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2019-09-09T20:10:45Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/beagle/commit/cf58285635b69dd4fa88af05342c88db299a4e51">cf582856</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2019-09-09T20:19:22Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove folders not used
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#5deb5056c0326ef2fa7706bf604aee0190919ece">
beagleutil/ChromInterval.java
</a>
</li>
<li class="file-stats">
<a href="#b35797e1b11f8d20e90b3d56030212885a937712">
beagleutil/IntInterval.java
</a>
</li>
<li class="file-stats">
<a href="#f3681b06dae45d0dfe680fe6a7cd8ca5cd04094b">
<span class="new-file">
+
beagleutil/PbwtUpdater.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#16719bc23bce502b2ebc67f8f38b13b159126355">
haplotype/HapPair.java
→
blbutil/DoubleArray.java
</a>
</li>
<li class="file-stats">
<a href="#08657c75a9a9746475e49445932865fc0544632d">
blbutil/FloatArray.java
</a>
</li>
<li class="file-stats">
<a href="#1928aebe75a42243fe3f56cf57a32c12bb414d3e">
blbutil/InputIt.java
</a>
</li>
<li class="file-stats">
<a href="#569d1e1ae30f252e98526e6aa870ed406131b290">
blbutil/Utilities.java
</a>
</li>
<li class="file-stats">
<a href="#923ab2081306a60ce903c2304d7d5d6f3224175c">
bref/Bref3Reader.java
</a>
</li>
<li class="file-stats">
<a href="#8858d04c3e071f8148d52b04a39944b5f4560a7a">
bref/SeqCoder3.java
</a>
</li>
<li class="file-stats">
<a href="#11cbb4ac57c191672ba7d7793b1a643356e13832">
debian/beagle-doc.doc-base
</a>
</li>
<li class="file-stats">
<a href="#ed124504208923d1916384d14b122bd861ddea4f">
debian/beagle-doc.install
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#3f33d564a0973e6e3ed5f94104fc2a215f746ec5">
debian/patches/01_Update_htsjtk.patch
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242">
debian/source/include-binaries
</a>
</li>
<li class="file-stats">
<a href="#e1250afca617ba6b8cb26f9db6c9f54edd45b099">
debian/upstream.docs/README
</a>
</li>
<li class="file-stats">
<a href="#aa251a2bbc4710e01c82e59ea95518f7688e63e9">
debian/upstream.docs/beagle_5.0.pdf
→
debian/upstream.docs/beagle_5.1.pdf
</a>
</li>
<li class="file-stats">
<a href="#2c67f0396400cf929c0bd079032f65da8e21650c">
debian/upstream.docs/release_notes
</a>
</li>
<li class="file-stats">
<a href="#9b282dc1f612e13f56bc2c3badc1f9c3e71ac538">
debian/upstream.docs/run.beagle.example
</a>
</li>
<li class="file-stats">
<a href="#373b03ef1c58a3e23feb091695a2467fa61c4063">
<span class="deleted-file">
−
haplotype/BitHapPair.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#2ad3c2f9ba6ca719872022b5f4e5f2741da7808d">
<span class="deleted-file">
−
haplotype/WrappedHapPair.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#d431de7a0c4ce83c756519ac2461da10c7d77d1d">
<span class="new-file">
+
imp/CodedSteps.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#67a867e14e93b445b6c7f4b319e9a70c9961e9a7">
imp/HaplotypeCoder.java
</a>
</li>
<li class="file-stats">
<a href="#923f1b8e82851d3ec572b6c0fe2053ba7176c20c">
imp/ImpData.java
</a>
</li>
<li class="file-stats">
<a href="#3ca7c61e1782c0aafcd8bc57803302b434469b7e">
imp/ImpIbs.java
</a>
</li>
<li class="file-stats">
<a href="#1dac241016f8d99d1172c89fd0ce0b82695d5929">
imp/ImpLSBaum.java
</a>
</li>
<li class="file-stats">
<a href="#315086b42467cd64d67b45236c874d197c068244">
imp/ImpStates.java
</a>
</li>
<li class="file-stats">
<a href="#d158c3582076a802a226c9ef95c7781d71642267">
imp/ImputedVcfWriter.java
</a>
</li>
<li class="file-stats">
<a href="#5d0b9ec9c97b4cb59643ae2a931842687f9062ed">
imp/RefHapHash.java
</a>
</li>
<li class="file-stats">
<a href="#f476aeb05c4d494ef711eb392393ad6a239dfba0">
ints/IntArray.java
</a>
</li>
</ul>
<h5>The diff was not included because it is too large.</h5>
</div>
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—
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<a href="https://salsa.debian.org/med-team/beagle/compare/e2876f35d59fc6302aa69bd6d1f14861fd796016...cf58285635b69dd4fa88af05342c88db299a4e51">View it on GitLab</a>.
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