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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/picard-tools" style="color: #1068bf;">Debian Med / picard-tools</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/picard-tools/-/commit/ac518bb5f410586638e4af3f2a8c885ac740b525" style="color: #1068bf;">ac518bb5</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2022-11-01T20:28:47+01:00 </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 2.27.5+dfsg</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/5cddd0f0e2b23363f4d6ac99d0d0b97d716cd498" style="color: #1068bf;">5cddd0f0</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2022-11-01T20:29:45+01:00 </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/2.27.5+dfsg'
Update to upstream version '2.27.5+dfsg'
with Debian dir 3ac603ec8efc74ef4cc46effe338afacc68b4e26</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/fdca5f8f73c26c6a936e24b793431285e55782af" style="color: #1068bf;">fdca5f8f</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2022-11-01T20:31:55+01:00 </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/picard-tools/-/commit/62d788f3387206607371bce12c3b09f7275f7752" style="color: #1068bf;">62d788f3</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2022-11-02T17:40:53+01:00 </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;'>Skipping tests which cannot run because of old Gradle not providing --add-opens
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/5ea0b2a01fcbcfa4a6046963188bf24895ca9653" style="color: #1068bf;">5ea0b2a0</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2022-11-02T17:41:35+01:00 </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;'>Skipping a test because of a byte changing when switching to OpenJDK17
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/18bda0d1f14744258040d27808f3f24cabf15396" style="color: #1068bf;">18bda0d1</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2022-11-02T17:42:06+01:00 </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;'>Adding a versioned B-D on libhtsjdk-java because of a change in the ABI
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/8d269aa692afd529ecbe90593584e0aceaf4ef20" style="color: #1068bf;">8d269aa6</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2022-11-02T17:44:32+01:00 </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/picard-tools/-/commit/1837ad947e238b54842108138b7cbf970ac3b24c" style="color: #1068bf;">1837ad94</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2022-11-03T21:03:24+01:00 </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;'>Marking the 60- patch as Forwarded: not-needed
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/17b4d41e1a69db9dd581f8cd3fa1c8f6cf8a085d" style="color: #1068bf;">17b4d41e</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2022-11-04T11:07:15+01:00 </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;'>Excluding the BamToBfq class from the jar to be conservative, as its test is possibly problematic with OpenJDK17
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/90670e8ba7605bee8ad05f2a77a6c49fdcbf1bf1" style="color: #1068bf;">90670e8b</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2022-11-04T11:10:10+01:00 </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="#f07866736216be0ee2aba49e392191aeae700a35" style="color: #1068bf;">
build.gradle
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1" style="color: #1068bf;">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2" style="color: #1068bf;">
debian/control
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</li>
<li class="file-stats">
<a href="#e186644cad34bbb8e38eb75706855e6cd177ad48" style="color: #1068bf;">
debian/patches/10-build.xml.patch
</a>
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<li class="file-stats">
<a href="#4416da23ca69dd7403c07c230b77bb0c32e0abb1" style="color: #1068bf;">
debian/patches/30-tests-fix-dataprovider.patch
</a>
</li>
<li class="file-stats">
<a href="#267b223587f808a65b35e2693e029c59fb4476cf" style="color: #1068bf;">
debian/patches/60-tests-exclude-network.patch
</a>
</li>
<li class="file-stats">
<a href="#2338e60d4382624824f4ac493301417b621e0a9d" style="color: #1068bf;">
debian/patches/fix_unreadabletests.patch
</a>
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<li class="file-stats">
<a href="#fc59194b64ff6e3314b8876b2d65744728f49562" style="color: #1068bf;">
<span class="new-file">
+
debian/patches/gradle_openjdk17_incompatibility.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#e56a62236fb9214df6dc57c88905f4cf21035bf2" style="color: #1068bf;">
<span class="new-file">
+
debian/patches/omit_BamToBfq.patch
</span>
</a>
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<li class="file-stats">
<a href="#a19ab181f42f2952911fb425a841f9a77adf945f" style="color: #1068bf;">
debian/patches/remove_google_nio.patch
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96" style="color: #1068bf;">
debian/patches/series
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<li class="file-stats">
<a href="#1fa2570ced8b3c33e4b3bd1f563ab3786ec64e29" style="color: #1068bf;">
src/main/java/picard/cmdline/CommandLineProgram.java
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<li class="file-stats">
<a href="#f7d76d352dfb807611c35d4412191ed995aa7003" style="color: #1068bf;">
src/main/java/picard/fingerprint/CrosscheckFingerprints.java
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<li class="file-stats">
<a href="#b8553f759ce8bc72a7ed6f6994097c2fc323b375" style="color: #1068bf;">
src/main/java/picard/fingerprint/FingerprintChecker.java
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<li class="file-stats">
<a href="#6d29efa301dfe7d55a00774547f4cf67aea4ef28" style="color: #1068bf;">
src/main/java/picard/util/SequenceDictionaryUtils.java
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<li class="file-stats">
<a href="#e49bb5587beb891c29297afe9cf94c80c95edd7e" style="color: #1068bf;">
src/test/java/picard/analysis/artifacts/CollectSequencingArtifactMetricsTest.java
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<li class="file-stats">
<a href="#6dac1c7c1b4d9022ddd3bc5f57a44bb077b0983c" style="color: #1068bf;">
src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
</a>
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<li class="file-stats">
<a href="#e1d370246779010899b4d52a55c98c9ac1af3784" style="color: #1068bf;">
src/test/java/picard/analysis/replicates/CollectIndependentReplicatesMetricTest.java
</a>
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<li class="file-stats">
<a href="#1e6b578642f95f7a451ba037531db2fafb4b5701" style="color: #1068bf;">
src/test/java/picard/fastq/BamToBfqTest.java
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<li class="file-stats">
<a href="#05be7520b4dd89a3de09be1dbab026d6561fd3b1" style="color: #1068bf;">
src/test/java/picard/fingerprint/CrosscheckFingerprintsTest.java
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<li class="file-stats">
<a href="#8e47b09e231ce09b8b2b713f2020679c7cc00327" style="color: #1068bf;">
src/test/java/picard/fingerprint/FingerprintCheckerTest.java
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<li class="file-stats">
<a href="#41e770699927a5a3306b5a5722b75be3e3ae1299" style="color: #1068bf;">
src/test/java/picard/illumina/CheckIlluminaDirectoryTest.java
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<li class="file-stats">
<a href="#4a3455d3b3da89fba102450e92ca3771afab474e" style="color: #1068bf;">
src/test/java/picard/illumina/CollectIlluminaBasecallingMetricsTest.java
</a>
</li>
<li class="file-stats">
<a href="#e1b7610ac081822bc869b241576e7cb24565e95a" style="color: #1068bf;">
src/test/java/picard/illumina/ExtractIlluminaBarcodesTest.java
</a>
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<li class="file-stats">
<a href="#98e96985ec6ebe536f106ab2bb736999afc79ff9" style="color: #1068bf;">
src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java
</a>
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<li class="file-stats">
<a href="#a09216193085cd02d8bb25e1c7a366cf40058c11" style="color: #1068bf;">
src/test/java/picard/illumina/IlluminaLaneMetricsCollectorTest.java
</a>
</li>
<li class="file-stats">
<a href="#5266112e051618c9a333e2b3a23bb5ae66a1d756" style="color: #1068bf;">
src/test/java/picard/illumina/parser/BclParserTest.java
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<li class="file-stats">
<a href="#a795b3663ce9176b8ec9a3b2d6be1522e27f1abe" style="color: #1068bf;">
src/test/java/picard/illumina/parser/IlluminaFileUtilTest.java
</a>
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<li class="file-stats">
<a href="#85dfc66eaf47ac9c1c3161200f4a5b3cb5f42375" style="color: #1068bf;">
src/test/java/picard/metrics/CollectRrbsMetricsTest.java
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<li class="file-stats">
<a href="#2fd364663723790d1032a20b6431f11595ce86b7" style="color: #1068bf;">
src/test/java/picard/sam/CramCompatibilityTest.java
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</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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