[med-svn] [Git][med-team/picard-tools][upstream] New upstream version 3.1.1+dfsg

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch upstream at Debian Med / picard-tools


Commits:
c1ab316e by Pierre Gruet at 2023-12-14T13:16:36+01:00
New upstream version 3.1.1+dfsg
- - - - -


30 changed files:

- + .gitattributes
- + .github/workflows/cloud_tests.yml
- .gitignore
- build.gradle
- gradle/wrapper/gradle-wrapper.properties
- gradlew
- src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java
- src/main/java/picard/analysis/CollectOxoGMetrics.java
- src/main/java/picard/analysis/CollectWgsMetrics.java
- src/main/java/picard/analysis/SinglePassSamProgram.java
- src/main/java/picard/analysis/directed/CollectTargetedMetrics.java
- src/main/java/picard/analysis/replicates/CollectIndependentReplicateMetrics.java
- src/main/java/picard/cmdline/CommandLineProgram.java
- src/main/java/picard/cmdline/PicardCommandLine.java
- src/main/java/picard/fingerprint/CheckFingerprint.java
- src/main/java/picard/fingerprint/CrosscheckFingerprints.java
- src/main/java/picard/fingerprint/Fingerprint.java
- src/main/java/picard/fingerprint/FingerprintChecker.java
- src/main/java/picard/illumina/IlluminaBasecallsToFastq.java
- src/main/java/picard/illumina/MarkIlluminaAdapters.java
- src/main/java/picard/illumina/parser/readers/FilterFileReader.java
- + src/main/java/picard/nio/DeleteRecursive.java
- + src/main/java/picard/nio/GATKBucketUtils.java
- + src/main/java/picard/nio/GATKIOUtils.java
- + src/main/java/picard/nio/GATKUtils.java
- src/main/java/picard/nio/PicardHtsPath.java
- src/main/java/picard/reference/ExtractSequences.java
- src/main/java/picard/sam/FastqToSam.java
- src/main/java/picard/sam/MergeBamAlignment.java
- src/main/java/picard/sam/markduplicates/MarkDuplicates.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/commit/c1ab316e8d2d59c90e9504e26b97b563315c8daf

-- 
View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/commit/c1ab316e8d2d59c90e9504e26b97b563315c8daf
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20231216/f8ed5dd1/attachment.htm>