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<h3>
Olivier Sallou pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/picard-tools">Debian Med / picard-tools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/commit/ebc5863a824a4ddb1e24754f070e6d109a2c22e5">ebc5863a</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2019-01-25T10:43:57Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.18.25+dfsg</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
Dockerfile
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<li class="file-stats">
<a href="#f07866736216be0ee2aba49e392191aeae700a35">
build.gradle
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<li class="file-stats">
<a href="#23366f98715d6c32e5528d491010c0875a482b37">
<span class="new-file">
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src/main/java/picard/sam/AddOATag.java
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<li class="file-stats">
<a href="#27b373658b0266838a2e7b5abf9e09f5c4da3488">
src/main/java/picard/sam/markduplicates/MarkDuplicates.java
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<li class="file-stats">
<a href="#29126ce694b74453b952ea35f1defd61b5dc1b83">
src/main/java/picard/sam/markduplicates/util/AbstractMarkDuplicatesCommandLineProgram.java
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<li class="file-stats">
<a href="#cf498877f67ccdc131c3b4a9aaa43351b05b4275">
src/main/java/picard/sam/markduplicates/util/LibraryIdGenerator.java
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<li class="file-stats">
<a href="#dc629c42db1f7d3a87978e3c165dbd25e8d1cd12">
src/main/java/picard/sam/markduplicates/util/OpticalDuplicateFinder.java
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<li class="file-stats">
<a href="#010bcae9b8de038f9a24b4cb14c96f7d30fc26f1">
src/main/java/picard/sam/util/PGTagArgumentCollection.java
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<li class="file-stats">
<a href="#8b287224d553b22d66d660772b240c33a9b9687d">
src/main/java/picard/util/LiftoverUtils.java
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<li class="file-stats">
<a href="#0b1e0dfde316c2b041f0de2be4a8f01acf9367dc">
src/main/java/picard/vcf/LiftoverVcf.java
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<li class="file-stats">
<a href="#b5f0a8370564ee26f164cb9f90d1730eec48f989">
<span class="new-file">
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src/test/java/picard/sam/AddOATagTest.java
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<li class="file-stats">
<a href="#36e06a696460a20fb2b5692fada38d91da45e3cc">
src/test/java/picard/sam/CompareSAMsTest.java
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<li class="file-stats">
<a href="#a99995537fa97a684145e0505ea4f1444dd94225">
src/test/java/picard/sam/ValidateSamFileTest.java
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<li class="file-stats">
<a href="#1c4ab9040306a67f03ebb4112d94cc35b530275e">
src/test/java/picard/sam/markduplicates/AbstractMarkDuplicatesCommandLineProgramTester.java
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<li class="file-stats">
<a href="#470265788ca56d9b8cbbe06cca8688f1f5f4a605">
<span class="new-file">
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src/test/java/picard/sam/markduplicates/MarkDuplicatesSetSizeHistogramTest.java
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<li class="file-stats">
<a href="#d743ed3cb9352eeba7be3579d617e162b69cc5f3">
<span class="new-file">
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src/test/java/picard/sam/markduplicates/MarkDuplicatesSetSizeHistogramTester.java
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<li class="file-stats">
<a href="#764bed357174db7399f519cd73e09029ed9e6a9a">
src/test/java/picard/sam/markduplicates/UmiAwareMarkDuplicatesWithMateCigarTester.java
</a>
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<li class="file-stats">
<a href="#95d8805670a10395e931bc9861cd4d779eecb0fe">
src/test/java/picard/sam/markduplicates/util/OpticalDuplicateFinderTest.java
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</li>
<li class="file-stats">
<a href="#9b61479b138e0828830ad8e1bf311e6211bb1976">
src/test/java/picard/sam/testers/SamFileTester.java
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<li class="file-stats">
<a href="#e6b8ac7829c30ddf0e78348a6f4b3e9668bd2135">
src/test/java/picard/util/LiftoverVcfTest.java
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<li class="file-stats">
<a href="#7c6a6a4225d618f44d19097c6b79b6f725fc1bf3">
src/test/java/picard/vcf/VcfTestUtils.java
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<li class="file-stats">
<a href="#241d46656003e41ecc30714407fd364e238c6968">
testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list
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</li>
<li class="file-stats">
<a href="#f5037b1a191456b998645d02f34fe33671d56c41">
testdata/picard/analysis/directed/CollectHsMetrics/lowbaseq.sam
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</li>
<li class="file-stats">
<a href="#35f6835b86c07dfeded9339cdbdd3a5c48089429">
testdata/picard/analysis/directed/CollectHsMetrics/lowmapq.sam
</a>
</li>
<li class="file-stats">
<a href="#4f3bed60bcf499fa6fe8d810ae896a211da96843">
testdata/picard/analysis/directed/CollectHsMetrics/overlapping.sam
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</li>
<li class="file-stats">
<a href="#423431a6f0c12b2804e49b6bd5f93f937e7d1737">
testdata/picard/analysis/directed/CollectHsMetrics/single-short-read.sam
</a>
</li>
<li class="file-stats">
<a href="#f5aa890ffdea695bb7bb7a0f7c2f1ccb7d196a85">
testdata/picard/analysis/directed/CollectHsMetrics/two-small.interval_list
</a>
</li>
<li class="file-stats">
<a href="#6ff32ea86c3ba8c4caee817d1627419ed9ba634d">
testdata/picard/fingerprint/reference.dict
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<li class="file-stats">
<a href="#8caf1c07fa15b254f0fee9670d4fe5b3f1f0c18f">
testdata/picard/illumina/151T8B8B151T_cbcl/sams/1102.CACCTAGTACTCGAGT.sam
</a>
</li>
<li class="file-stats">
<a href="#f11b2ae315bcd89d1eaeca9037a1e5237b5a2c9a">
testdata/picard/illumina/151T8B8B151T_cbcl/sams/1102.CCCCGCTTTTGCGTGT.sam
</a>
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</ul>
<h5>The diff was not included because it is too large.</h5>
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