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GitLab

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<h3>

Michael R. Crusoe 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/a51591b391fe3a248a9e1ddc74a654c204764350">a51591b3</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2021-01-07T13:41:43+01:00</i>

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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.24.0+dfsg</pre>

</li>

</ul>

<h4>30 changed files:</h4>

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<li class="file-stats">

<a href="#bac4c9ac8d5063b8b48c84e1a30915ee1d4b4523">

src/main/java/picard/analysis/AlignmentSummaryMetrics.java

</a>

</li>

<li class="file-stats">

<a href="#39ad2a42470243aa1402488d16e8309995fc1180">

src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java

</a>

</li>

<li class="file-stats">

<a href="#3a02115cc24686ccecd94ec7f340c5890a553d38">

src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.java

</a>

</li>

<li class="file-stats">

<a href="#8d7507e76526876f60daef574438762bd6f57ab0">

src/main/java/picard/analysis/CollectBaseDistributionByCycle.java

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</li>

<li class="file-stats">

<a href="#39018791387cf476a9ea4511dd7a82d4982e3c05">

src/main/java/picard/analysis/CollectGcBiasMetrics.java

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<li class="file-stats">

<a href="#a8427986ca1c000c6402307f4ef77043d503630e">

src/main/java/picard/analysis/CollectInsertSizeMetrics.java

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<li class="file-stats">

<a href="#2269f0b41b877093e5ef84c96198be511137ddbc">

src/main/java/picard/analysis/CollectMultipleMetrics.java

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<li class="file-stats">

<a href="#ef73529293175de94b68d4817a681e5643b34dd8">

src/main/java/picard/analysis/CollectRnaSeqMetrics.java

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<li class="file-stats">

<a href="#13f54df4e2b29414eecb5c0cbc1da4d3e02dc14e">

src/main/java/picard/analysis/CollectRrbsMetrics.java

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<li class="file-stats">

<a href="#ef17ffbbef833877458003eb2f12fc07610dfc1e">

src/main/java/picard/analysis/CollectWgsMetrics.java

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<li class="file-stats">

<a href="#9a97429e0fb33ada2f86ffefa4c68b6a1554dab7">

src/main/java/picard/analysis/CollectWgsMetricsWithNonZeroCoverage.java

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</li>

<li class="file-stats">

<a href="#da9ff87ef6c58326bf722021f76a9882a5eea09c">

src/main/java/picard/analysis/MeanQualityByCycle.java

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<li class="file-stats">

<a href="#8d0504dc5db7e6ffe8a19828bf6d32a8aff6f8dc">

src/main/java/picard/analysis/QualityScoreDistribution.java

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<li class="file-stats">

<a href="#a4eadc1086ad98cf8ee663d0279108246675300e">

src/main/java/picard/analysis/directed/PanelMetricsBase.java

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</li>

<li class="file-stats">

<a href="#7dc078e8a631cb6833fea5fe97f4d605fadaef7f">

src/main/java/picard/analysis/directed/TargetMetricsCollector.java

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<li class="file-stats">

<a href="#ad1f1dc5e8b9664bb405dbc8386d79b194eada83">

src/main/java/picard/analysis/replicates/CollectIndependentReplicateMetrics.java

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</li>

<li class="file-stats">

<a href="#f91c189fd4550d2b3a19984cf8214fc36e993efb">

src/main/java/picard/arrays/GtcToVcf.java

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<li class="file-stats">

<a href="#1fa2570ced8b3c33e4b3bd1f563ab3786ec64e29">

src/main/java/picard/cmdline/CommandLineProgram.java

</a>

</li>

<li class="file-stats">

<a href="#275e1a3adda92e2755d0c2f78a9802f1c7460f96">

<span class="deleted-file">

−

src/main/java/picard/illumina/parser/ClusterIntensityFileReader.java

</span>

</a>

</li>

<li class="file-stats">

<a href="#20dc8786dd862a59374a77bb4650068fe097b466">

<span class="deleted-file">

−

src/main/java/picard/illumina/parser/FourChannelIntensityData.java

</span>

</a>

</li>

<li class="file-stats">

<a href="#3d226ee21322a8c38428ca7889d26099c1bac15d">

src/main/java/picard/illumina/parser/IlluminaData.java

</a>

</li>

<li class="file-stats">

<a href="#3f586535541951e4a364bbc04b2891adb85930fd">

src/main/java/picard/illumina/parser/ReadData.java

</a>

</li>

<li class="file-stats">

<a href="#71cfe8301c6ffbf3a0d8c4e7f06d8d7bbab2d6cd">

src/main/java/picard/sam/BuildBamIndex.java

</a>

</li>

<li class="file-stats">

<a href="#1b665c5e0a5fc18aea02668714885fae5d776aea">

src/main/java/picard/sam/SamErrorMetric/CollectSamErrorMetrics.java

</a>

</li>

<li class="file-stats">

<a href="#dfce5d14fe42247461ea8220e644d29cb15ce7a7">

src/main/java/picard/sam/SamErrorMetric/ReadBaseStratification.java

</a>

</li>

<li class="file-stats">

<a href="#a6846a3645e1f6b1318cc73c0d6fd268c2c97997">

src/main/java/picard/sam/ValidateSamFile.java

</a>

</li>

<li class="file-stats">

<a href="#d8a06c7ca3aa05f7ea80334288df8f0f9c5e711a">

src/main/java/picard/sam/util/PhysicalLocation.java

</a>

</li>

<li class="file-stats">

<a href="#7b8c8bdd576e9d3a0df135db87180469ffbaea30">

src/main/java/picard/sam/util/ReadNameParser.java

</a>

</li>

<li class="file-stats">

<a href="#192759cddd7a04a212bb94980e062008ad977e97">

src/main/java/picard/util/IntervalListTools.java

</a>

</li>

<li class="file-stats">

<a href="#8b4cede99831e731a77cc89cd119ec3afb7f8616">

src/main/java/picard/vcf/MendelianViolations/FindMendelianViolations.java

</a>

</li>

</ul>

<h5>The diff was not included because it is too large.</h5>

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