[med-svn] [Git][med-team/htsjdk][upstream] New upstream version 4.3.0+dfsg
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Fri Dec 26 07:26:31 GMT 2025
Pierre Gruet pushed to branch upstream at Debian Med / htsjdk
Commits:
395c9dfd by Pierre Gruet at 2025-12-23T15:04:55+01:00
New upstream version 4.3.0+dfsg
- - - - -
1378 changed files:
- .github/workflows/tests.yml
- .gitignore
- README.md
- build.gradle
- scripts/install-samtools.sh
- src/main/java/htsjdk/beta/codecs/hapref/fasta/FASTACodecV1_0.java
- src/main/java/htsjdk/beta/codecs/hapref/fasta/FASTADecoderV1_0.java
- + src/main/java/htsjdk/beta/codecs/reads/cram/cramV3_1/CRAMCodecV3_1.java
- + src/main/java/htsjdk/beta/codecs/reads/cram/cramV3_1/CRAMDecoderV3_1.java
- + src/main/java/htsjdk/beta/codecs/reads/cram/cramV3_1/CRAMEncoderV3_1.java
- src/main/java/htsjdk/beta/codecs/variants/vcf/VCFCodec.java
- src/main/java/htsjdk/beta/io/bundle/BundleResourceType.java
- src/main/java/htsjdk/beta/plugin/registry/HaploidReferenceResolver.java
- src/main/java/htsjdk/beta/plugin/registry/HtsCodecResolver.java
- src/main/java/htsjdk/beta/plugin/registry/HtsDefaultRegistry.java
- src/main/java/htsjdk/beta/plugin/registry/ReadsResolver.java
- src/main/java/htsjdk/beta/plugin/variants/VariantsBundle.java
- src/main/java/htsjdk/samtools/MemoryMappedFileBuffer.java
- src/main/java/htsjdk/samtools/SamPairUtil.java
- src/main/java/htsjdk/samtools/cram/common/CramVersions.java
- src/main/java/htsjdk/samtools/cram/compression/BZIP2ExternalCompressor.java
- + src/main/java/htsjdk/samtools/cram/compression/CompressionUtils.java
- src/main/java/htsjdk/samtools/cram/compression/ExternalCompressor.java
- src/main/java/htsjdk/samtools/cram/compression/GZIPExternalCompressor.java
- src/main/java/htsjdk/samtools/cram/compression/LZMAExternalCompressor.java
- src/main/java/htsjdk/samtools/cram/compression/RANSExternalCompressor.java → src/main/java/htsjdk/samtools/cram/compression/RANS4x8ExternalCompressor.java
- + src/main/java/htsjdk/samtools/cram/compression/RANSNx16ExternalCompressor.java
- src/main/java/htsjdk/samtools/cram/compression/RAWExternalCompressor.java
- + src/main/java/htsjdk/samtools/cram/compression/fqzcomp/FQZCompDecode.java
- + src/main/java/htsjdk/samtools/cram/compression/fqzcomp/FQZCompEncode.java
- + src/main/java/htsjdk/samtools/cram/compression/fqzcomp/FQZCompExternalCompressor.java
- + src/main/java/htsjdk/samtools/cram/compression/fqzcomp/FQZGlobalFlags.java
- + src/main/java/htsjdk/samtools/cram/compression/fqzcomp/FQZModels.java
- + src/main/java/htsjdk/samtools/cram/compression/fqzcomp/FQZParam.java
- + src/main/java/htsjdk/samtools/cram/compression/fqzcomp/FQZParams.java
- + src/main/java/htsjdk/samtools/cram/compression/fqzcomp/FQZState.java
- + src/main/java/htsjdk/samtools/cram/compression/fqzcomp/FQZUtils.java
- + src/main/java/htsjdk/samtools/cram/compression/nametokenisation/NameTokenisationDecode.java
- + src/main/java/htsjdk/samtools/cram/compression/nametokenisation/NameTokenisationEncode.java
- + src/main/java/htsjdk/samtools/cram/compression/nametokenisation/NameTokeniserExternalCompressor.java
- + src/main/java/htsjdk/samtools/cram/compression/nametokenisation/TokenStreams.java
- + src/main/java/htsjdk/samtools/cram/compression/nametokenisation/tokens/EncodeToken.java
- + src/main/java/htsjdk/samtools/cram/compression/range/ByteModel.java
- + src/main/java/htsjdk/samtools/cram/compression/range/Constants.java
- + src/main/java/htsjdk/samtools/cram/compression/range/RangeCoder.java
- + src/main/java/htsjdk/samtools/cram/compression/range/RangeDecode.java
- + src/main/java/htsjdk/samtools/cram/compression/range/RangeEncode.java
- + src/main/java/htsjdk/samtools/cram/compression/range/RangeExternalCompressor.java
- + src/main/java/htsjdk/samtools/cram/compression/range/RangeParams.java
- src/main/java/htsjdk/samtools/cram/compression/rans/ArithmeticDecoder.java
- src/main/java/htsjdk/samtools/cram/compression/rans/Constants.java
- − src/main/java/htsjdk/samtools/cram/compression/rans/D04.java
- − src/main/java/htsjdk/samtools/cram/compression/rans/D14.java
- − src/main/java/htsjdk/samtools/cram/compression/rans/E04.java
- − src/main/java/htsjdk/samtools/cram/compression/rans/E14.java
- − src/main/java/htsjdk/samtools/cram/compression/rans/FC.java
- − src/main/java/htsjdk/samtools/cram/compression/rans/Frequencies.java
- − src/main/java/htsjdk/samtools/cram/compression/rans/RANS.java
- + src/main/java/htsjdk/samtools/cram/compression/rans/RANSDecode.java
- src/main/java/htsjdk/samtools/cram/compression/rans/RANSDecodingSymbol.java
- + src/main/java/htsjdk/samtools/cram/compression/rans/RANSEncode.java
- src/main/java/htsjdk/samtools/cram/compression/rans/RANSEncodingSymbol.java
- + src/main/java/htsjdk/samtools/cram/compression/rans/RANSParams.java
- src/main/java/htsjdk/samtools/cram/compression/rans/Utils.java
- + src/main/java/htsjdk/samtools/cram/compression/rans/rans4x8/RANS4x8Decode.java
- + src/main/java/htsjdk/samtools/cram/compression/rans/rans4x8/RANS4x8Encode.java
- + src/main/java/htsjdk/samtools/cram/compression/rans/rans4x8/RANS4x8Params.java
- + src/main/java/htsjdk/samtools/cram/compression/rans/ransnx16/RANSNx16Decode.java
- + src/main/java/htsjdk/samtools/cram/compression/rans/ransnx16/RANSNx16Encode.java
- + src/main/java/htsjdk/samtools/cram/compression/rans/ransnx16/RANSNx16Params.java
- src/main/java/htsjdk/samtools/cram/encoding/writer/CramRecordWriter.java
- + src/main/java/htsjdk/samtools/cram/structure/CRAMCodecModelContext.java
- src/main/java/htsjdk/samtools/cram/structure/CompressionHeaderEncodingMap.java
- src/main/java/htsjdk/samtools/cram/structure/CompressorCache.java
- src/main/java/htsjdk/samtools/cram/structure/Slice.java
- src/main/java/htsjdk/samtools/cram/structure/SliceBlocksWriteStreams.java
- src/main/java/htsjdk/samtools/cram/structure/block/Block.java
- src/main/java/htsjdk/samtools/cram/structure/block/BlockCompressionMethod.java
- src/main/java/htsjdk/samtools/reference/AbstractFastaSequenceFile.java
- src/main/java/htsjdk/samtools/reference/AbstractIndexedFastaSequenceFile.java
- src/main/java/htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.java
- src/main/java/htsjdk/samtools/reference/FastaSequenceFile.java
- src/main/java/htsjdk/samtools/reference/IndexedFastaSequenceFile.java
- src/main/java/htsjdk/samtools/reference/ReferenceSequenceFile.java
- src/main/java/htsjdk/samtools/reference/ReferenceSequenceFileFactory.java
- src/main/java/htsjdk/samtools/reference/ReferenceSequenceFileWalker.java
- src/main/java/htsjdk/samtools/util/FileExtensions.java
- src/main/java/htsjdk/samtools/util/GZIIndex.java
- src/main/java/htsjdk/tribble/gff/Gff3BaseData.java
- src/main/java/htsjdk/tribble/gff/Gff3Feature.java
- src/main/resources/META-INF/services/htsjdk.beta.plugin.HtsCodec
- + src/test/java/htsjdk/beta/codecs/hapref/fasta/HaploidReferenceResolverTest.java
- + src/test/java/htsjdk/beta/codecs/reads/cram/HtsCRAMCodec31Test.java
- src/test/java/htsjdk/samtools/CRAMAllEncodingStrategiesTest.java
- src/test/java/htsjdk/samtools/CRAMEdgeCasesTest.java
- src/test/java/htsjdk/samtools/SamPairUtilTest.java
- + src/test/java/htsjdk/samtools/cram/CRAM31Tests.java
- + src/test/java/htsjdk/samtools/cram/CRAMInteropTestUtils.java
- + src/test/java/htsjdk/samtools/cram/FQZCompInteropTest.java
- + src/test/java/htsjdk/samtools/cram/NameTokenizationInteropTest.java
- + src/test/java/htsjdk/samtools/cram/RANSInteropTest.java
- + src/test/java/htsjdk/samtools/cram/RangeInteropTest.java
- src/test/java/htsjdk/samtools/cram/build/CramIOTest.java
- src/test/java/htsjdk/samtools/cram/build/SliceFactoryTest.java
- src/test/java/htsjdk/samtools/cram/compression/CompressorCacheTest.java
- src/test/java/htsjdk/samtools/cram/compression/ExternalCompressionTest.java
- + src/test/java/htsjdk/samtools/cram/compression/nametokenisation/NameTokenisationTest.java
- + src/test/java/htsjdk/samtools/cram/compression/range/RangeTest.java
- src/test/java/htsjdk/samtools/cram/compression/rans/RansTest.java
- src/test/java/htsjdk/samtools/cram/structure/SliceBlockReadStreamTest.java
- src/test/java/htsjdk/samtools/cram/structure/SliceBlockWriteStreamTest.java
- src/test/java/htsjdk/samtools/cram/structure/SliceBlocksTest.java
- src/test/java/htsjdk/samtools/cram/structure/StructureTestUtils.java
- src/test/java/htsjdk/samtools/cram/structure/block/BlockTest.java
- + src/test/java/htsjdk/samtools/reference/AbstractFastaSequenceFileTest.java
- src/test/java/htsjdk/samtools/reference/AbstractIndexedFastaSequenceFileTest.java
- src/test/java/htsjdk/samtools/reference/ReferenceSequenceFileFactoryTests.java
- src/test/java/htsjdk/tribble/gff/Gff3CodecTest.java
- src/test/java/htsjdk/utils/SamtoolsTestUtils.java
- src/test/java/htsjdk/utils/SamtoolsTestUtilsTest.java
- src/test/java/htsjdk/variant/variantcontext/writer/VCFWriterUnitTest.java
- + src/test/resources/htsjdk/hts-specs/test/README.md
- + src/test/resources/htsjdk/hts-specs/test/SAMtags/LICENSE
- + src/test/resources/htsjdk/hts-specs/test/SAMtags/MM-chebi.sam
- + src/test/resources/htsjdk/hts-specs/test/SAMtags/MM-chebi.txt
- + src/test/resources/htsjdk/hts-specs/test/SAMtags/MM-double.sam
- + src/test/resources/htsjdk/hts-specs/test/SAMtags/MM-double.txt
- + src/test/resources/htsjdk/hts-specs/test/SAMtags/MM-explicit.sam
- + src/test/resources/htsjdk/hts-specs/test/SAMtags/MM-explicit.txt
- + src/test/resources/htsjdk/hts-specs/test/SAMtags/MM-multi.sam
- + src/test/resources/htsjdk/hts-specs/test/SAMtags/MM-multi.txt
- + src/test/resources/htsjdk/hts-specs/test/SAMtags/MM-orient.sam
- + src/test/resources/htsjdk/hts-specs/test/SAMtags/MM-orient.txt
- + src/test/resources/htsjdk/hts-specs/test/SAMtags/README.md
- + src/test/resources/htsjdk/hts-specs/test/SAMtags/parse_mm.pl
- + src/test/resources/htsjdk/hts-specs/test/bam/LICENSE
- + src/test/resources/htsjdk/hts-specs/test/bam/passed/level-1.bam
- + src/test/resources/htsjdk/hts-specs/test/bam/passed/level-9.bam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/LICENSE
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/README.md
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/failed/0000_empty_noeof.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/failed/0000_empty_noeof.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0001_empty_eof.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0001_empty_eof.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0100_header1.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0100_header1.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0101_header2.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0101_header2.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0200_cmpr_hdr.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0200_cmpr_hdr.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0300_unmapped.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0300_unmapped.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0301_unmapped.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0301_unmapped.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0302_unmapped.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0302_unmapped.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0303_unmapped.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0303_unmapped.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0400_mapped.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0400_mapped.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0401_mapped.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0401_mapped.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0402_mapped.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0402_mapped.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0403_mapped.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0403_mapped.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0500_mapped.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0500_mapped.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0501_mapped.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0501_mapped.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0502_mapped.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0502_mapped.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0503_mapped.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0503_mapped.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0504_mapped.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0504_mapped.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0505_mapped.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0505_mapped.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0506_mapped.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0506_mapped.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0507_mapped.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0507_mapped.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0600_mapped.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0600_mapped.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0601_mapped.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0601_mapped.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0700_tag.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0700_tag.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0701_tag.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0701_tag.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0702_tag.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0702_tag.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0703_tag.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0703_tag.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0704_tag.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0704_tag.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0705_tag.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0705_tag.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0706_tag.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0706_tag.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0707_tag.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0707_tag.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0708_tag.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0708_tag.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0709_tag.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0709_tag.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0710_tag.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0710_tag.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0800_ctr.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0800_ctr.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0801_ctr.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0801_ctr.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0802_ctr.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0802_ctr.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0900_comp_raw.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0900_comp_raw.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0901_comp_gz.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0901_comp_gz.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0902_comp_bz2.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0902_comp_bz2.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0903_comp_lzma.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0903_comp_lzma.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0904_comp_rans0.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0904_comp_rans0.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0905_comp_rans1.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/0905_comp_rans1.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/1000_name.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/1000_name.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/1001_name.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/1001_name.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/1002_qual.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/1002_qual.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/1003_qual.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/1003_qual.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/1004_qual.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/1004_qual.sam
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/1005_qual.cram
- + src/test/resources/htsjdk/hts-specs/test/cram/3.0/passed/1005_qual.sam
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- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_011.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_012.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_013.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_014.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_015.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_016.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_017.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_018.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_019.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_020.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_021.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_022.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_023.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_024.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_025.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_026.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_027.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_028.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_029.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_030.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_031.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_032.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_format_033.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_000.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_001.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_002.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_003.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_004.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_005.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_006.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_007.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_008.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_009.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_010.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_011.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_012.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_013.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_014.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_015.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_016.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_017.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_018.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_019.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_020.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_021.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_022.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_023.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_024.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_025.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_026.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_027.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_028.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_029.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_030.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_031.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_032.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_033.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_034.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_035.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_036.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_037.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_038.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_039.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_040.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_041.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_info_042.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_meta_000.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_meta_001.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_meta_002.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_meta_003.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_pedigree_000.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_pedigree_001.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_pedigree_002.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_pedigree_003.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_pedigreedb_000.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_pedigreedb_001.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_pedigreedb_002.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_sample_000.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_sample_001.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_sample_002.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/failed/failed_meta_sample_003.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/complexfile_passed_000.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_body_alt.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_body_chrom.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_body_filter.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_body_id.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_body_info.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_body_pos.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_body_qual.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_body_ref.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_body_samples.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_fileformat_header_000.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_fileformat_header_001.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_fileformat_header_002.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_meta_alt.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_meta_assembly.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_meta_contig.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_meta_format.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_meta_info.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_meta_meta.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_meta_pedigree.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_meta_pedigreedb.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_meta_sample.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_ploidy_000.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_ploidy_001.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.3/passed/passed_symbolic_duplicates.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/4.5/passed/zero_length_LAA.vcf
- + src/test/resources/htsjdk/hts-specs/test/vcf/LICENSE
- + src/test/resources/htsjdk/hts-specs/test/vcf/README.md
The diff was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/commit/395c9dfdaa72b49a24a2f7f1ff7b3a6d8910be95
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View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/commit/395c9dfdaa72b49a24a2f7f1ff7b3a6d8910be95
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