[med-svn] [Git][med-team/htsjdk][upstream] New upstream version 4.0.2+dfsg

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch upstream at Debian Med / htsjdk


Commits:
0c5275b1 by Pierre Gruet at 2023-12-01T11:11:26+01:00
New upstream version 4.0.2+dfsg
- - - - -


30 changed files:

- .github/workflows/tests.yml
- README.md
- build.gradle
- src/main/java/htsjdk/beta/io/bundle/BundleJSON.java
- src/main/java/htsjdk/samtools/BamFileIoUtils.java
- src/main/java/htsjdk/samtools/Defaults.java
- src/main/java/htsjdk/samtools/SAMReadGroupRecord.java
- src/main/java/htsjdk/samtools/SAMRecord.java
- src/main/java/htsjdk/samtools/SAMRecordIterator.java
- src/main/java/htsjdk/samtools/SAMRecordSetBuilder.java
- src/main/java/htsjdk/samtools/SAMUtils.java
- src/main/java/htsjdk/samtools/SamFileValidator.java
- src/main/java/htsjdk/samtools/TextTagCodec.java
- src/main/java/htsjdk/samtools/cram/structure/Slice.java
- src/main/java/htsjdk/samtools/util/AbstractProgressLogger.java
- src/main/java/htsjdk/samtools/util/BlockCompressedInputStream.java
- src/main/java/htsjdk/samtools/util/FileExtensions.java
- src/main/java/htsjdk/samtools/util/IOUtil.java
- src/main/java/htsjdk/samtools/util/Interval.java
- src/main/java/htsjdk/samtools/util/htsget/HtsgetErrorResponse.java
- src/main/java/htsjdk/samtools/util/htsget/HtsgetPOSTRequest.java
- src/main/java/htsjdk/samtools/util/htsget/HtsgetResponse.java
- + src/main/java/htsjdk/tribble/NamedFeature.java
- src/main/java/htsjdk/tribble/bed/BEDFeature.java
- src/main/java/htsjdk/variant/variantcontext/Allele.java
- src/main/java/htsjdk/variant/variantcontext/Genotype.java
- src/main/java/htsjdk/variant/vcf/VCFCodec.java
- src/main/java/htsjdk/variant/vcf/VCFHeaderVersion.java
- src/test/java/htsjdk/beta/io/bundle/BundleJSONTest.java
- + src/test/java/htsjdk/samtools/BamFileIoUtilsUnitTest.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/commit/0c5275b15d2b8aad0dec0be9856d0761f1ef26f3

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View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/commit/0c5275b15d2b8aad0dec0be9856d0761f1ef26f3
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