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<div class="content">
<h3 style="margin-top: 20px; margin-bottom: 10px;">
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/snpeff" style="color: #1068bf; text-decoration: none;">Debian Med / snpeff</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
<ul>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/snpeff/-/commit/f8c46e3345981473d8e79a8c57239f3d631fa9d4" style="color: #1068bf; text-decoration: none;">f8c46e33</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-06-02T17:18:06+02:00</i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Mangling in debian/watch
uversionmangle is to range versions correctly: for instance dpkg ranges
5.1+dfsg after 5.1d+dfsg, whereas it ranges 5.1+dfsg before 5.1+d+dfsg.
filenamemangle is written following recommendations on uscan (1) man page.
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/snpeff/-/commit/10ccfdda307f9bb03cb0d21848cd819edbb33ef0" style="color: #1068bf; text-decoration: none;">10ccfdda</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-06-02T17:22:06+02:00</i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Updating the list of files to exclude when repacking
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/snpeff/-/commit/3a21e7f88559157ed83b022daf37e891c39046d2" style="color: #1068bf; text-decoration: none;">3a21e7f8</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-06-02T17:24:37+02:00</i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>New upstream version 5.1+d+dfsg</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/snpeff/-/commit/f85dafeb13eec51aff1356b19a8f097bd2c9b620" style="color: #1068bf; text-decoration: none;">f85dafeb</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-06-02T17:27:03+02:00</i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Update upstream source from tag 'upstream/5.1+d+dfsg'
Update to upstream version '5.1+d+dfsg'
with Debian dir 20705bd86572acb0329f5b0453b84c340b97278c</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/snpeff/-/commit/f8102c5a96b98c9be355d93c0e03717848ad9f87" style="color: #1068bf; text-decoration: none;">f8102c5a</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-06-02T17:28:44+02:00</i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Raising Standards version to 4.6.1 (no change)
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/snpeff/-/commit/47c1a62d0c94868dda352004a424536cc9589002" style="color: #1068bf; text-decoration: none;">47c1a62d</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-06-02T17:29:28+02:00</i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Refreshing patches
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/snpeff/-/commit/86b76b7a8a9bdfee129042bc2f3ed76d6f134922" style="color: #1068bf; text-decoration: none;">86b76b7a</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-06-02T20:40:49+02:00</i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>(Build-)depending only on needed -doc packages
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/snpeff/-/commit/7cd83d17a4b7da7c9c754f1c06b1cf8402bebbfb" style="color: #1068bf; text-decoration: none;">7cd83d17</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-06-02T20:41:44+02:00</i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Updating changelog
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/snpeff/-/commit/04d3e1ffd8c62ac80975c4f235f5559f2db04db1" style="color: #1068bf; text-decoration: none;">04d3e1ff</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-06-02T21:41:01+02:00</i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Upload to unstable
</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#ed51fbed4951b0ce36af52f88a70a524f29a427b" style="color: #1068bf; text-decoration: none;">
README_release.md
</a>
</li>
<li class="file-stats">
<a href="#aa923c4e771f6330bc047232250d254c1eed38e3" style="color: #1068bf; text-decoration: none;">
config/snpEff.ENSEMBL_105.config
</a>
</li>
<li class="file-stats">
<a href="#8569cc11bfac4243e678a8e5f9acc47f75ad4ef7" style="color: #1068bf; text-decoration: none;">
config/snpEff.ENSEMBL_BFMPP_52.config
</a>
</li>
<li class="file-stats">
<a href="#3b9d0b31e272f1cc8b2e8ee6deda70ce25b806e5" style="color: #1068bf; text-decoration: none;">
<span class="new-file">
+
config/snpEff.FLYBASE_FB2022_02.config
</span>
</a>
</li>
<li class="file-stats">
<a href="#47cc5ea4264ea2f7621b478691296be7b66d8727" style="color: #1068bf; text-decoration: none;">
config/snpEff.config
</a>
</li>
<li class="file-stats">
<a href="#fcd0f37617c726fe6d62c7d0b6e3377c49bfb17b" style="color: #1068bf; text-decoration: none;">
config/snpEff.dbs.config
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1" style="color: #1068bf; text-decoration: none;">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2" style="color: #1068bf; text-decoration: none;">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb" style="color: #1068bf; text-decoration: none;">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#94bfc9b7b2edebd4dc49a7edd537fcb53d71efa6" style="color: #1068bf; text-decoration: none;">
debian/patches/update_launching_script_and_config_file_for_Debian.patch
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79" style="color: #1068bf; text-decoration: none;">
debian/watch
</a>
</li>
<li class="file-stats">
<a href="#bb47f94ec4ef676d9476b58d752b21c3dd37c210" style="color: #1068bf; text-decoration: none;">
docs/examples/index.html
</a>
</li>
<li class="file-stats">
<a href="#8c0d6b0dca5817118d2f528acb81b643d000c69a" style="color: #1068bf; text-decoration: none;">
docs/index.html
</a>
</li>
<li class="file-stats">
<a href="#41309f3083d517bd6b273059e71c4c3e25f3e458" style="color: #1068bf; text-decoration: none;">
docs/sitemap.xml.gz
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</li>
<li class="file-stats">
<a href="#e7eac1063274854e2bd2cbfdf50b75e57d5b72aa" style="color: #1068bf; text-decoration: none;">
docs/versions.txt
</a>
</li>
<li class="file-stats">
<a href="#a39ddb14dc438b3e36c7ef81f9d455bc6dd6febc" style="color: #1068bf; text-decoration: none;">
galaxy/tool-data/snpEff_genomes.loc
</a>
</li>
<li class="file-stats">
<a href="#18435e9731326cca1752f95c6eb594baa7527e67" style="color: #1068bf; text-decoration: none;">
galaxy/tool-data/snpEff_genomes.loc.sample
</a>
</li>
<li class="file-stats">
<a href="#b030bc94168fc6c01406ef34eb31b9d38648b3b6" style="color: #1068bf; text-decoration: none;">
scripts_build/data/GRCh37.RefSeq/download_RefSeq_NCBI.sh
</a>
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<li class="file-stats">
<a href="#813c4031dc6ee84ff3fc013c0b20e3520668ed2e" style="color: #1068bf; text-decoration: none;">
scripts_build/data/GRCh38.RefSeq/download_RefSeq_NCBI.sh
</a>
</li>
<li class="file-stats">
<a href="#cfe63d04c881323fa6cdf24ee25bc3d5421fa81d" style="color: #1068bf; text-decoration: none;">
src/bds/download/downloadEnsemblBulk.bds
</a>
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<a href="#afd50b4ce6efc12a52687c80b92cdae4dca5dba9" style="color: #1068bf; text-decoration: none;">
src/bds/download/downloadGenome.bds
</a>
</li>
<li class="file-stats">
<a href="#cb97482d6cd9f0510073ea41925c0a0f3d29e9eb" style="color: #1068bf; text-decoration: none;">
src/bds/download/downloadMane.bds
</a>
</li>
<li class="file-stats">
<a href="#48755847f6f1b48371cfb02883d6bb80469fea7c" style="color: #1068bf; text-decoration: none;">
src/bds/download/downloadOther.bds
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</li>
<li class="file-stats">
<a href="#0217223bf67b5f28108f4cfa5381eca14294c812" style="color: #1068bf; text-decoration: none;">
src/bds/download/downloadUcsc.bds
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</li>
<li class="file-stats">
<a href="#0b81e1dee9f1c0fb58c789602684b9c7428cf290" style="color: #1068bf; text-decoration: none;">
src/bds/make.bds
</a>
</li>
<li class="file-stats">
<a href="#c25564673103c5980f0cec750b5e7c4acf10fbf0" style="color: #1068bf; text-decoration: none;">
src/docs/examples.md
</a>
</li>
<li class="file-stats">
<a href="#6f29ed189525c96d3c522590163c5ac2593ce218" style="color: #1068bf; text-decoration: none;">
src/docs/index.html
</a>
</li>
<li class="file-stats">
<a href="#8679d84b139e71b6747cd0be0883d7dc9c42c79a" style="color: #1068bf; text-decoration: none;">
src/main/java/org/snpeff/SnpEff.java
</a>
</li>
<li class="file-stats">
<a href="#893d90bed25b329abd5c28383ac58c15d773960e" style="color: #1068bf; text-decoration: none;">
src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdBuild.java
</a>
</li>
<li class="file-stats">
<a href="#36e345b1edd8470324b860a043749ff0b9b67843" style="color: #1068bf; text-decoration: none;">
src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdCds.java
</a>
</li>
</ul>
<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: 0.875rem;">The diff was not included because it is too large.</h5>
</div>
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