[med-svn] [Git][med-team/htsjdk][master] 11 commits: Raising Standards version to 4.7.4

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / htsjdk


Commits:
affa340a by Pierre Gruet at 2026-05-29T07:30:57+02:00
Raising Standards version to 4.7.4

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339a8686 by Pierre Gruet at 2026-05-29T07:31:53+02:00
New upstream version 5.0.0+dfsg
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7d591e24 by Pierre Gruet at 2026-05-29T07:32:04+02:00
Update upstream source from tag 'upstream/5.0.0+dfsg'

Update to upstream version '5.0.0+dfsg'
with Debian dir 275b138b6638112858bf4bfdc7699e812cca8582
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6faa1500 by Pierre Gruet at 2026-05-29T13:14:28+02:00
Updating d/copyright

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a7cfbeed by Pierre Gruet at 2026-05-29T13:15:17+02:00
Removing obsolete skip-non-installable restrictions in d/t/control

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a49f2ceb by Pierre Gruet at 2026-05-29T13:17:49+02:00
Refreshing patches

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f31b791f by Pierre Gruet at 2026-05-29T13:35:59+02:00
Using the standard inflater/deflater

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044ee0a8 by Pierre Gruet at 2026-05-29T13:36:15+02:00
Deactivating a test requiring too much memory

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5e1dadea by Pierre Gruet at 2026-05-29T13:36:43+02:00
Ignoring dependency on libdeflate

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90ac01e8 by Pierre Gruet at 2026-05-29T13:36:53+02:00
Updating changelog

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3bf1c160 by Pierre Gruet at 2026-05-29T13:37:04+02:00
Upload to unstable

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1264 changed files:

- + .git-blame-ignore-revs
- .github/workflows/tests.yml
- .gitignore
- − .travis.yml
- + CHANGELOG.md
- + CONTRIBUTING.md
- README.md
- build.gradle
- − build.xml
- debian/changelog
- debian/control
- debian/copyright
- debian/maven.ignoreRules
- debian/patches/10-build.xml.patch
- debian/patches/100-fix-java11
- debian/patches/13-skip_network_tests
- debian/patches/150-use-rhino-as-JS-engine.patch
- debian/patches/160-mkdirs-before-creating-tempPaths.patch
- debian/patches/171-use-org-kordamp-json.patch
- debian/patches/190-newest-vcf.patch
- debian/patches/20-fix-version.patch
- debian/patches/200-accept-samtools-version.patch
- + debian/patches/210-no-fulcrumgenomics-inflater-in-debian.patch
- + debian/patches/220-test-with-too-much-memory.patch
- debian/patches/30-disable-scalatest.patch
- debian/patches/60-enable-tests
- debian/patches/70-removesometests-testng.patch
- debian/patches/90-disable-testftp.patch
- debian/patches/92-disable-testhttp.patch
- debian/patches/series
- debian/tests/control
- gradle/wrapper/gradle-wrapper.properties
- gradlew
- + gradlew.bat
- − java-style-eclipse.xml
- − java-style-intellij.xml
- src/main/java/htsjdk/annotations/BetaAPI.java
- src/main/java/htsjdk/annotations/InternalAPI.java
- 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/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/BAMDecoderOptions.java
- src/main/java/htsjdk/beta/codecs/reads/bam/BAMEncoder.java
- src/main/java/htsjdk/beta/codecs/reads/bam/BAMEncoderOptions.java
- src/main/java/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMCodecV1_0.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/CRAMDecoderOptions.java
- src/main/java/htsjdk/beta/codecs/reads/cram/CRAMEncoder.java
- src/main/java/htsjdk/beta/codecs/reads/cram/CRAMEncoderOptions.java
- src/main/java/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMCodecV2_1.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/CRAMCodecV3_0.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/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/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/SAMCodecV1_0.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/VCFCodec.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
- src/main/java/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFCodecV3_2.java
- src/main/java/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFDecoderV3_2.java
- src/main/java/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFEncoderV3_2.java
- src/main/java/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFCodecV3_3.java
- src/main/java/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFDecoderV3_3.java
- src/main/java/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFEncoderV3_3.java
- src/main/java/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFCodecV4_0.java
- src/main/java/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFDecoderV4_0.java
- src/main/java/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFEncoderV4_0.java
- src/main/java/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFCodecV4_1.java
- src/main/java/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFDecoderV4_1.java
- src/main/java/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFEncoderV4_1.java
- src/main/java/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFCodecV4_2.java
- src/main/java/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFDecoderV4_2.java
- src/main/java/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFEncoderV4_2.java
- src/main/java/htsjdk/beta/codecs/variants/vcf/vcfv4_3/VCFCodecV4_3.java
- src/main/java/htsjdk/beta/codecs/variants/vcf/vcfv4_3/VCFDecoderV4_3.java
- src/main/java/htsjdk/beta/exception/HtsjdkPluginException.java
- src/main/java/htsjdk/beta/io/IOPathUtils.java
- src/main/java/htsjdk/beta/io/bundle/Bundle.java
- src/main/java/htsjdk/beta/io/bundle/BundleBuilder.java
- src/main/java/htsjdk/beta/io/bundle/BundleJSON.java
- src/main/java/htsjdk/beta/io/bundle/BundleResource.java
- src/main/java/htsjdk/beta/io/bundle/BundleResourceBase.java
- src/main/java/htsjdk/beta/io/bundle/BundleResourceType.java
- src/main/java/htsjdk/beta/io/bundle/IOPathResource.java
- src/main/java/htsjdk/beta/io/bundle/InputStreamResource.java
- src/main/java/htsjdk/beta/io/bundle/OutputStreamResource.java
- src/main/java/htsjdk/beta/io/bundle/SeekableStreamResource.java
- src/main/java/htsjdk/beta/io/bundle/SignatureStream.java
- src/main/java/htsjdk/beta/package-info.java
- src/main/java/htsjdk/beta/plugin/HtsCodec.java
- src/main/java/htsjdk/beta/plugin/HtsContentType.java
- src/main/java/htsjdk/beta/plugin/HtsDecoder.java
- src/main/java/htsjdk/beta/plugin/HtsDecoderOptions.java
- src/main/java/htsjdk/beta/plugin/HtsEncoder.java
- src/main/java/htsjdk/beta/plugin/HtsEncoderOptions.java
- src/main/java/htsjdk/beta/plugin/HtsHeader.java
- src/main/java/htsjdk/beta/plugin/HtsRecord.java
- src/main/java/htsjdk/beta/plugin/HtsVersion.java
- src/main/java/htsjdk/beta/plugin/IOUtils.java
- src/main/java/htsjdk/beta/plugin/hapref/HapRefDecoderOptions.java
- src/main/java/htsjdk/beta/plugin/hapref/HaploidReferenceCodec.java
- src/main/java/htsjdk/beta/plugin/hapref/HaploidReferenceDecoder.java
- src/main/java/htsjdk/beta/plugin/hapref/HaploidReferenceDecoderOptions.java
- src/main/java/htsjdk/beta/plugin/hapref/HaploidReferenceEncoder.java
- src/main/java/htsjdk/beta/plugin/hapref/HaploidReferenceEncoderOptions.java
- src/main/java/htsjdk/beta/plugin/hapref/HaploidReferenceFormats.java
- src/main/java/htsjdk/beta/plugin/interval/HtsIntervalUtils.java
- src/main/java/htsjdk/beta/plugin/interval/HtsQuery.java
- src/main/java/htsjdk/beta/plugin/interval/HtsQueryInterval.java
- src/main/java/htsjdk/beta/plugin/reads/ReadsBundle.java
- src/main/java/htsjdk/beta/plugin/reads/ReadsCodec.java
- src/main/java/htsjdk/beta/plugin/reads/ReadsDecoder.java
- src/main/java/htsjdk/beta/plugin/reads/ReadsDecoderOptions.java
- src/main/java/htsjdk/beta/plugin/reads/ReadsEncoder.java
- src/main/java/htsjdk/beta/plugin/reads/ReadsEncoderOptions.java
- src/main/java/htsjdk/beta/plugin/reads/ReadsFormats.java
- src/main/java/htsjdk/beta/plugin/reads/ReadsQuery.java
- src/main/java/htsjdk/beta/plugin/registry/HaploidReferenceResolver.java
- src/main/java/htsjdk/beta/plugin/registry/HtsCodecRegistry.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/registry/VariantsResolver.java
- src/main/java/htsjdk/beta/plugin/variants/VariantsBundle.java
- src/main/java/htsjdk/beta/plugin/variants/VariantsCodec.java
- src/main/java/htsjdk/beta/plugin/variants/VariantsDecoder.java
- src/main/java/htsjdk/beta/plugin/variants/VariantsDecoderOptions.java
- src/main/java/htsjdk/beta/plugin/variants/VariantsEncoder.java
- src/main/java/htsjdk/beta/plugin/variants/VariantsEncoderOptions.java
- src/main/java/htsjdk/io/AsyncWriterPool.java
- src/main/java/htsjdk/io/HtsPath.java
- src/main/java/htsjdk/io/IOPath.java
- src/main/java/htsjdk/samtools/AbstractBAMFileIndex.java
- src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java
- src/main/java/htsjdk/samtools/AlignmentBlock.java
- src/main/java/htsjdk/samtools/AsyncSAMFileWriter.java
- src/main/java/htsjdk/samtools/BAMFileConstants.java
- src/main/java/htsjdk/samtools/BAMFileReader.java
- src/main/java/htsjdk/samtools/BAMFileSpan.java
- src/main/java/htsjdk/samtools/BAMFileWriter.java
- src/main/java/htsjdk/samtools/BAMIndex.java
- src/main/java/htsjdk/samtools/BAMIndexContent.java
- src/main/java/htsjdk/samtools/BAMIndexMerger.java
- src/main/java/htsjdk/samtools/BAMIndexMetaData.java
- src/main/java/htsjdk/samtools/BAMIndexWriter.java
- src/main/java/htsjdk/samtools/BAMIndexer.java
- src/main/java/htsjdk/samtools/BAMIteratorFilter.java
- src/main/java/htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilter.java
- src/main/java/htsjdk/samtools/BAMRecord.java
- src/main/java/htsjdk/samtools/BAMRecordCodec.java
- src/main/java/htsjdk/samtools/BAMSBIIndexer.java
- src/main/java/htsjdk/samtools/BAMStartingAtIteratorFilter.java
- src/main/java/htsjdk/samtools/BAMStreamWriter.java
- + src/main/java/htsjdk/samtools/BamConverter.java
- src/main/java/htsjdk/samtools/BamFileIoUtils.java
- src/main/java/htsjdk/samtools/BamIndexValidator.java
- src/main/java/htsjdk/samtools/Bin.java
- src/main/java/htsjdk/samtools/BinList.java
- src/main/java/htsjdk/samtools/BinaryBAMIndexWriter.java
- src/main/java/htsjdk/samtools/BinaryTagCodec.java
- src/main/java/htsjdk/samtools/BinningIndexBuilder.java
- src/main/java/htsjdk/samtools/BinningIndexContent.java
- src/main/java/htsjdk/samtools/BrowseableBAMIndex.java
- src/main/java/htsjdk/samtools/CRAMBAIIndexer.java
- src/main/java/htsjdk/samtools/CRAMCRAIIndexer.java
- src/main/java/htsjdk/samtools/CRAMContainerStreamWriter.java
- src/main/java/htsjdk/samtools/CRAMFileReader.java
- src/main/java/htsjdk/samtools/CRAMFileWriter.java
- src/main/java/htsjdk/samtools/CRAMIndexer.java
- src/main/java/htsjdk/samtools/CRAMIterator.java
- src/main/java/htsjdk/samtools/CSIIndex.java
- src/main/java/htsjdk/samtools/CachingBAMFileIndex.java
- src/main/java/htsjdk/samtools/CachingBamFileIndexOptimizedForMerging.java
- src/main/java/htsjdk/samtools/ChainedDownsamplingIterator.java
- src/main/java/htsjdk/samtools/Chunk.java
- src/main/java/htsjdk/samtools/Cigar.java
- src/main/java/htsjdk/samtools/CigarElement.java
- src/main/java/htsjdk/samtools/CigarOperator.java
- src/main/java/htsjdk/samtools/ComparableSamRecordIterator.java
- src/main/java/htsjdk/samtools/CompressedIndexFileBuffer.java
- src/main/java/htsjdk/samtools/ConstantMemoryDownsamplingIterator.java
- src/main/java/htsjdk/samtools/CoordinateSortedPairInfoMap.java
- src/main/java/htsjdk/samtools/CustomReaderFactory.java
- src/main/java/htsjdk/samtools/DefaultSAMRecordFactory.java
- src/main/java/htsjdk/samtools/Defaults.java
- src/main/java/htsjdk/samtools/DiskBasedBAMFileIndex.java
- src/main/java/htsjdk/samtools/DownsamplingIterator.java
- src/main/java/htsjdk/samtools/DownsamplingIteratorFactory.java
- src/main/java/htsjdk/samtools/DuplicateScoringStrategy.java
- src/main/java/htsjdk/samtools/DuplicateSet.java
- src/main/java/htsjdk/samtools/DuplicateSetIterator.java
- src/main/java/htsjdk/samtools/FileTruncatedException.java
- src/main/java/htsjdk/samtools/GenomicIndexUtil.java
- src/main/java/htsjdk/samtools/HighAccuracyDownsamplingIterator.java
- src/main/java/htsjdk/samtools/HtsgetBAMFileReader.java
- src/main/java/htsjdk/samtools/IndexFileBuffer.java
- src/main/java/htsjdk/samtools/IndexFileBufferFactory.java
- src/main/java/htsjdk/samtools/IndexStreamBuffer.java
- src/main/java/htsjdk/samtools/LinearIndex.java
- src/main/java/htsjdk/samtools/MemoryMappedFileBuffer.java
- src/main/java/htsjdk/samtools/MergingSamRecordIterator.java
- src/main/java/htsjdk/samtools/QueryInterval.java
- src/main/java/htsjdk/samtools/RandomAccessFileBuffer.java
- src/main/java/htsjdk/samtools/ReservedTagConstants.java
- src/main/java/htsjdk/samtools/SAMBinaryTagAndUnsignedArrayValue.java
- src/main/java/htsjdk/samtools/SAMBinaryTagAndValue.java
- src/main/java/htsjdk/samtools/SAMException.java
- src/main/java/htsjdk/samtools/SAMFileHeader.java
- src/main/java/htsjdk/samtools/SAMFileWriter.java
- src/main/java/htsjdk/samtools/SAMFileWriterFactory.java
- src/main/java/htsjdk/samtools/SAMFileWriterImpl.java
- src/main/java/htsjdk/samtools/SAMFlag.java
- src/main/java/htsjdk/samtools/SAMFormatException.java
- src/main/java/htsjdk/samtools/SAMHeaderRecordComparator.java
- src/main/java/htsjdk/samtools/SAMLineParser.java
- src/main/java/htsjdk/samtools/SAMProgramRecord.java
- src/main/java/htsjdk/samtools/SAMReadGroupRecord.java
- src/main/java/htsjdk/samtools/SAMRecord.java
- src/main/java/htsjdk/samtools/SAMRecordComparator.java
- src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java
- src/main/java/htsjdk/samtools/SAMRecordDuplicateComparator.java
- src/main/java/htsjdk/samtools/SAMRecordFactory.java
- src/main/java/htsjdk/samtools/SAMRecordIterator.java
- src/main/java/htsjdk/samtools/SAMRecordQueryHashComparator.java
- src/main/java/htsjdk/samtools/SAMRecordQueryNameComparator.java
- src/main/java/htsjdk/samtools/SAMRecordSetBuilder.java
- src/main/java/htsjdk/samtools/SAMSequenceDictionary.java
- src/main/java/htsjdk/samtools/SAMSequenceDictionaryCodec.java
- src/main/java/htsjdk/samtools/SAMSequenceRecord.java
- src/main/java/htsjdk/samtools/SAMSortOrderChecker.java
- src/main/java/htsjdk/samtools/SAMTag.java
- src/main/java/htsjdk/samtools/SAMTagUtil.java
- src/main/java/htsjdk/samtools/SAMTestUtil.java
- src/main/java/htsjdk/samtools/SAMTextHeaderCodec.java
- src/main/java/htsjdk/samtools/SAMTextReader.java
- src/main/java/htsjdk/samtools/SAMTextWriter.java
- src/main/java/htsjdk/samtools/SAMUtils.java
- src/main/java/htsjdk/samtools/SAMValidationError.java
- src/main/java/htsjdk/samtools/SBIIndex.java
- src/main/java/htsjdk/samtools/SBIIndexMerger.java
- src/main/java/htsjdk/samtools/SBIIndexWriter.java
- src/main/java/htsjdk/samtools/SQTagUtil.java
- − src/main/java/htsjdk/samtools/SRAFileReader.java
- − src/main/java/htsjdk/samtools/SRAIndex.java
- − src/main/java/htsjdk/samtools/SRAIterator.java
- src/main/java/htsjdk/samtools/SamFileHeaderMerger.java
- src/main/java/htsjdk/samtools/SamFileValidator.java
- src/main/java/htsjdk/samtools/SamFiles.java
- src/main/java/htsjdk/samtools/SamFlagField.java
- src/main/java/htsjdk/samtools/SamIndexes.java
- src/main/java/htsjdk/samtools/SamInputResource.java
- src/main/java/htsjdk/samtools/SamPairUtil.java
- src/main/java/htsjdk/samtools/SamReader.java
- src/main/java/htsjdk/samtools/SamReaderFactory.java
- src/main/java/htsjdk/samtools/SamStreams.java
- src/main/java/htsjdk/samtools/SecondaryAlignmentSkippingIterator.java
- src/main/java/htsjdk/samtools/SecondaryOrSupplementarySkippingIterator.java
- src/main/java/htsjdk/samtools/StreamInflatingIndexingOutputStream.java
- src/main/java/htsjdk/samtools/TextCigarCodec.java
- src/main/java/htsjdk/samtools/TextTagCodec.java
- src/main/java/htsjdk/samtools/TextualBAMIndexWriter.java
- src/main/java/htsjdk/samtools/apps/TimeRandomAccessFile.java
- src/main/java/htsjdk/samtools/cram/BAIEntry.java
- src/main/java/htsjdk/samtools/cram/CRAIEntry.java
- src/main/java/htsjdk/samtools/cram/CRAIIndex.java
- src/main/java/htsjdk/samtools/cram/CRAIIndexMerger.java
- src/main/java/htsjdk/samtools/cram/CRAMException.java
- + src/main/java/htsjdk/samtools/cram/CramComparison.java
- + src/main/java/htsjdk/samtools/cram/CramConverter.java
- + src/main/java/htsjdk/samtools/cram/CramStats.java
- src/main/java/htsjdk/samtools/cram/build/CRAMReferenceRegion.java
- src/main/java/htsjdk/samtools/cram/build/CompressionHeaderFactory.java
- src/main/java/htsjdk/samtools/cram/build/ContainerFactory.java
- src/main/java/htsjdk/samtools/cram/build/CramContainerHeaderIterator.java
- src/main/java/htsjdk/samtools/cram/build/CramContainerIterator.java
- src/main/java/htsjdk/samtools/cram/build/CramIO.java
- src/main/java/htsjdk/samtools/cram/build/CramSpanContainerIterator.java
- src/main/java/htsjdk/samtools/cram/build/SliceFactory.java
- src/main/java/htsjdk/samtools/cram/build/Utils.java
- src/main/java/htsjdk/samtools/cram/common/CRAMVersion.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/RANS4x8ExternalCompressor.java
- src/main/java/htsjdk/samtools/cram/compression/RANSNx16ExternalCompressor.java
- + src/main/java/htsjdk/samtools/cram/compression/TrialCompressor.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/RANS4x8Decode.java
- + src/main/java/htsjdk/samtools/cram/compression/rans/RANS4x8Encode.java
- src/main/java/htsjdk/samtools/cram/compression/rans/rans4x8/RANS4x8Params.java → src/main/java/htsjdk/samtools/cram/compression/rans/RANS4x8Params.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/ransnx16/RANSNx16Decode.java → src/main/java/htsjdk/samtools/cram/compression/rans/RANSNx16Decode.java
- + src/main/java/htsjdk/samtools/cram/compression/rans/RANSNx16Encode.java
- src/main/java/htsjdk/samtools/cram/compression/rans/ransnx16/RANSNx16Params.java → src/main/java/htsjdk/samtools/cram/compression/rans/RANSNx16Params.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/ransnx16/RANSNx16Encode.java
- src/main/java/htsjdk/samtools/cram/digest/AbstractSerialDigest.java
- src/main/java/htsjdk/samtools/cram/digest/ByteSumCombine.java
- src/main/java/htsjdk/samtools/cram/digest/ContentDigests.java
- src/main/java/htsjdk/samtools/cram/digest/Crc32Hasher.java
- src/main/java/htsjdk/samtools/cram/digest/IntegerSumCombine.java
- src/main/java/htsjdk/samtools/cram/digest/MessageDigestHasher.java
- src/main/java/htsjdk/samtools/cram/digest/SERIES.java
- src/main/java/htsjdk/samtools/cram/encoding/ByteArrayLenCodec.java
- src/main/java/htsjdk/samtools/cram/encoding/ByteArrayLenEncoding.java
- src/main/java/htsjdk/samtools/cram/encoding/CRAMCodec.java
- src/main/java/htsjdk/samtools/cram/encoding/CRAMEncoding.java
- src/main/java/htsjdk/samtools/cram/encoding/EncodingFactory.java
- src/main/java/htsjdk/samtools/cram/encoding/core/BetaIntegerCodec.java
- src/main/java/htsjdk/samtools/cram/encoding/core/BetaIntegerEncoding.java
- src/main/java/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanByteCodec.java
- src/main/java/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanByteEncoding.java
- src/main/java/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanIntegerCodec.java
- src/main/java/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanIntegerEncoding.java
- src/main/java/htsjdk/samtools/cram/encoding/core/CoreCodec.java
- src/main/java/htsjdk/samtools/cram/encoding/core/GammaIntegerCodec.java
- src/main/java/htsjdk/samtools/cram/encoding/core/GammaIntegerEncoding.java
- src/main/java/htsjdk/samtools/cram/encoding/core/SubexponentialIntegerCodec.java
- src/main/java/htsjdk/samtools/cram/encoding/core/SubexponentialIntegerEncoding.java
- src/main/java/htsjdk/samtools/cram/encoding/core/experimental/ExperimentalCodec.java
- src/main/java/htsjdk/samtools/cram/encoding/core/experimental/GolombIntegerCodec.java
- src/main/java/htsjdk/samtools/cram/encoding/core/experimental/GolombIntegerEncoding.java
- src/main/java/htsjdk/samtools/cram/encoding/core/experimental/GolombLongCodec.java
- src/main/java/htsjdk/samtools/cram/encoding/core/experimental/GolombLongEncoding.java
- src/main/java/htsjdk/samtools/cram/encoding/core/experimental/GolombRiceIntegerCodec.java
- src/main/java/htsjdk/samtools/cram/encoding/core/experimental/GolombRiceIntegerEncoding.java
- src/main/java/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanBitCode.java
- src/main/java/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanCanoncialCodeGenerator.java
- src/main/java/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanLeaf.java
- src/main/java/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanNode.java
- src/main/java/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanParams.java
- src/main/java/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanParamsCalculator.java
- src/main/java/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanTree.java
- src/main/java/htsjdk/samtools/cram/encoding/external/ByteArrayStopCodec.java
- src/main/java/htsjdk/samtools/cram/encoding/external/ByteArrayStopEncoding.java
- src/main/java/htsjdk/samtools/cram/encoding/external/ExternalByteArrayCodec.java
- src/main/java/htsjdk/samtools/cram/encoding/external/ExternalByteArrayEncoding.java
- src/main/java/htsjdk/samtools/cram/encoding/external/ExternalByteCodec.java
- src/main/java/htsjdk/samtools/cram/encoding/external/ExternalByteEncoding.java
- src/main/java/htsjdk/samtools/cram/encoding/external/ExternalCodec.java
- src/main/java/htsjdk/samtools/cram/encoding/external/ExternalIntegerCodec.java
- src/main/java/htsjdk/samtools/cram/encoding/external/ExternalIntegerEncoding.java
- src/main/java/htsjdk/samtools/cram/encoding/external/ExternalLongCodec.java
- src/main/java/htsjdk/samtools/cram/encoding/external/ExternalLongEncoding.java
- src/main/java/htsjdk/samtools/cram/encoding/reader/CramRecordReader.java
- src/main/java/htsjdk/samtools/cram/encoding/reader/DataSeriesReader.java
- src/main/java/htsjdk/samtools/cram/encoding/readfeatures/BaseQualityScore.java
- src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Bases.java
- src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Deletion.java
- src/main/java/htsjdk/samtools/cram/encoding/readfeatures/HardClip.java
- src/main/java/htsjdk/samtools/cram/encoding/readfeatures/InsertBase.java
- src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Insertion.java
- src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Padding.java
- src/main/java/htsjdk/samtools/cram/encoding/readfeatures/ReadBase.java
- src/main/java/htsjdk/samtools/cram/encoding/readfeatures/RefSkip.java
- src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Scores.java
- src/main/java/htsjdk/samtools/cram/encoding/readfeatures/SoftClip.java
- src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Substitution.java
- src/main/java/htsjdk/samtools/cram/encoding/writer/CramRecordWriter.java
- src/main/java/htsjdk/samtools/cram/encoding/writer/DataSeriesWriter.java
- src/main/java/htsjdk/samtools/cram/io/BitInputStream.java
- src/main/java/htsjdk/samtools/cram/io/BitOutputStream.java
- + src/main/java/htsjdk/samtools/cram/io/CRAMByteReader.java
- + src/main/java/htsjdk/samtools/cram/io/CRAMByteWriter.java
- src/main/java/htsjdk/samtools/cram/io/CRC32InputStream.java
- src/main/java/htsjdk/samtools/cram/io/CRC32OutputStream.java
- src/main/java/htsjdk/samtools/cram/io/CountingInputStream.java
- src/main/java/htsjdk/samtools/cram/io/CramInt.java
- src/main/java/htsjdk/samtools/cram/io/CramIntArray.java
- src/main/java/htsjdk/samtools/cram/io/DefaultBitInputStream.java
- src/main/java/htsjdk/samtools/cram/io/DefaultBitOutputStream.java
- src/main/java/htsjdk/samtools/cram/io/ITF8.java
- src/main/java/htsjdk/samtools/cram/io/InputStreamUtils.java
- src/main/java/htsjdk/samtools/cram/io/LTF8.java
- src/main/java/htsjdk/samtools/cram/ref/CRAMLazyReferenceSource.java
- src/main/java/htsjdk/samtools/cram/ref/CRAMReferenceSource.java
- src/main/java/htsjdk/samtools/cram/ref/EnaRefService.java
- src/main/java/htsjdk/samtools/cram/ref/ReferenceContext.java
- src/main/java/htsjdk/samtools/cram/ref/ReferenceSource.java
- src/main/java/htsjdk/samtools/cram/structure/AlignmentContext.java
- src/main/java/htsjdk/samtools/cram/structure/AlignmentSpan.java
- src/main/java/htsjdk/samtools/cram/structure/CRAMCodecModelContext.java
- + src/main/java/htsjdk/samtools/cram/structure/CRAMCompressionProfile.java
- src/main/java/htsjdk/samtools/cram/structure/CRAMCompressionRecord.java
- src/main/java/htsjdk/samtools/cram/structure/CRAMEncodingStrategy.java
- src/main/java/htsjdk/samtools/cram/structure/CRAMRecordReadFeatures.java
- src/main/java/htsjdk/samtools/cram/structure/CompressionHeader.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/CompressorDescriptor.java
- src/main/java/htsjdk/samtools/cram/structure/Container.java
- src/main/java/htsjdk/samtools/cram/structure/ContainerHeader.java
- src/main/java/htsjdk/samtools/cram/structure/CramHeader.java
- src/main/java/htsjdk/samtools/cram/structure/DataSeries.java
- src/main/java/htsjdk/samtools/cram/structure/EncodingDescriptor.java
- src/main/java/htsjdk/samtools/cram/structure/ReadTag.java
- src/main/java/htsjdk/samtools/cram/structure/Slice.java
- src/main/java/htsjdk/samtools/cram/structure/SliceBlocks.java
- src/main/java/htsjdk/samtools/cram/structure/SliceBlocksReadStreams.java
- src/main/java/htsjdk/samtools/cram/structure/SliceBlocksWriteStreams.java
- src/main/java/htsjdk/samtools/cram/structure/SubstitutionBase.java
- src/main/java/htsjdk/samtools/cram/structure/SubstitutionMatrix.java
- + src/main/java/htsjdk/samtools/cram/structure/TagKeyCache.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/cram/structure/block/BlockContentType.java
- src/main/java/htsjdk/samtools/example/ExampleSamUsage.java
- src/main/java/htsjdk/samtools/example/PrintReadsExample.java
- src/main/java/htsjdk/samtools/fastq/AsyncFastqWriter.java
- src/main/java/htsjdk/samtools/fastq/BasicFastqWriter.java
- src/main/java/htsjdk/samtools/fastq/FastqConstants.java
- src/main/java/htsjdk/samtools/fastq/FastqEncoder.java
- src/main/java/htsjdk/samtools/fastq/FastqReader.java
- src/main/java/htsjdk/samtools/fastq/FastqRecord.java
- src/main/java/htsjdk/samtools/fastq/FastqWriter.java
- src/main/java/htsjdk/samtools/fastq/FastqWriterFactory.java
- src/main/java/htsjdk/samtools/filter/AbstractJavascriptFilter.java
- src/main/java/htsjdk/samtools/filter/AggregateFilter.java
- src/main/java/htsjdk/samtools/filter/AlignedFilter.java
- src/main/java/htsjdk/samtools/filter/DuplicateReadFilter.java
- src/main/java/htsjdk/samtools/filter/FailsVendorReadQualityFilter.java
- src/main/java/htsjdk/samtools/filter/FilteringIterator.java
- src/main/java/htsjdk/samtools/filter/FilteringSamIterator.java
- src/main/java/htsjdk/samtools/filter/InsertSizeFilter.java
- src/main/java/htsjdk/samtools/filter/IntervalFilter.java
- src/main/java/htsjdk/samtools/filter/IntervalKeepPairFilter.java
- src/main/java/htsjdk/samtools/filter/InvertFilter.java
- src/main/java/htsjdk/samtools/filter/JavascriptSamRecordFilter.java
- src/main/java/htsjdk/samtools/filter/NotPrimaryAlignmentFilter.java
- src/main/java/htsjdk/samtools/filter/OverclippedReadFilter.java
- src/main/java/htsjdk/samtools/filter/ReadNameFilter.java
- src/main/java/htsjdk/samtools/filter/SamRecordFilter.java
- src/main/java/htsjdk/samtools/filter/SecondaryAlignmentFilter.java
- src/main/java/htsjdk/samtools/filter/SecondaryOrSupplementaryFilter.java
- src/main/java/htsjdk/samtools/filter/SolexaNoiseFilter.java
- src/main/java/htsjdk/samtools/filter/TagFilter.java
- src/main/java/htsjdk/samtools/filter/WholeReadClippedFilter.java
- src/main/java/htsjdk/samtools/liftover/Chain.java
- src/main/java/htsjdk/samtools/liftover/LiftOver.java
- src/main/java/htsjdk/samtools/metrics/Header.java
- src/main/java/htsjdk/samtools/metrics/MetricBase.java
- src/main/java/htsjdk/samtools/metrics/MetricsFile.java
- src/main/java/htsjdk/samtools/metrics/StringHeader.java
- src/main/java/htsjdk/samtools/metrics/VersionHeader.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/FastaReferenceWriter.java
- src/main/java/htsjdk/samtools/reference/FastaReferenceWriterBuilder.java
- src/main/java/htsjdk/samtools/reference/FastaSequenceFile.java
- src/main/java/htsjdk/samtools/reference/FastaSequenceIndex.java
- src/main/java/htsjdk/samtools/reference/FastaSequenceIndexCreator.java
- src/main/java/htsjdk/samtools/reference/FastaSequenceIndexEntry.java
- src/main/java/htsjdk/samtools/reference/IndexedFastaSequenceFile.java
- src/main/java/htsjdk/samtools/reference/ReferenceSequence.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/reference/SamLocusAndReferenceIterator.java
- src/main/java/htsjdk/samtools/seekablestream/ISeekableStreamFactory.java
- src/main/java/htsjdk/samtools/seekablestream/SeekableBufferedStream.java
- src/main/java/htsjdk/samtools/seekablestream/SeekableFTPStream.java
- src/main/java/htsjdk/samtools/seekablestream/SeekableFTPStreamHelper.java
- src/main/java/htsjdk/samtools/seekablestream/SeekableFileStream.java
- src/main/java/htsjdk/samtools/seekablestream/SeekableHTTPStream.java
- src/main/java/htsjdk/samtools/seekablestream/SeekableMemoryStream.java
- src/main/java/htsjdk/samtools/seekablestream/SeekablePathStream.java
- src/main/java/htsjdk/samtools/seekablestream/SeekableStream.java
- src/main/java/htsjdk/samtools/seekablestream/SeekableStreamFactory.java
- src/main/java/htsjdk/samtools/seekablestream/UserPasswordInput.java
- − src/main/java/htsjdk/samtools/sra/ReferenceCache.java
- − src/main/java/htsjdk/samtools/sra/SRAAccession.java
- − src/main/java/htsjdk/samtools/sra/SRAAlignmentIterator.java
- − src/main/java/htsjdk/samtools/sra/SRAIndexedSequenceFile.java
- − src/main/java/htsjdk/samtools/sra/SRALazyRecord.java
- − src/main/java/htsjdk/samtools/sra/SRAUnalignmentIterator.java
- − src/main/java/htsjdk/samtools/sra/SRAUtils.java
- src/main/java/htsjdk/samtools/util/AbstractAsyncWriter.java
- src/main/java/htsjdk/samtools/util/AbstractLocusInfo.java
- src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java
- src/main/java/htsjdk/samtools/util/AbstractProgressLogger.java
- src/main/java/htsjdk/samtools/util/AbstractRecordAndOffset.java
- src/main/java/htsjdk/samtools/util/AsciiWriter.java
- src/main/java/htsjdk/samtools/util/AsyncBlockCompressedInputStream.java
- src/main/java/htsjdk/samtools/util/AsyncBufferedIterator.java
- src/main/java/htsjdk/samtools/util/BinaryCodec.java
- src/main/java/htsjdk/samtools/util/BlockCompressedFilePointerUtil.java
- src/main/java/htsjdk/samtools/util/BlockCompressedInputStream.java
- src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java
- src/main/java/htsjdk/samtools/util/BlockCompressedStreamConstants.java
- src/main/java/htsjdk/samtools/util/BlockGunzipper.java
- src/main/java/htsjdk/samtools/util/BufferedLineReader.java
- src/main/java/htsjdk/samtools/util/CigarUtil.java
- src/main/java/htsjdk/samtools/util/CloseableIterator.java
- src/main/java/htsjdk/samtools/util/CloserUtil.java
- src/main/java/htsjdk/samtools/util/CollectionUtil.java
- src/main/java/htsjdk/samtools/util/ComparableTuple.java
- src/main/java/htsjdk/samtools/util/CoordMath.java
- src/main/java/htsjdk/samtools/util/CoordSpanInputSteam.java
- src/main/java/htsjdk/samtools/util/CustomGzipOutputStream.java
- src/main/java/htsjdk/samtools/util/DateParser.java
- src/main/java/htsjdk/samtools/util/DiskBackedQueue.java
- src/main/java/htsjdk/samtools/util/EdgeReadIterator.java
- src/main/java/htsjdk/samtools/util/EdgingRecordAndOffset.java
- src/main/java/htsjdk/samtools/util/FastLineReader.java
- src/main/java/htsjdk/samtools/util/FileAppendStreamLRUCache.java
- src/main/java/htsjdk/samtools/util/FileExtensions.java
- src/main/java/htsjdk/samtools/util/FormatUtil.java
- src/main/java/htsjdk/samtools/util/GZIIndex.java
- + src/main/java/htsjdk/samtools/util/GzipCodec.java
- src/main/java/htsjdk/samtools/util/Histogram.java
- src/main/java/htsjdk/samtools/util/HttpUtils.java
- src/main/java/htsjdk/samtools/util/IOUtil.java
- src/main/java/htsjdk/samtools/util/Interval.java
- src/main/java/htsjdk/samtools/util/IntervalCodec.java
- src/main/java/htsjdk/samtools/util/IntervalCoordinateComparator.java
- src/main/java/htsjdk/samtools/util/IntervalList.java
- src/main/java/htsjdk/samtools/util/IntervalListReferenceSequenceMask.java
- src/main/java/htsjdk/samtools/util/IntervalListWriter.java
- src/main/java/htsjdk/samtools/util/IntervalTree.java
- src/main/java/htsjdk/samtools/util/IntervalTreeMap.java
- src/main/java/htsjdk/samtools/util/IntervalUtil.java
- src/main/java/htsjdk/samtools/util/IterableOnceIterator.java
- src/main/java/htsjdk/samtools/util/Iterables.java
- src/main/java/htsjdk/samtools/util/Lazy.java
- src/main/java/htsjdk/samtools/util/ListMap.java
- src/main/java/htsjdk/samtools/util/Locatable.java
- src/main/java/htsjdk/samtools/util/LocationAware.java
- src/main/java/htsjdk/samtools/util/Locus.java
- src/main/java/htsjdk/samtools/util/Log.java
- src/main/java/htsjdk/samtools/util/Md5CalculatingInputStream.java
- src/main/java/htsjdk/samtools/util/Md5CalculatingOutputStream.java
- src/main/java/htsjdk/samtools/util/MergingIterator.java
- src/main/java/htsjdk/samtools/util/Murmur3.java
- src/main/java/htsjdk/samtools/util/OverlapDetector.java
- src/main/java/htsjdk/samtools/util/PeekIterator.java
- src/main/java/htsjdk/samtools/util/PeekableIterator.java
- src/main/java/htsjdk/samtools/util/PositionalOutputStream.java
- src/main/java/htsjdk/samtools/util/ProcessExecutor.java
- src/main/java/htsjdk/samtools/util/ProgressLogger.java
- src/main/java/htsjdk/samtools/util/ProgressLoggerInterface.java
- src/main/java/htsjdk/samtools/util/QualityEncodingDetector.java
- src/main/java/htsjdk/samtools/util/QualityUtil.java
- src/main/java/htsjdk/samtools/util/ResourceLimitedMap.java
- src/main/java/htsjdk/samtools/util/RuntimeEOFException.java
- src/main/java/htsjdk/samtools/util/RuntimeIOException.java
- src/main/java/htsjdk/samtools/util/RuntimeScriptException.java
- src/main/java/htsjdk/samtools/util/SAMRecordPrefetchingIterator.java
- src/main/java/htsjdk/samtools/util/SamConstants.java
- src/main/java/htsjdk/samtools/util/SamLocusIterator.java
- src/main/java/htsjdk/samtools/util/SamRecordIntervalIteratorFactory.java
- src/main/java/htsjdk/samtools/util/SamRecordTrackingBuffer.java
- src/main/java/htsjdk/samtools/util/SamRecordWithOrdinal.java
- src/main/java/htsjdk/samtools/util/SequenceUtil.java
- src/main/java/htsjdk/samtools/util/SnappyLoader.java
- src/main/java/htsjdk/samtools/util/SnappyLoaderInternal.java
- src/main/java/htsjdk/samtools/util/SolexaQualityConverter.java
- src/main/java/htsjdk/samtools/util/SortingCollection.java
- src/main/java/htsjdk/samtools/util/SortingLongCollection.java
- src/main/java/htsjdk/samtools/util/StopWatch.java
- src/main/java/htsjdk/samtools/util/StringUtil.java
- src/main/java/htsjdk/samtools/util/TempStreamFactory.java
- src/main/java/htsjdk/samtools/util/TestUtil.java
- src/main/java/htsjdk/samtools/util/TrimmingUtil.java
- src/main/java/htsjdk/samtools/util/ftp/FTPClient.java
- src/main/java/htsjdk/samtools/util/ftp/FTPReply.java
- src/main/java/htsjdk/samtools/util/ftp/FTPStream.java
- src/main/java/htsjdk/samtools/util/ftp/FTPUtils.java
- src/main/java/htsjdk/samtools/util/htsget/HtsgetErrorResponse.java
- src/main/java/htsjdk/samtools/util/htsget/HtsgetMalformedResponseException.java
- src/main/java/htsjdk/samtools/util/htsget/HtsgetPOSTRequest.java
- src/main/java/htsjdk/samtools/util/htsget/HtsgetRequest.java
- src/main/java/htsjdk/samtools/util/htsget/HtsgetResponse.java
- src/main/java/htsjdk/samtools/util/nio/DeleteOnExitPathHook.java
- src/main/java/htsjdk/samtools/util/zip/DeflaterFactory.java
- src/main/java/htsjdk/samtools/util/zip/InflaterFactory.java
- + src/main/java/htsjdk/samtools/util/zip/LibdeflateDeflater.java
- + src/main/java/htsjdk/samtools/util/zip/LibdeflateInflater.java
- src/main/java/htsjdk/tribble/AbstractFeatureCodec.java
- src/main/java/htsjdk/tribble/AbstractFeatureReader.java
- src/main/java/htsjdk/tribble/AsciiFeatureCodec.java
- src/main/java/htsjdk/tribble/BinaryFeatureCodec.java
- src/main/java/htsjdk/tribble/Feature.java
- src/main/java/htsjdk/tribble/FeatureCodec.java
- src/main/java/htsjdk/tribble/FeatureCodecHeader.java
- src/main/java/htsjdk/tribble/FeatureReader.java
- src/main/java/htsjdk/tribble/IntervalList/IntervalListCodec.java
- src/main/java/htsjdk/tribble/MutableFeature.java
- src/main/java/htsjdk/tribble/NameAwareCodec.java
- src/main/java/htsjdk/tribble/NamedFeature.java
- src/main/java/htsjdk/tribble/TabixFeatureReader.java
- src/main/java/htsjdk/tribble/Tribble.java
- src/main/java/htsjdk/tribble/TribbleException.java
- src/main/java/htsjdk/tribble/TribbleIndexedFeatureReader.java
- src/main/java/htsjdk/tribble/annotation/Strand.java
- src/main/java/htsjdk/tribble/bed/BEDCodec.java
- src/main/java/htsjdk/tribble/bed/BEDFeature.java
- src/main/java/htsjdk/tribble/bed/FullBEDFeature.java
- src/main/java/htsjdk/tribble/bed/SimpleBEDFeature.java
- src/main/java/htsjdk/tribble/example/CountRecords.java
- src/main/java/htsjdk/tribble/example/ExampleBinaryCodec.java
- src/main/java/htsjdk/tribble/example/IndexToTable.java
- src/main/java/htsjdk/tribble/example/IndicesAreEqual.java
- src/main/java/htsjdk/tribble/example/ProfileIndexReading.java
- src/main/java/htsjdk/tribble/exception/CodecLineParsingException.java
- src/main/java/htsjdk/tribble/exception/UnsortedFileException.java
- src/main/java/htsjdk/tribble/gff/Gff3BaseData.java
- src/main/java/htsjdk/tribble/gff/Gff3Codec.java
- src/main/java/htsjdk/tribble/gff/Gff3Constants.java
- src/main/java/htsjdk/tribble/gff/Gff3Feature.java
- src/main/java/htsjdk/tribble/gff/Gff3FeatureImpl.java
- src/main/java/htsjdk/tribble/gff/Gff3Writer.java
- src/main/java/htsjdk/tribble/gff/SequenceRegion.java
- src/main/java/htsjdk/tribble/index/AbstractIndex.java
- src/main/java/htsjdk/tribble/index/Block.java
- src/main/java/htsjdk/tribble/index/ChrIndex.java
- src/main/java/htsjdk/tribble/index/DynamicIndexCreator.java
- src/main/java/htsjdk/tribble/index/Index.java
- src/main/java/htsjdk/tribble/index/IndexCreator.java
- src/main/java/htsjdk/tribble/index/IndexFactory.java
- src/main/java/htsjdk/tribble/index/TribbleIndexCreator.java
- src/main/java/htsjdk/tribble/index/interval/Interval.java
- src/main/java/htsjdk/tribble/index/interval/IntervalIndexCreator.java
- src/main/java/htsjdk/tribble/index/interval/IntervalTree.java
- src/main/java/htsjdk/tribble/index/interval/IntervalTreeIndex.java
- src/main/java/htsjdk/tribble/index/linear/LinearIndex.java
- src/main/java/htsjdk/tribble/index/linear/LinearIndexCreator.java
- src/main/java/htsjdk/tribble/index/tabix/AllRefsTabixIndexCreator.java
- src/main/java/htsjdk/tribble/index/tabix/StreamBasedTabixIndexCreator.java
- src/main/java/htsjdk/tribble/index/tabix/TabixFormat.java
- src/main/java/htsjdk/tribble/index/tabix/TabixIndex.java
- src/main/java/htsjdk/tribble/index/tabix/TabixIndexCreator.java
- src/main/java/htsjdk/tribble/index/tabix/TabixIndexMerger.java
- src/main/java/htsjdk/tribble/readers/AsciiLineReader.java
- src/main/java/htsjdk/tribble/readers/AsciiLineReaderIterator.java
- src/main/java/htsjdk/tribble/readers/BlockCompressedAsciiLineReader.java
- src/main/java/htsjdk/tribble/readers/LineIteratorImpl.java
- src/main/java/htsjdk/tribble/readers/LineReader.java
- src/main/java/htsjdk/tribble/readers/LongLineBufferedReader.java
- src/main/java/htsjdk/tribble/readers/Positional.java
- src/main/java/htsjdk/tribble/readers/PositionalBufferedStream.java
- src/main/java/htsjdk/tribble/readers/SynchronousLineReader.java
- src/main/java/htsjdk/tribble/readers/TabixIteratorLineReader.java
- src/main/java/htsjdk/tribble/readers/TabixReader.java
- src/main/java/htsjdk/tribble/util/FTPHelper.java
- src/main/java/htsjdk/tribble/util/HTTPHelper.java
- src/main/java/htsjdk/tribble/util/LittleEndianInputStream.java
- src/main/java/htsjdk/tribble/util/LittleEndianOutputStream.java
- src/main/java/htsjdk/tribble/util/MathUtils.java
- src/main/java/htsjdk/tribble/util/ParsingUtils.java
- src/main/java/htsjdk/tribble/util/TabixUtils.java
- src/main/java/htsjdk/tribble/util/URLHelper.java
- src/main/java/htsjdk/tribble/util/URLHelperFactory.java
- src/main/java/htsjdk/tribble/util/popgen/HardyWeinbergCalculation.java
- src/main/java/htsjdk/utils/ClassFinder.java
- src/main/java/htsjdk/utils/ValidationUtils.java
- src/main/java/htsjdk/variant/bcf2/BCF2Codec.java
- src/main/java/htsjdk/variant/bcf2/BCF2Decoder.java
- src/main/java/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.java
- src/main/java/htsjdk/variant/bcf2/BCF2LazyGenotypesDecoder.java
- src/main/java/htsjdk/variant/bcf2/BCF2Type.java
- src/main/java/htsjdk/variant/bcf2/BCF2Utils.java
- src/main/java/htsjdk/variant/bcf2/BCFVersion.java
- src/main/java/htsjdk/variant/example/PrintVariantsExample.java
- src/main/java/htsjdk/variant/utils/BinomialCoefficientUtil.java
- src/main/java/htsjdk/variant/utils/GeneralUtils.java
- src/main/java/htsjdk/variant/utils/SAMSequenceDictionaryExtractor.java
- src/main/java/htsjdk/variant/utils/VCFHeaderReader.java
- src/main/java/htsjdk/variant/variantcontext/Allele.java
- src/main/java/htsjdk/variant/variantcontext/CommonInfo.java
- src/main/java/htsjdk/variant/variantcontext/FastGenotype.java
- src/main/java/htsjdk/variant/variantcontext/Genotype.java
- src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java
- src/main/java/htsjdk/variant/variantcontext/GenotypeJEXLContext.java
- src/main/java/htsjdk/variant/variantcontext/GenotypeLikelihoods.java
- src/main/java/htsjdk/variant/variantcontext/GenotypeNumLikelihoodsCache.java
- src/main/java/htsjdk/variant/variantcontext/GenotypeType.java
- src/main/java/htsjdk/variant/variantcontext/GenotypesContext.java
- src/main/java/htsjdk/variant/variantcontext/JEXLMap.java
- src/main/java/htsjdk/variant/variantcontext/JexlMissingValueTreatment.java
- src/main/java/htsjdk/variant/variantcontext/LazyGenotypesContext.java
- src/main/java/htsjdk/variant/variantcontext/SimpleAllele.java
- src/main/java/htsjdk/variant/variantcontext/StructuralVariantType.java
- src/main/java/htsjdk/variant/variantcontext/VariantContext.java
- src/main/java/htsjdk/variant/variantcontext/VariantContextBuilder.java
- src/main/java/htsjdk/variant/variantcontext/VariantContextComparator.java
- src/main/java/htsjdk/variant/variantcontext/VariantContextUtils.java
- src/main/java/htsjdk/variant/variantcontext/VariantJEXLContext.java
- src/main/java/htsjdk/variant/variantcontext/filter/CompoundFilter.java
- src/main/java/htsjdk/variant/variantcontext/filter/FilteringIterator.java
- src/main/java/htsjdk/variant/variantcontext/filter/FilteringVariantContextIterator.java
- src/main/java/htsjdk/variant/variantcontext/filter/GenotypeQualityFilter.java
- src/main/java/htsjdk/variant/variantcontext/filter/HeterozygosityFilter.java
- src/main/java/htsjdk/variant/variantcontext/filter/JavascriptVariantFilter.java
- src/main/java/htsjdk/variant/variantcontext/filter/VariantContextFilter.java
- src/main/java/htsjdk/variant/variantcontext/writer/AsyncVariantContextWriter.java
- src/main/java/htsjdk/variant/variantcontext/writer/BCF2Encoder.java
- src/main/java/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.java
- src/main/java/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.java
- src/main/java/htsjdk/variant/variantcontext/writer/BCF2FieldWriterManager.java
- src/main/java/htsjdk/variant/variantcontext/writer/BCF2Writer.java
- src/main/java/htsjdk/variant/variantcontext/writer/IndexingVariantContextWriter.java
- src/main/java/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.java
- src/main/java/htsjdk/variant/variantcontext/writer/Options.java
- src/main/java/htsjdk/variant/variantcontext/writer/SortingVariantContextWriter.java
- src/main/java/htsjdk/variant/variantcontext/writer/SortingVariantContextWriterBase.java
- src/main/java/htsjdk/variant/variantcontext/writer/VCFWriter.java
- src/main/java/htsjdk/variant/variantcontext/writer/VariantContextWriter.java
- src/main/java/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.java
- src/main/java/htsjdk/variant/vcf/AbstractVCFCodec.java
- src/main/java/htsjdk/variant/vcf/VCF3Codec.java
- src/main/java/htsjdk/variant/vcf/VCFAltHeaderLine.java
- src/main/java/htsjdk/variant/vcf/VCFCodec.java
- src/main/java/htsjdk/variant/vcf/VCFCompoundHeaderLine.java
- src/main/java/htsjdk/variant/vcf/VCFConstants.java
- src/main/java/htsjdk/variant/vcf/VCFContigHeaderLine.java
- src/main/java/htsjdk/variant/vcf/VCFEncoder.java
- src/main/java/htsjdk/variant/vcf/VCFFileReader.java
- src/main/java/htsjdk/variant/vcf/VCFFilterHeaderLine.java
- src/main/java/htsjdk/variant/vcf/VCFFormatHeaderLine.java
- src/main/java/htsjdk/variant/vcf/VCFHeader.java
- src/main/java/htsjdk/variant/vcf/VCFHeaderLine.java
- src/main/java/htsjdk/variant/vcf/VCFHeaderLineCount.java
- src/main/java/htsjdk/variant/vcf/VCFHeaderLineTranslator.java
- src/main/java/htsjdk/variant/vcf/VCFHeaderLineType.java
- src/main/java/htsjdk/variant/vcf/VCFHeaderVersion.java
- src/main/java/htsjdk/variant/vcf/VCFIDHeaderLine.java
- src/main/java/htsjdk/variant/vcf/VCFInfoHeaderLine.java
- src/main/java/htsjdk/variant/vcf/VCFIterator.java
- src/main/java/htsjdk/variant/vcf/VCFIteratorBuilder.java
- src/main/java/htsjdk/variant/vcf/VCFMetaHeaderLine.java
- src/main/java/htsjdk/variant/vcf/VCFPedigreeHeaderLine.java
- src/main/java/htsjdk/variant/vcf/VCFPercentEncodedTextTransformer.java
- src/main/java/htsjdk/variant/vcf/VCFReader.java
- src/main/java/htsjdk/variant/vcf/VCFRecordCodec.java
- src/main/java/htsjdk/variant/vcf/VCFSampleHeaderLine.java
- src/main/java/htsjdk/variant/vcf/VCFSimpleHeaderLine.java
- src/main/java/htsjdk/variant/vcf/VCFStandardHeaderLines.java
- src/main/java/htsjdk/variant/vcf/VCFTextTransformer.java
- src/main/java/htsjdk/variant/vcf/VCFUtils.java
- src/test/java/htsjdk/HtsjdkTest.java
- src/test/java/htsjdk/TestClassDependenceTest.java
- src/test/java/htsjdk/TestDataProviders.java
- src/test/java/htsjdk/beta/codecs/hapref/fasta/HaploidReferenceResolverTest.java
- src/test/java/htsjdk/beta/codecs/hapref/fasta/HtsFASTACodecTest.java
- src/test/java/htsjdk/beta/codecs/reads/bam/BAMDecoderOptionsTest.java
- src/test/java/htsjdk/beta/codecs/reads/bam/BAMEncoderOptionsTest.java
- src/test/java/htsjdk/beta/codecs/reads/bam/HtsBAMCodecTest.java
- src/test/java/htsjdk/beta/codecs/reads/bam/HtsBAMDecoderQueryTest.java
- src/test/java/htsjdk/beta/codecs/reads/cram/CRAMDecoderOptionsTest.java
- src/test/java/htsjdk/beta/codecs/reads/cram/CRAMEncoderOptionsTest.java
- src/test/java/htsjdk/beta/codecs/reads/cram/HtsCRAMCodec21Test.java
- src/test/java/htsjdk/beta/codecs/reads/cram/HtsCRAMCodec30And21QueryTest.java
- src/test/java/htsjdk/beta/codecs/reads/cram/HtsCRAMCodec30Test.java
- src/test/java/htsjdk/beta/codecs/reads/cram/HtsCRAMCodec31Test.java
- src/test/java/htsjdk/beta/codecs/reads/htsget/HtsgetBAM/HtsgetBAMCodecTest.java
- src/test/java/htsjdk/beta/codecs/reads/sam/SAMCodecV1_0Test.java
- src/test/java/htsjdk/beta/codecs/variants/vcf/HtsVCFCodecTest.java
- src/test/java/htsjdk/beta/io/bundle/BundleJSONTest.java
- src/test/java/htsjdk/beta/io/bundle/BundleResourceTest.java
- src/test/java/htsjdk/beta/io/bundle/BundleResourceTestData.java
- src/test/java/htsjdk/beta/io/bundle/BundleTest.java
- src/test/java/htsjdk/beta/io/bundle/InputStreamResourceTest.java
- src/test/java/htsjdk/beta/io/bundle/OutputStreamResourceTest.java
- src/test/java/htsjdk/beta/io/bundle/SeekableStreamResourceTest.java
- src/test/java/htsjdk/beta/io/bundle/SignatureStreamTest.java
- src/test/java/htsjdk/beta/plugin/HtsVersionTest.java
- src/test/java/htsjdk/beta/plugin/reads/ReadsBundleTest.java
- src/test/java/htsjdk/beta/plugin/reads/ReadsDecoderOptionsTest.java
- src/test/java/htsjdk/beta/plugin/registry/HtsCodecRegistryTest.java
- src/test/java/htsjdk/beta/plugin/registry/HtsCodecResolverTest.java
- src/test/java/htsjdk/beta/plugin/registry/HtsReadsCodecTest.java
- src/test/java/htsjdk/beta/plugin/registry/testcodec/HtsTestCodec.java
- src/test/java/htsjdk/beta/plugin/registry/testcodec/HtsTestCodecFormats.java
- src/test/java/htsjdk/beta/plugin/registry/testcodec/HtsTestDecoder.java
- src/test/java/htsjdk/beta/plugin/registry/testcodec/HtsTestEncoder.java
- src/test/java/htsjdk/beta/plugin/variants/VariantsBundleTest.java
- src/test/java/htsjdk/io/AsyncWriterPoolTest.java
- src/test/java/htsjdk/io/HtsPathUnitTest.java
- src/test/java/htsjdk/io/IOPathUtilsTest.java
- src/test/java/htsjdk/samtools/AbstractBAMFileIndexTest.java
- src/test/java/htsjdk/samtools/BAMCigarOverflowTest.java
- src/test/java/htsjdk/samtools/BAMFileIndexTest.java
- src/test/java/htsjdk/samtools/BAMFileReaderTest.java
- src/test/java/htsjdk/samtools/BAMFileSpanTest.java
- src/test/java/htsjdk/samtools/BAMFileWriterTest.java
- src/test/java/htsjdk/samtools/BAMIndexValidatorTest.java
- src/test/java/htsjdk/samtools/BAMIndexWriterTest.java
- src/test/java/htsjdk/samtools/BAMIteratorTest.java
- src/test/java/htsjdk/samtools/BAMMergerTest.java
- src/test/java/htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilterTest.java
- src/test/java/htsjdk/samtools/BAMRemoteFileTest.java
- src/test/java/htsjdk/samtools/BAMSBIIndexerTest.java
- src/test/java/htsjdk/samtools/BaiEqualityChecker.java
- src/test/java/htsjdk/samtools/BamFileIoUtilsUnitTest.java
- src/test/java/htsjdk/samtools/BinTest.java
- src/test/java/htsjdk/samtools/BinningIndexBuilderTest.java
- src/test/java/htsjdk/samtools/CRAMAllEncodingStrategiesTest.java
- src/test/java/htsjdk/samtools/CRAMBAIIndexerTest.java
- src/test/java/htsjdk/samtools/CRAMCRAIIndexerTest.java
- src/test/java/htsjdk/samtools/CRAMComplianceTest.java
- src/test/java/htsjdk/samtools/CRAMContainerStreamWriterTest.java
- src/test/java/htsjdk/samtools/CRAMEdgeCasesTest.java
- src/test/java/htsjdk/samtools/CRAMFileBAIIndexTest.java
- src/test/java/htsjdk/samtools/CRAMFileCRAIIndexTest.java
- src/test/java/htsjdk/samtools/CRAMFileReaderTest.java
- src/test/java/htsjdk/samtools/CRAMFileWriterTest.java
- src/test/java/htsjdk/samtools/CRAMFileWriterWithIndexTest.java
- src/test/java/htsjdk/samtools/CRAMIndexPermutationsTests.java
- src/test/java/htsjdk/samtools/CRAMIndexQueryTest.java
- src/test/java/htsjdk/samtools/CRAMIndexTestHelper.java
- src/test/java/htsjdk/samtools/CRAMIteratorTest.java
- src/test/java/htsjdk/samtools/CRAMMergerTest.java
- src/test/java/htsjdk/samtools/CRAMReferencelessTest.java
- src/test/java/htsjdk/samtools/CRAMSliceMD5Test.java
- src/test/java/htsjdk/samtools/CRAMTestUtils.java
- src/test/java/htsjdk/samtools/CSIIndexTest.java
- src/test/java/htsjdk/samtools/CachingBAMFileIndexTest.java
- src/test/java/htsjdk/samtools/ChunkTest.java
- src/test/java/htsjdk/samtools/CigarCodecTest.java
- src/test/java/htsjdk/samtools/CigarOperatorUnitTest.java
- src/test/java/htsjdk/samtools/CigarTest.java
- src/test/java/htsjdk/samtools/CramContainerHeaderIteratorTest.java
- src/test/java/htsjdk/samtools/DownsamplingIteratorTests.java
- src/test/java/htsjdk/samtools/DuplicateScoringStrategyTest.java
- src/test/java/htsjdk/samtools/DuplicateSetIteratorTest.java
- src/test/java/htsjdk/samtools/GenomicIndexUtilTest.java
- src/test/java/htsjdk/samtools/HtsgetBAMFileReaderTest.java
- src/test/java/htsjdk/samtools/HtsjdkTestUtils.java
- src/test/java/htsjdk/samtools/LongReadsTest.java
- src/test/java/htsjdk/samtools/MergingSamRecordIteratorGroupCollisionTest.java
- src/test/java/htsjdk/samtools/MergingSamRecordIteratorTest.java
- src/test/java/htsjdk/samtools/PathInputResourceTest.java
- src/test/java/htsjdk/samtools/ProgramRecordChainingTest.java
- src/test/java/htsjdk/samtools/QueryIntervalTest.java
- src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java
- src/test/java/htsjdk/samtools/SAMFileHeaderTest.java
- src/test/java/htsjdk/samtools/SAMFileWriterFactoryTest.java
- src/test/java/htsjdk/samtools/SAMFileWriterTest.java
- src/test/java/htsjdk/samtools/SAMIntegerTagTest.java
- src/test/java/htsjdk/samtools/SAMProgramRecordTest.java
- src/test/java/htsjdk/samtools/SAMReadGroupRecordTest.java
- src/test/java/htsjdk/samtools/SAMRecordDuplicateComparatorTest.java
- src/test/java/htsjdk/samtools/SAMRecordQueryHashComparatorTest.java
- src/test/java/htsjdk/samtools/SAMRecordQueryNameComparatorTest.java
- src/test/java/htsjdk/samtools/SAMRecordSetBuilderTest.java
- src/test/java/htsjdk/samtools/SAMRecordUnitTest.java
- src/test/java/htsjdk/samtools/SAMSequenceDictionaryCodecTest.java
- src/test/java/htsjdk/samtools/SAMSequenceDictionaryTest.java
- src/test/java/htsjdk/samtools/SAMSequenceRecordTest.java
- src/test/java/htsjdk/samtools/SAMTextReaderTest.java
- src/test/java/htsjdk/samtools/SAMTextWriterTest.java
- src/test/java/htsjdk/samtools/SAMUtilsTest.java
- src/test/java/htsjdk/samtools/SamFileHeaderMergerTest.java
- src/test/java/htsjdk/samtools/SamFilesTest.java
- src/test/java/htsjdk/samtools/SamFlagFieldTest.java
- src/test/java/htsjdk/samtools/SamHeaderRecordComparatorTest.java
- src/test/java/htsjdk/samtools/SamIndexesTest.java
- src/test/java/htsjdk/samtools/SamPairUtilTest.java
- src/test/java/htsjdk/samtools/SamReaderFactoryTest.java
- src/test/java/htsjdk/samtools/SamReaderSortTest.java
- src/test/java/htsjdk/samtools/SamReaderTest.java
- src/test/java/htsjdk/samtools/SamSpecIntTest.java
- src/test/java/htsjdk/samtools/SamStreamsTest.java
- src/test/java/htsjdk/samtools/SequenceNameTruncationAndValidationTest.java
- src/test/java/htsjdk/samtools/TextTagCodecTest.java
- src/test/java/htsjdk/samtools/ValidateSamFileTest.java
- src/test/java/htsjdk/samtools/cram/BAIEntryTest.java
- src/test/java/htsjdk/samtools/cram/CRAIEntryTest.java
- src/test/java/htsjdk/samtools/cram/CRAIIndexTest.java
- + src/test/java/htsjdk/samtools/cram/CRAIQueryTest.java
- − src/test/java/htsjdk/samtools/cram/CRAM31Tests.java
- src/test/java/htsjdk/samtools/cram/CRAMInteropTestUtils.java
- src/test/java/htsjdk/samtools/cram/CRAMVersionTest.java
- + src/test/java/htsjdk/samtools/cram/CramComparisonTest.java
- src/test/java/htsjdk/samtools/cram/FQZCompInteropTest.java
- src/test/java/htsjdk/samtools/cram/LosslessRoundTripTest.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/CompressionHeaderFactoryTest.java
- src/test/java/htsjdk/samtools/cram/build/ContainerFactoryTest.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/CodecRoundTripPropertyTest.java
- + src/test/java/htsjdk/samtools/cram/compression/CompressionUtilsTest.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/TrialCompressorTest.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/cram31/CRAM31ArchiveFidelityTest.java
- + src/test/java/htsjdk/samtools/cram/cram31/CRAM31FastFidelityTest.java
- + src/test/java/htsjdk/samtools/cram/cram31/CRAM31FidelityTestBase.java
- + src/test/java/htsjdk/samtools/cram/cram31/CRAM31NormalFidelityTest.java
- + src/test/java/htsjdk/samtools/cram/cram31/CRAM31SmallFidelityTest.java
- src/test/java/htsjdk/samtools/cram/encoding/ByteArrayLenCodecTest.java
- src/test/java/htsjdk/samtools/cram/encoding/ByteArrayLenEncodingTest.java
- src/test/java/htsjdk/samtools/cram/encoding/CramRecordWriterReaderTest.java
- src/test/java/htsjdk/samtools/cram/encoding/DataSeriesReaderTest.java
- src/test/java/htsjdk/samtools/cram/encoding/DataSeriesWriterTest.java
- src/test/java/htsjdk/samtools/cram/encoding/ReadFeaturesTest.java
- src/test/java/htsjdk/samtools/cram/encoding/core/BetaIntegerCodecTest.java
- src/test/java/htsjdk/samtools/cram/encoding/core/BetaIntegerEncodingTest.java
- src/test/java/htsjdk/samtools/cram/encoding/core/CanoncialHuffmanByteEncodingTest.java
- src/test/java/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanIntegerEncodingTest.java
- src/test/java/htsjdk/samtools/cram/encoding/core/GammaIntegerCodecTest.java
- src/test/java/htsjdk/samtools/cram/encoding/core/GammaIntegerEncodingTest.java
- src/test/java/htsjdk/samtools/cram/encoding/core/HuffmanTest.java
- src/test/java/htsjdk/samtools/cram/encoding/core/SubexponentialIntegerCodecTest.java
- src/test/java/htsjdk/samtools/cram/encoding/core/SubexponentialIntegerEncodingTest.java
- src/test/java/htsjdk/samtools/cram/encoding/external/ByteArrayStopCodecTest.java
- src/test/java/htsjdk/samtools/cram/encoding/external/ByteArrayStopEncodingTest.java
- src/test/java/htsjdk/samtools/cram/encoding/external/ExternalByteArrayCodecTest.java
- src/test/java/htsjdk/samtools/cram/encoding/external/ExternalByteCodecTest.java
- src/test/java/htsjdk/samtools/cram/encoding/external/ExternalCodecEquivalenceTest.java
- src/test/java/htsjdk/samtools/cram/encoding/external/ExternalEncodingTest.java
- src/test/java/htsjdk/samtools/cram/encoding/external/ExternalIntegerCodecTest.java
- src/test/java/htsjdk/samtools/cram/encoding/external/ExternalLongCodecTest.java
- + src/test/java/htsjdk/samtools/cram/io/CRAMByteReaderWriterTest.java
- src/test/java/htsjdk/samtools/cram/io/CramIntArrayTest.java
- src/test/java/htsjdk/samtools/cram/io/CramIntTest.java
- src/test/java/htsjdk/samtools/cram/io/IOTestCases.java
- src/test/java/htsjdk/samtools/cram/io/ITF8Test.java
- src/test/java/htsjdk/samtools/cram/io/InputStreamUtilsTest.java
- src/test/java/htsjdk/samtools/cram/io/LTF8Test.java
- src/test/java/htsjdk/samtools/cram/ref/CRAMReferenceRegionTest.java
- src/test/java/htsjdk/samtools/cram/ref/EnaRefServiceTest.java
- src/test/java/htsjdk/samtools/cram/ref/ReferenceContextTest.java
- src/test/java/htsjdk/samtools/cram/ref/ReferenceSourceTest.java
- + src/test/java/htsjdk/samtools/cram/spec30/HtsSpecsComplianceTestBase.java
- + src/test/java/htsjdk/samtools/cram/spec30/Spec30CompressionTest.java
- + src/test/java/htsjdk/samtools/cram/spec30/Spec30ContainerTest.java
- + src/test/java/htsjdk/samtools/cram/spec30/Spec30CornerCaseTest.java
- + src/test/java/htsjdk/samtools/cram/spec30/Spec30DataLayoutTest.java
- + src/test/java/htsjdk/samtools/cram/spec30/Spec30EmbeddedRefTest.java
- + src/test/java/htsjdk/samtools/cram/spec30/Spec30FileDefinitionTest.java
- + src/test/java/htsjdk/samtools/cram/spec30/Spec30HeaderTest.java
- + src/test/java/htsjdk/samtools/cram/spec30/Spec30IndexTest.java
- + src/test/java/htsjdk/samtools/cram/spec30/Spec30LevelTest.java
- + src/test/java/htsjdk/samtools/cram/spec30/Spec30LossyTest.java
- + src/test/java/htsjdk/samtools/cram/spec30/Spec30MappedNoRefTest.java
- + src/test/java/htsjdk/samtools/cram/spec30/Spec30MappedWithRefTest.java
- + src/test/java/htsjdk/samtools/cram/spec30/Spec30MultiContainerTest.java
- + src/test/java/htsjdk/samtools/cram/spec30/Spec30RoundTripBasicTest.java
- + src/test/java/htsjdk/samtools/cram/spec30/Spec30RoundTripIndexTest.java
- + src/test/java/htsjdk/samtools/cram/spec30/Spec30RoundTripTagsAndLayoutTest.java
- + src/test/java/htsjdk/samtools/cram/spec30/Spec30SliceTagTest.java
- + src/test/java/htsjdk/samtools/cram/spec30/Spec30TagTest.java
- + src/test/java/htsjdk/samtools/cram/spec30/Spec30UnmappedTest.java
- + src/test/java/htsjdk/samtools/cram/spec30/Spec31ComplianceTest.java
- src/test/java/htsjdk/samtools/cram/structure/AlignmentContextTest.java
- src/test/java/htsjdk/samtools/cram/structure/AlignmentSpanTest.java
- + src/test/java/htsjdk/samtools/cram/structure/CRAMCompressionProfileTest.java
- src/test/java/htsjdk/samtools/cram/structure/CRAMCompressionRecordTest.java
- src/test/java/htsjdk/samtools/cram/structure/CRAMRecordTestHelper.java
- src/test/java/htsjdk/samtools/cram/structure/CRAMStructureTestHelper.java
- src/test/java/htsjdk/samtools/cram/structure/CompressionHeaderEncodingMapTest.java
- src/test/java/htsjdk/samtools/cram/structure/ContainerTest.java
- src/test/java/htsjdk/samtools/cram/structure/DataSeriesTest.java
- src/test/java/htsjdk/samtools/cram/structure/ReadTagTest.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/SliceTests.java
- src/test/java/htsjdk/samtools/cram/structure/StructureTestUtils.java
- src/test/java/htsjdk/samtools/cram/structure/SubstitutionMatrixTest.java
- + src/test/java/htsjdk/samtools/cram/structure/TagKeyCacheTest.java
- src/test/java/htsjdk/samtools/cram/structure/block/BlockTest.java
- src/test/java/htsjdk/samtools/cram/structure/block/CRAMRecordReadFeaturesTest.java
- src/test/java/htsjdk/samtools/fastq/BasicFastqWriterTest.java
- src/test/java/htsjdk/samtools/fastq/FastqEncoderTest.java
- src/test/java/htsjdk/samtools/fastq/FastqRecordTest.java
- src/test/java/htsjdk/samtools/filter/FailsVendorReadQualityFilterTest.java
- src/test/java/htsjdk/samtools/filter/InsertSizeFilterTest.java
- src/test/java/htsjdk/samtools/filter/IntervalFilterTest.java
- src/test/java/htsjdk/samtools/filter/IntervalKeepPairFilterTest.java
- src/test/java/htsjdk/samtools/filter/JavascriptSamRecordFilterTest.java
- src/test/java/htsjdk/samtools/filter/MappingQualityFilterTest.java
- src/test/java/htsjdk/samtools/filter/OverclippedReadFilterTest.java
- src/test/java/htsjdk/samtools/filter/ReadNameFilterTest.java
- src/test/java/htsjdk/samtools/filter/SecondaryAlignmentFilterTest.java
- src/test/java/htsjdk/samtools/filter/SecondaryOrSupplementaryFilterTest.java
- src/test/java/htsjdk/samtools/filter/SolexaNoiseFilterTest.java
- src/test/java/htsjdk/samtools/filter/TagFilterTest.java
- src/test/java/htsjdk/samtools/liftover/LiftOverTest.java
- src/test/java/htsjdk/samtools/metrics/MetricBaseTest.java
- src/test/java/htsjdk/samtools/metrics/MetricsFileTest.java
- src/test/java/htsjdk/samtools/metrics/StringHeaderTest.java
- src/test/java/htsjdk/samtools/metrics/VersionHeaderTest.java
- src/test/java/htsjdk/samtools/reference/AbstractFastaSequenceFileTest.java
- src/test/java/htsjdk/samtools/reference/AbstractIndexedFastaSequenceFileTest.java
- src/test/java/htsjdk/samtools/reference/FakeReferenceSequenceFile.java
- src/test/java/htsjdk/samtools/reference/FastaReferenceWriterTest.java
- src/test/java/htsjdk/samtools/reference/FastaSequenceFileTest.java
- src/test/java/htsjdk/samtools/reference/FastaSequenceIndexCreatorTest.java
- src/test/java/htsjdk/samtools/reference/FastaSequenceIndexTest.java
- src/test/java/htsjdk/samtools/reference/InMemoryReferenceSequenceFile.java
- src/test/java/htsjdk/samtools/reference/ReferenceSequenceFileFactoryTests.java
- src/test/java/htsjdk/samtools/reference/ReferenceSequenceFileWalkerTest.java
- src/test/java/htsjdk/samtools/reference/ReferenceSequenceTests.java
- src/test/java/htsjdk/samtools/reference/SamLocusAndReferenceIteratorTest.java
- src/test/java/htsjdk/samtools/seekablestream/ByteArraySeekableStreamTest.java
- src/test/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java
- src/test/java/htsjdk/samtools/seekablestream/SeekableFTPStreamTest.java
- src/test/java/htsjdk/samtools/seekablestream/SeekableFileStreamTest.java
- src/test/java/htsjdk/samtools/seekablestream/SeekableMemoryStreamTest.java
- src/test/java/htsjdk/samtools/seekablestream/SeekablePathStreamTest.java
- src/test/java/htsjdk/samtools/seekablestream/SeekableStreamFactoryTest.java
- src/test/java/htsjdk/samtools/seekablestream/SeekableStreamGZIPinputStreamIntegrationTest.java
- src/test/java/htsjdk/samtools/seekablestream/SeekableStreamTest.java
- − src/test/java/htsjdk/samtools/sra/AbstractSRATest.java
- − src/test/java/htsjdk/samtools/sra/SRAAccessionTest.java
- − src/test/java/htsjdk/samtools/sra/SRAIndexTest.java
- − src/test/java/htsjdk/samtools/sra/SRALazyRecordTest.java
- − src/test/java/htsjdk/samtools/sra/SRAQueryTest.java
- − src/test/java/htsjdk/samtools/sra/SRAReferenceTest.java
- − src/test/java/htsjdk/samtools/sra/SRATest.java
- src/test/java/htsjdk/samtools/util/AbstractLocusInfoTest.java
- src/test/java/htsjdk/samtools/util/AbstractLocusIteratorTestTemplate.java
- src/test/java/htsjdk/samtools/util/AbstractRecordAndOffsetTest.java
- src/test/java/htsjdk/samtools/util/AsyncBlockCompressedInputStreamTest.java
- src/test/java/htsjdk/samtools/util/AsyncBufferedIteratorTest.java
- src/test/java/htsjdk/samtools/util/AsyncWriterTest.java
- src/test/java/htsjdk/samtools/util/BinaryCodecTest.java
- src/test/java/htsjdk/samtools/util/BlockCompressedFilePointerUtilTest.java
- src/test/java/htsjdk/samtools/util/BlockCompressedInputStreamTest.java
- src/test/java/htsjdk/samtools/util/BlockCompressedOutputStreamTest.java
- src/test/java/htsjdk/samtools/util/BlockCompressedTerminatorTest.java
- src/test/java/htsjdk/samtools/util/BufferedLineReaderTest.java
- src/test/java/htsjdk/samtools/util/CigarElementUnitTest.java
- src/test/java/htsjdk/samtools/util/CigarUtilTest.java
- src/test/java/htsjdk/samtools/util/CloseableIteratorTest.java
- src/test/java/htsjdk/samtools/util/CodeUtilTest.java
- src/test/java/htsjdk/samtools/util/ComparableTupleTest.java
- src/test/java/htsjdk/samtools/util/CoordSpanInputSteamTest.java
- src/test/java/htsjdk/samtools/util/DateParserTest.java
- src/test/java/htsjdk/samtools/util/DiskBackedQueueTest.java
- src/test/java/htsjdk/samtools/util/EdgeReadIteratorTest.java
- src/test/java/htsjdk/samtools/util/EdgingRecordAndOffsetTest.java
- src/test/java/htsjdk/samtools/util/GZIIndexTest.java
- + src/test/java/htsjdk/samtools/util/GzipCodecTest.java
- src/test/java/htsjdk/samtools/util/HistogramTest.java
- src/test/java/htsjdk/samtools/util/HtsgetRequestUnitTest.java
- src/test/java/htsjdk/samtools/util/HtsgetResponseUnitTest.java
- src/test/java/htsjdk/samtools/util/HttpUtilsTest.java
- src/test/java/htsjdk/samtools/util/IOUtilTest.java
- src/test/java/htsjdk/samtools/util/IntervalCodecTest.java
- src/test/java/htsjdk/samtools/util/IntervalListTest.java
- src/test/java/htsjdk/samtools/util/IntervalListWriterTest.java
- src/test/java/htsjdk/samtools/util/IntervalTest.java
- src/test/java/htsjdk/samtools/util/IntervalTreeMapTest.java
- src/test/java/htsjdk/samtools/util/IntervalTreeTest.java
- src/test/java/htsjdk/samtools/util/IntervalUtilTest.java
- src/test/java/htsjdk/samtools/util/Iso8601DateTest.java
- src/test/java/htsjdk/samtools/util/IupacTest.java
- src/test/java/htsjdk/samtools/util/LocatableUnitTest.java
- src/test/java/htsjdk/samtools/util/LogTest.java
- src/test/java/htsjdk/samtools/util/Md5CalculatingOutputStreamTest.java
- src/test/java/htsjdk/samtools/util/MergingIteratorTest.java
- src/test/java/htsjdk/samtools/util/OverlapDetectorTest.java
- src/test/java/htsjdk/samtools/util/PositionalOutputStreamTest.java
- src/test/java/htsjdk/samtools/util/QualityEncodingDetectorTest.java
- src/test/java/htsjdk/samtools/util/QuietTestWrapper.java
- src/test/java/htsjdk/samtools/util/RelativeIso8601DateTest.java
- src/test/java/htsjdk/samtools/util/SAMRecordPrefetchingIteratorTest.java
- src/test/java/htsjdk/samtools/util/SamLocusIteratorTest.java
- src/test/java/htsjdk/samtools/util/SequenceUtilTest.java
- src/test/java/htsjdk/samtools/util/SnappyLoaderUnitTest.java
- src/test/java/htsjdk/samtools/util/SolexaQualityConverterTest.java
- src/test/java/htsjdk/samtools/util/SortingCollectionTest.java
- src/test/java/htsjdk/samtools/util/SortingLongCollectionTest.java
- src/test/java/htsjdk/samtools/util/TrimmingUtilTest.java
- src/test/java/htsjdk/samtools/util/TupleTest.java
- + src/test/java/htsjdk/samtools/util/zip/LibdeflateTest.java
- src/test/java/htsjdk/testutil/streams/SeekableByteChannelFromBuffer.java
- src/test/java/htsjdk/tribble/AbstractFeatureReaderTest.java
- src/test/java/htsjdk/tribble/AsciiFeatureCodecTest.java
- src/test/java/htsjdk/tribble/BinaryFeaturesTest.java
- src/test/java/htsjdk/tribble/FeatureReaderTest.java
- src/test/java/htsjdk/tribble/IntervalList/IntervalListCodecTest.java
- src/test/java/htsjdk/tribble/TestUtils.java
- src/test/java/htsjdk/tribble/TribbleIndexedFeatureReaderTest.java
- src/test/java/htsjdk/tribble/TribbleTest.java
- src/test/java/htsjdk/tribble/VCFRedirectCodec.java
- src/test/java/htsjdk/tribble/annotation/StrandTest.java
- src/test/java/htsjdk/tribble/bed/BEDCodecTest.java
- src/test/java/htsjdk/tribble/gff/Gff3CodecTest.java
- src/test/java/htsjdk/tribble/gff/Gff3FeatureTest.java
- src/test/java/htsjdk/tribble/gff/Gff3WriterTest.java
- src/test/java/htsjdk/tribble/index/IndexFactoryTest.java
- src/test/java/htsjdk/tribble/index/IndexTest.java
- src/test/java/htsjdk/tribble/index/interval/IntervalTreeTest.java
- src/test/java/htsjdk/tribble/index/linear/LinearIndexTest.java
- src/test/java/htsjdk/tribble/index/tabix/TabixIndexTest.java
- src/test/java/htsjdk/tribble/index/tabix/TbiEqualityChecker.java
- src/test/java/htsjdk/tribble/readers/AsciiLineReaderTest.java
- src/test/java/htsjdk/tribble/readers/BlockCompressedAsciiLineReaderTest.java
- src/test/java/htsjdk/tribble/readers/LongLineBufferedReaderTest.java
- src/test/java/htsjdk/tribble/readers/PositionalBufferedStreamTest.java
- src/test/java/htsjdk/tribble/readers/ReaderTest.java
- src/test/java/htsjdk/tribble/readers/SynchronousLineReaderUnitTest.java
- src/test/java/htsjdk/tribble/readers/TabixReaderTest.java
- src/test/java/htsjdk/tribble/util/ParsingUtilsTest.java
- src/test/java/htsjdk/tribble/util/ftp/FTPClientTest.java
- src/test/java/htsjdk/tribble/util/ftp/FTPUtilsTest.java
- src/test/java/htsjdk/tribble/util/popgen/HardyWeinbergCalculationTest.java
- src/test/java/htsjdk/utils/ClassFinderTest.java
- src/test/java/htsjdk/utils/SamtoolsTestUtils.java
- src/test/java/htsjdk/utils/SamtoolsTestUtilsTest.java
- src/test/java/htsjdk/utils/TestNGUtils.java
- src/test/java/htsjdk/utils/TestNGUtilsTest.java
- src/test/java/htsjdk/variant/PrintVariantsExampleTest.java
- src/test/java/htsjdk/variant/VariantBaseTest.java
- src/test/java/htsjdk/variant/bcf2/BCF2EncoderDecoderUnitTest.java
- src/test/java/htsjdk/variant/bcf2/BCF2UtilsUnitTest.java
- src/test/java/htsjdk/variant/bcf2/BCF2VersionTest.java
- src/test/java/htsjdk/variant/bcf2/BCF2WriterUnitTest.java
- src/test/java/htsjdk/variant/bcf2/BCFCodecTest.java
- src/test/java/htsjdk/variant/utils/SAMSequenceDictionaryExtractorTest.java
- src/test/java/htsjdk/variant/utils/VCFHeaderReaderTest.java
- src/test/java/htsjdk/variant/variantcontext/AlleleUnitTest.java
- src/test/java/htsjdk/variant/variantcontext/GenotypeBuilderTest.java
- src/test/java/htsjdk/variant/variantcontext/GenotypeLikelihoodsUnitTest.java
- src/test/java/htsjdk/variant/variantcontext/GenotypeUnitTest.java
- src/test/java/htsjdk/variant/variantcontext/GenotypesContextUnitTest.java
- src/test/java/htsjdk/variant/variantcontext/VariantContextBuilderTest.java
- src/test/java/htsjdk/variant/variantcontext/VariantContextTestProvider.java
- src/test/java/htsjdk/variant/variantcontext/VariantContextUnitTest.java
- src/test/java/htsjdk/variant/variantcontext/VariantJEXLContextUnitTest.java
- src/test/java/htsjdk/variant/variantcontext/filter/CompoundFilterTest.java
- src/test/java/htsjdk/variant/variantcontext/filter/FilteringVariantContextIteratorTest.java
- src/test/java/htsjdk/variant/variantcontext/filter/GenotypeQualityFilterTest.java
- src/test/java/htsjdk/variant/variantcontext/filter/HeterozygosityFilterTest.java
- src/test/java/htsjdk/variant/variantcontext/filter/JavascriptVariantFilterTest.java
- src/test/java/htsjdk/variant/variantcontext/filter/PassingVariantFilterTest.java
- src/test/java/htsjdk/variant/variantcontext/filter/SnpFilterTest.java
- src/test/java/htsjdk/variant/variantcontext/writer/AsyncVariantContextWriterUnitTest.java
- src/test/java/htsjdk/variant/variantcontext/writer/TabixOnTheFlyIndexCreationTest.java
- src/test/java/htsjdk/variant/variantcontext/writer/VCFWriterUnitTest.java
- src/test/java/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilderUnitTest.java
- src/test/java/htsjdk/variant/variantcontext/writer/VariantContextWritersUnitTest.java
- src/test/java/htsjdk/variant/vcf/AbstractVCFCodecTest.java
- src/test/java/htsjdk/variant/vcf/IndexFactoryUnitTest.java
- src/test/java/htsjdk/variant/vcf/VCFCodec42FeaturesTest.java
- src/test/java/htsjdk/variant/vcf/VCFCodec43FeaturesTest.java
- src/test/java/htsjdk/variant/vcf/VCFCompoundHeaderLineUnitTest.java
- src/test/java/htsjdk/variant/vcf/VCFEncoderTest.java
- src/test/java/htsjdk/variant/vcf/VCFFileReaderTest.java
- src/test/java/htsjdk/variant/vcf/VCFHeaderLineTranslatorUnitTest.java
- src/test/java/htsjdk/variant/vcf/VCFHeaderLineUnitTest.java
- src/test/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java
- src/test/java/htsjdk/variant/vcf/VCFHeaderVersionTest.java
- src/test/java/htsjdk/variant/vcf/VCFIteratorTest.java
- src/test/java/htsjdk/variant/vcf/VCFMergerTest.java
- src/test/java/htsjdk/variant/vcf/VCFStandardHeaderLinesUnitTest.java
- src/test/java/htsjdk/variant/vcf/VCFTextTransformerTest.java
- src/test/java/htsjdk/variant/vcf/VCFUtilsTest.java
- src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram
- src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram.crai
- src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.first.8000.bam
- + src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.first.8000.bam.bai
- src/test/resources/htsjdk/samtools/cram/amb#amb.sam
- src/test/resources/htsjdk/samtools/cram/auxf#values.sam
- src/test/resources/htsjdk/samtools/cram/c1#bounds.sam
- src/test/resources/htsjdk/samtools/cram/c1#clip.sam
- src/test/resources/htsjdk/samtools/cram/c1#noseq.sam
- src/test/resources/htsjdk/samtools/cram/c1#pad1.sam
- src/test/resources/htsjdk/samtools/cram/c1#pad2.sam
- src/test/resources/htsjdk/samtools/cram/c1#pad3.sam
- src/test/resources/htsjdk/samtools/cram/c1#unknown.sam
- src/test/resources/htsjdk/samtools/cram/c1WithRG.bam
- + src/test/resources/htsjdk/samtools/cram/c1WithRG.bam.bai
- src/test/resources/htsjdk/samtools/cram/c2#pad.sam
- src/test/resources/htsjdk/samtools/cram/ce#1.sam
- src/test/resources/htsjdk/samtools/cram/ce#1000.sam
- src/test/resources/htsjdk/samtools/cram/ce#2.sam
- src/test/resources/htsjdk/samtools/cram/ce#5.sam
- src/test/resources/htsjdk/samtools/cram/ce#5b.sam
- src/test/resources/htsjdk/samtools/cram/ce#large_seq.sam
- src/test/resources/htsjdk/samtools/cram/ce#supp.sam
- src/test/resources/htsjdk/samtools/cram/ce#tag_depadded.sam
- src/test/resources/htsjdk/samtools/cram/ce#tag_padded.sam
- src/test/resources/htsjdk/samtools/cram/ce#unmap.sam
- src/test/resources/htsjdk/samtools/cram/ce#unmap1.sam
- src/test/resources/htsjdk/samtools/cram/ce#unmap2.sam
- src/test/resources/htsjdk/samtools/cram/mateResolutionTest1.sam
- src/test/resources/htsjdk/samtools/cram/mateResolutionTest2.sam
- src/test/resources/htsjdk/samtools/cram/md#1.sam
- src/test/resources/htsjdk/samtools/cram/xx#large_aux.sam
- src/test/resources/htsjdk/samtools/cram/xx#large_aux2.sam
- src/test/resources/htsjdk/samtools/cram/xx#minimal.sam
- src/test/resources/htsjdk/samtools/cram/xx#pair.sam
- src/test/resources/htsjdk/samtools/cram/xx#repeated.sam
- src/test/resources/htsjdk/samtools/cram/xx#rg.sam
- src/test/resources/htsjdk/samtools/cram/xx#tlen.sam
- src/test/resources/htsjdk/samtools/cram/xx#tlen2.sam
- src/test/resources/htsjdk/samtools/cram/xx#triplet.sam
- src/test/resources/htsjdk/samtools/cram/xx#unsorted.sam
- − src/test/resources/htsjdk/samtools/samFilter01.js
- − src/test/resources/htsjdk/samtools/samFilter02.js
- − src/test/resources/htsjdk/samtools/sra/test_archive.sra
- − src/test/resources/htsjdk/variant/variantFilter01.js
- − src/test/resources/htsjdk/variant/variantFilter02.js
- − src/test/resources/testng.xml
- + validation/.gitignore
- + validation/README.md
- + validation/Snakefile
- + validation/config.yaml
- + validation/pixi.lock
- + validation/pixi.toml
- + validation/samples.tsv
- + validation/test_datasets.tsv


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/compare/92700f65e5920e1be412fca6450485d23800e2ca...3bf1c1609f8bf38b2e44d7c7bdae8eb765939cbc

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View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/compare/92700f65e5920e1be412fca6450485d23800e2ca...3bf1c1609f8bf38b2e44d7c7bdae8eb765939cbc
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