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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/libgoby-java">Debian Med / libgoby-java</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/02da56598e67eaca2ff3ac81c285670fc76d12ad">02da5659</a></strong>
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<span>by Pierre Gruet</span>
<i>at 2021-08-10T14:09:34+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Forwarding patches
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<h4>6 changed files:</h4>
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<li class="file-stats">
<a href="#8585405484f09930892f52fc8586f799991520f7">
debian/patches/adding_dependencies.patch
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<li class="file-stats">
<a href="#feb3f16505e2aaa666cfa5d5bbefd0d3cde765d8">
debian/patches/catch_IOException_LineIterator.patch
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<li class="file-stats">
<a href="#9d449b8baa51e3c14c1e21ddb68b41a7ef737cd8">
debian/patches/goby_script.patch
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<li class="file-stats">
<a href="#e5c767c2890f75ce61cf5fdf32589ce66eb14a98">
debian/patches/inclusions_in_SplitTranscriptsMode.patch
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<li class="file-stats">
<a href="#77eab9699a307dbdc1aaabb9972b3e27a0b81aa3">
debian/patches/protoc.patch
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<li class="file-stats">
<a href="#ef745f5cc2f1850f044372eaa52b7f53ca4cc69f">
debian/patches/using_correct_SamReader_api.patch
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<h4>Changes:</h4>
<li id="8585405484f09930892f52fc8586f799991520f7">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/02da56598e67eaca2ff3ac81c285670fc76d12ad#8585405484f09930892f52fc8586f799991520f7"><strong>debian/patches/adding_dependencies.patch</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: Adding missing dependencies to <span class="idiff left right">goby-io/</span>pom.xml</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Adding missing dependencies to <span class="idiff left">the various </span>pom.xml<span class="idiff right"> files</span></span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/CampagneLaboratory/goby3/issues/6</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2020-10-31</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<td class="new_line diff-line-num" data-linenumber="6" 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="LC6" class="line" lang="diff">--- a/goby-io/pom.xml</span>
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<li id="feb3f16505e2aaa666cfa5d5bbefd0d3cde765d8">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/02da56598e67eaca2ff3ac81c285670fc76d12ad#feb3f16505e2aaa666cfa5d5bbefd0d3cde765d8"><strong>debian/patches/catch_IOException_LineIterator.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: Catch the IOException launched by close() method of LineIterator</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: <span class="idiff left right">no</span></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: <span class="idiff left right">https://github.com/CampagneLaboratory/goby3/issues/7</span></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2020-11-03</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">--- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/EmpiricalPMode.java</span>
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<li id="9d449b8baa51e3c14c1e21ddb68b41a7ef737cd8">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/02da56598e67eaca2ff3ac81c285670fc76d12ad#9d449b8baa51e3c14c1e21ddb68b41a7ef737cd8"><strong>debian/patches/goby_script.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: modifying the launcher script to account for Debian paths</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: no<span class="idiff left right">t-needed</span></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2021-08-08</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">--- a/goby</span>
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<li id="e5c767c2890f75ce61cf5fdf32589ce66eb14a98">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/02da56598e67eaca2ff3ac81c285670fc76d12ad#e5c767c2890f75ce61cf5fdf32589ce66eb14a98"><strong>debian/patches/inclusions_in_SplitTranscriptsMode.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: reading class GeneTranscriptRelationships from Goby archive</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"> The above-named class is in the archive of Goby and thus does not need to be read elsewhere.</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: <span class="idiff left right">no</span></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: <span class="idiff left right">https://github.com/CampagneLaboratory/goby3/issues/8</span></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 2020-11-02</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff">--- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/SplitTranscriptsMode.java</span>
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<li id="77eab9699a307dbdc1aaabb9972b3e27a0b81aa3">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/02da56598e67eaca2ff3ac81c285670fc76d12ad#77eab9699a307dbdc1aaabb9972b3e27a0b81aa3"><strong>debian/patches/protoc.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: Using Debian-packaged protoc compiler</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2020-08-24</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">--- a/goby-io/pom.xml</span>
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<li id="ef745f5cc2f1850f044372eaa52b7f53ca4cc69f">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/02da56598e67eaca2ff3ac81c285670fc76d12ad#ef745f5cc2f1850f044372eaa52b7f53ca4cc69f"><strong>debian/patches/using_correct_SamReader_api.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: using the correct SamReader api</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt@debian.org></span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Origin: https://sources.debian.org/src/fastqc/0.11.9+dfsg-4/debian/patches/htsjdk-api.patch</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: no<span class="idiff left right">t-needed</span></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 2020-11-06</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff">--- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMComparisonMode.java</span>
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