[med-svn] [Git][med-team/htsjdk][upstream] New upstream version 4.1.3+dfsg

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch upstream at Debian Med / htsjdk


Commits:
386fe92f by Pierre Gruet at 2024-10-09T09:45:19+02:00
New upstream version 4.1.3+dfsg
- - - - -


30 changed files:

- build.gradle
- gradle/wrapper/gradle-wrapper.properties
- gradlew
- scripts/install-samtools.sh
- src/main/java/htsjdk/beta/codecs/hapref/fasta/FASTADecoderV1_0.java
- src/main/java/htsjdk/beta/codecs/reads/ReadsCodecUtils.java
- src/main/java/htsjdk/beta/codecs/reads/bam/BAMCodec.java
- src/main/java/htsjdk/beta/codecs/reads/bam/BAMDecoder.java
- src/main/java/htsjdk/beta/codecs/reads/bam/BAMEncoder.java
- src/main/java/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMDecoderV1_0.java
- src/main/java/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMEncoderV1_0.java
- src/main/java/htsjdk/beta/codecs/reads/cram/CRAMCodec.java
- src/main/java/htsjdk/beta/codecs/reads/cram/CRAMDecoder.java
- src/main/java/htsjdk/beta/codecs/reads/cram/CRAMEncoder.java
- src/main/java/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMDecoderV2_1.java
- src/main/java/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMEncoderV2_1.java
- src/main/java/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMDecoderV3_0.java
- src/main/java/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMEncoderV3_0.java
- src/main/java/htsjdk/beta/codecs/reads/htsget/HtsgetBAMCodec.java
- src/main/java/htsjdk/beta/codecs/reads/htsget/HtsgetBAMDecoder.java
- src/main/java/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMCodecV1_2.java
- src/main/java/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMDecoderV1_2.java
- src/main/java/htsjdk/beta/codecs/reads/sam/SAMCodec.java
- src/main/java/htsjdk/beta/codecs/reads/sam/SAMDecoder.java
- src/main/java/htsjdk/beta/codecs/reads/sam/SAMEncoder.java
- src/main/java/htsjdk/beta/codecs/reads/sam/samV1_0/SAMDecoderV1_0.java
- src/main/java/htsjdk/beta/codecs/reads/sam/samV1_0/SAMEncoderV1_0.java
- src/main/java/htsjdk/beta/codecs/variants/vcf/VCFDecoder.java
- src/main/java/htsjdk/beta/codecs/variants/vcf/VCFEncoder.java
- src/main/java/htsjdk/beta/codecs/variants/vcf/VariantsCodecUtils.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/commit/386fe92fcd2e393e6042a9137b486ef4159c14c8

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View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/commit/386fe92fcd2e393e6042a9137b486ef4159c14c8
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