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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/snpeff">Debian Med / snpeff</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/c925d80830aef32ab71c1e3252fbb61f250f5115">c925d808</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-02-27T07:20:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Replacing the build timestamp using SOURCE_DATE_EPOCH to enhance build reproducibility
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/d8c6425172dc876e01ecc9d446c4c2d4cb20987f">d8c64251</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-03-17T18:12:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refreshing d/copyright and preparing to use a stripped orig tarball
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/71013c7eaea56bcb76738354565b08192b54f5f3">71013c7e</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-03-17T18:13:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Using Fastq* classes from biojava4-live
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/d19d6e58f908522b3752e4a832a896c0f1b25c3c">d19d6e58</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-03-17T18:19:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding myself to uploaders, using my debian.org email address
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/f2e6979aa3697feb442e865f5b52479689e8bce5">f2e6979a</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-03-17T18:19:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/56f72acc1ac97bd6619e7786486072ea944d4ab0">56f72acc</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-03-17T18:20:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 4.3t+dfsg1</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/33f0820d65217520848993e042fd8babe26165fa">33f0820d</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-03-17T18:22:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/4.3t+dfsg1'
Update to upstream version '4.3t+dfsg1'
with Debian dir 62c1ea37e67e89607fb224fe17a37716ff9f2b54</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/82b96a414a3841e333d77626378f9cd5e6c44221">82b96a41</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-03-17T21:06:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding a lintian override linked to embedded jquery
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
debian/README.Debian
</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="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#a0cbe1ff3da2e923ddd6b542f9b3843013a6590d">
<span class="new-file">
+
debian/libsnpeff-java-doc.lintian-overrides
</span>
</a>
</li>
<li class="file-stats">
<a href="#fc93cb17d5957919628da13ce0195e57878a1c59">
debian/manpages/snpEff.1
</a>
</li>
<li class="file-stats">
<a href="#dad1c764ef97fe56bf2081424eccb7987e4361c8">
debian/patches/adapting_to_htsjdk.patch
</a>
</li>
<li class="file-stats">
<a href="#090dbfdd4da905a27df6ad036a69314ac3c39e2d">
debian/patches/adding_scala_in_pom.patch
</a>
</li>
<li class="file-stats">
<a href="#bf0b334bdbece11ae40130c9c7a9fcd48161a57c">
debian/patches/alter_pom_for_debian_packaging.patch
</a>
</li>
<li class="file-stats">
<a href="#e55e63231c28bebd84d729b0952e9a5a0f9db6d9">
debian/patches/depending_on_biojava4.patch
</a>
</li>
<li class="file-stats">
<a href="#5d4bc5bec9cccce49eb00b14a49d6fa0feedbf70">
debian/patches/fix_tests.patch
</a>
</li>
<li class="file-stats">
<a href="#17563e1f4545f161f646a7b847a908f665bb1c7d">
debian/patches/replacing_akka_with_java_util_concurrent.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#94bfc9b7b2edebd4dc49a7edd537fcb53d71efa6">
debian/patches/update_launching_script_and_config_file_for_Debian.patch
</a>
</li>
<li class="file-stats">
<a href="#02c4552903646bc7019a3cc16081d7dbd6e042b3">
<span class="new-file">
+
debian/patches/use_fastq_from_biojava4.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
<li class="file-stats">
<a href="#d57fe81187ad19e322efcf6975b7ed7c0851f8c1">
<span class="deleted-file">
−
examples/1kg.head_chr1.filtered.vcf.gz
</span>
</a>
</li>
<li class="file-stats">
<a href="#d5c5eb7f56226b3775c48c217cf962964886e1a0">
<span class="deleted-file">
−
examples/1kg.head_chr1.vcf.gz
</span>
</a>
</li>
<li class="file-stats">
<a href="#5163530ebbb26190b10d1eeaacf9198e807b44ec">
<span class="deleted-file">
−
examples/cancer.ann.vcf
</span>
</a>
</li>
<li class="file-stats">
<a href="#cb24c66a5e78b51aceaba3360fe38cc831b9f103">
<span class="deleted-file">
−
examples/cancer.eff.vcf
</span>
</a>
</li>
<li class="file-stats">
<a href="#ce9f8668e14046eba0c5c48b699029256d4da853">
<span class="deleted-file">
−
examples/cancer.vcf
</span>
</a>
</li>
<li class="file-stats">
<a href="#833a261d38daf3f34a2c2863880680ddc6f51234">
<span class="deleted-file">
−
examples/cancer_pedigree.ann.vcf
</span>
</a>
</li>
<li class="file-stats">
<a href="#8f21abf72f89e47ae34ded976cadfadd7ce7af80">
<span class="deleted-file">
−
examples/cancer_pedigree.vcf
</span>
</a>
</li>
<li class="file-stats">
<a href="#dc7226c1c190895513cfc21cb4b97d3fcddccc7e">
<span class="deleted-file">
−
examples/example_motif.vcf
</span>
</a>
</li>
<li class="file-stats">
<a href="#032bf3c29ff41c3486a42d43a590be4b26493d24">
<span class="deleted-file">
−
examples/examples.sh
</span>
</a>
</li>
<li class="file-stats">
<a href="#c32b3753f361052cc1fd60fa17aac038cf79de29">
<span class="deleted-file">
−
examples/file.vcf
</span>
</a>
</li>
<li class="file-stats">
<a href="#0c69ce329cb6354d8301a45bc8de133c2b21f72b">
<span class="deleted-file">
−
examples/intervals.bed
</span>
</a>
</li>
<li class="file-stats">
<a href="#086c034bbc6295ca04771b6d7fe5afceb2894dda">
<span class="deleted-file">
−
examples/my_annotations.bed
</span>
</a>
</li>
<li class="file-stats">
<a href="#337ba62d544d666d5286f7cbb922b74fceb836af">
<span class="deleted-file">
−
examples/samples_cancer.txt
</span>
</a>
</li>
</ul>
<h5>The diff was not included because it is too large.</h5>
</div>
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