packagesListe der Dateien in Paket libhtsjdk-java-doc in resolute für Architektur all
/usr/share/doc-base/libhtsjdk-java-doc.libhtsjdk-java-doc /usr/share/doc/libhtsjdk-java-doc/changelog.Debian.gz /usr/share/doc/libhtsjdk-java-doc/copyright /usr/share/doc/libhtsjdk-java/api/allclasses-index.html /usr/share/doc/libhtsjdk-java/api/allpackages-index.html /usr/share/doc/libhtsjdk-java/api/constant-values.html /usr/share/doc/libhtsjdk-java/api/copy.svg /usr/share/doc/libhtsjdk-java/api/deprecated-list.html /usr/share/doc/libhtsjdk-java/api/element-list /usr/share/doc/libhtsjdk-java/api/help-doc.html /usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/BetaAPI.html /usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/InternalAPI.html /usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/FASTACodecV1_0.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/FASTADecoderV1_0.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/ReadsCodecUtils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMDecoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMDecoderOptions.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMEncoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMEncoderOptions.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMCodecV1_0.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMDecoderV1_0.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMEncoderV1_0.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMDecoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMDecoderOptions.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMEncoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMEncoderOptions.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMCodecV2_1.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMDecoderV2_1.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMEncoderV2_1.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMCodecV3_0.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMDecoderV3_0.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMEncoderV3_0.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_1/CRAMCodecV3_1.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_1/CRAMDecoderV3_1.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_1/CRAMEncoderV3_1.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_1/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_1/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/HtsgetBAMCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/HtsgetBAMDecoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMCodecV1_2.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMDecoderV1_2.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMDecoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMEncoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMCodecV1_0.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMDecoderV1_0.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMEncoderV1_0.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFDecoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFEncoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VariantsCodecUtils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFCodecV3_2.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFDecoderV3_2.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFEncoderV3_2.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFCodecV3_3.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFDecoderV3_3.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFEncoderV3_3.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFCodecV4_0.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFDecoderV4_0.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFEncoderV4_0.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFCodecV4_1.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFDecoderV4_1.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFEncoderV4_1.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFCodecV4_2.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFDecoderV4_2.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFEncoderV4_2.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/VCFCodecV4_3.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/VCFDecoderV4_3.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkException.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkIOException.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkPluginException.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkUnsupportedOperationException.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/IOPathUtils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/Bundle.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleBuilder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleJSON.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleResource.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleResourceBase.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleResourceType.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/IOPathResource.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/InputStreamResource.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/OutputStreamResource.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/SeekableStreamResource.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/SignatureStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsContentType.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsDecoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsDecoderOptions.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsEncoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsEncoderOptions.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsHeader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsRecord.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsVersion.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/IOUtils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/Upgradeable.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HapRefDecoderOptions.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceDecoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceDecoderOptions.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceEncoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceEncoderOptions.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceFormats.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsInterval.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsIntervalUtils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQuery.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQueryInterval.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQueryRule.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsBundle.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsDecoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsDecoderOptions.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsEncoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsEncoderOptions.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsFormats.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsQuery.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HaploidReferenceResolver.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsCodecRegistry.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsCodecResolver.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsDefaultRegistry.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/ReadsResolver.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/VariantsResolver.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsBundle.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsDecoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsDecoderOptions.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsEncoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsEncoderOptions.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsFormats.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/io/AsyncWriterPool.html /usr/share/doc/libhtsjdk-java/api/htsjdk/io/HtsPath.html /usr/share/doc/libhtsjdk-java/api/htsjdk/io/IOPath.html /usr/share/doc/libhtsjdk-java/api/htsjdk/io/Writer.html /usr/share/doc/libhtsjdk-java/api/htsjdk/io/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/io/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/AbstractBAMFileIndex.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/AbstractSAMHeaderRecord.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/AlignmentBlock.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileReader.BAMQueryFilteringIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileSpan.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndex.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndexMerger.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndexMetaData.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndexer.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMRecord.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMRecordCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMSBIIndexer.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMStartingAtIteratorFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMStreamWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BamFileIoUtils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BamIndexValidator.IndexValidationStringency.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BamIndexValidator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Bin.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinList.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinWithOffset.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinaryTagCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexBuilder.FeatureToBeIndexed.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexBuilder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexContent.BinList.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexContent.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BrowseableBAMIndex.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMBAIIndexer.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMCRAIIndexer.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMContainerStreamWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMFileReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMFileWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMIndexer.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CSIIndex.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Chunk.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Cigar.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CigarElement.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CigarOperator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CoordinateSortedPairInfoMap.Codec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CoordinateSortedPairInfoMap.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CustomReaderFactory.ICustomReaderFactory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CustomReaderFactory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DefaultSAMRecordFactory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Defaults.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DiskBasedBAMFileIndex.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DownsamplingIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DownsamplingIteratorFactory.Strategy.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DownsamplingIteratorFactory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateScoringStrategy.ScoringStrategy.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateScoringStrategy.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateSet.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateSetIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/FileTruncatedException.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/GenomicIndexUtil.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/HtsgetBAMFileReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/IndexMerger.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/LinearIndex.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/MergingSamRecordIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/NotPrimarySkippingIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/QueryInterval.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/ReservedTagConstants.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMBinaryTagAndUnsignedArrayValue.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMBinaryTagAndValue.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMException.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.GroupOrder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.PgIdGenerator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.SortOrder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileSource.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileSpan.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileWriterFactory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileWriterImpl.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFlag.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFormatException.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMHeaderRecordComparator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMLineParser.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMProgramRecord.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMReadGroupRecord.PlatformValue.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMReadGroupRecord.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecord.SAMTagAndValue.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecord.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordComparator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordCoordinateComparator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordDuplicateComparator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordFactory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordQueryHashComparator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordQueryNameComparator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordSetBuilder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSequenceDictionary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSequenceDictionaryCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSequenceRecord.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSortOrderChecker.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTag.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTagUtil.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTestUtil.SanityCheckFailedException.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTestUtil.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTextHeaderCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTextWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMUtils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMValidationError.Severity.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMValidationError.Type.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMValidationError.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndex.Header.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndex.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndexMerger.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndexWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SQTagUtil.SQBase.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SQTagUtil.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAFileReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIndex.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIterator.RecordRangeInfo.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileHeaderMerger.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileValidator.ValidationMetrics.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileValidator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFiles.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFlagField.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamIndexes.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamInputResource.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamPairUtil.PairOrientation.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamPairUtil.SetMateInfoIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamPairUtil.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.AssertingIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.Indexing.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.PrimitiveSamReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.PrimitiveSamReaderToSamReaderAdapter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.ReaderImplementation.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.Type.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReaderFactory.Option.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReaderFactory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamStreams.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SecondaryAlignmentSkippingIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SecondaryOrSupplementarySkippingIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/TagValueAndUnsignedArrayFlag.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/TextCigarCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/TextTagCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/ValidationStringency.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/TimeChannel.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/TimeRandomAccessFile.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/BAIEntry.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAIEntry.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAIIndex.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAIIndexMerger.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAMException.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CRAMReferenceRegion.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CompressionHeaderFactory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/ContainerFactory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramContainerHeaderIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramContainerIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramIO.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramSpanContainerIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/SliceFactory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/Utils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/CRAMVersion.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/CramVersions.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/MutableInt.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/BZIP2ExternalCompressor.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/CompressionUtils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/ExternalCompressor.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/GZIPExternalCompressor.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/LZMAExternalCompressor.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/RANS4x8ExternalCompressor.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/RANSNx16ExternalCompressor.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/RAWExternalCompressor.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/fqzcomp/FQZCompDecode.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/fqzcomp/FQZCompEncode.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/fqzcomp/FQZCompExternalCompressor.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/fqzcomp/FQZGlobalFlags.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/fqzcomp/FQZModels.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/fqzcomp/FQZParam.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/fqzcomp/FQZParams.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/fqzcomp/FQZState.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/fqzcomp/FQZUtils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/fqzcomp/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/fqzcomp/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/nametokenisation/NameTokenisationDecode.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/nametokenisation/NameTokenisationEncode.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/nametokenisation/NameTokeniserExternalCompressor.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/nametokenisation/TokenStreams.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/nametokenisation/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/nametokenisation/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/nametokenisation/tokens/EncodeToken.DupOrDiffToken.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/nametokenisation/tokens/EncodeToken.EndToken.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/nametokenisation/tokens/EncodeToken.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/nametokenisation/tokens/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/nametokenisation/tokens/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/range/ByteModel.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/range/Constants.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/range/RangeCoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/range/RangeDecode.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/range/RangeEncode.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/range/RangeExternalCompressor.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/range/RangeParams.ORDER.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/range/RangeParams.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/range/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/range/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/ArithmeticDecoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/Constants.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/RANSDecode.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/RANSDecodingSymbol.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/RANSEncode.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/RANSEncodingSymbol.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/RANSParams.ORDER.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/RANSParams.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/Utils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/rans4x8/RANS4x8Decode.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/rans4x8/RANS4x8Encode.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/rans4x8/RANS4x8Params.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/rans4x8/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/rans4x8/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/ransnx16/RANSNx16Decode.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/ransnx16/RANSNx16Encode.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/ransnx16/RANSNx16Params.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/ransnx16/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/ransnx16/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/ContentDigests.KNOWN_DIGESTS.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/ContentDigests.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/ByteArrayLenEncoding.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/CRAMCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/CRAMEncoding.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/EncodingFactory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/BetaIntegerCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/BetaIntegerEncoding.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanByteEncoding.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanIntegerEncoding.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CoreCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/GammaIntegerEncoding.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/SubexponentialIntegerEncoding.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/GolombIntegerEncoding.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/GolombLongEncoding.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/GolombRiceIntegerEncoding.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanBitCode.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanCanoncialCodeGenerator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanParams.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanParamsCalculator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ByteArrayStopEncoding.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteArrayCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteArrayEncoding.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteEncoding.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalEncoding.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalIntegerEncoding.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalLongEncoding.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/CramRecordReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/DataSeriesReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/BaseQualityScore.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Bases.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Deletion.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/HardClip.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/InsertBase.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Insertion.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Padding.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/ReadBase.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/ReadFeature.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/RefSkip.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Scores.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/SoftClip.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Substitution.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/CramRecordWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/DataSeriesWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/BitInputStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/BitOutputStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CRC32InputStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CRC32OutputStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CountingInputStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CramInt.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CramIntArray.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/DefaultBitInputStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/DefaultBitOutputStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/ITF8.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/InputStreamUtils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/LTF8.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/CRAMLazyReferenceSource.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/CRAMReferenceSource.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/EnaRefService.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/GaveUpException.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceContext.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceContextType.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceSource.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/AlignmentContext.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/AlignmentSpan.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMCodecModelContext.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMCompressionRecord.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMEncodingStrategy.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMRecordReadFeatures.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressionHeader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressionHeaderEncodingMap.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressorCache.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/Container.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/ContainerHeader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CramHeader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/DataSeries.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/DataSeriesType.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/EncodingDescriptor.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/EncodingID.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/ReadTag.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/Slice.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SliceBlocks.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SliceBlocksReadStreams.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SliceBlocksWriteStreams.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SubstitutionMatrix.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/Block.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/BlockCompressionMethod.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/BlockContentType.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/ExampleSamUsage.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/PrintReadsExample.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/AsyncFastqWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/BasicFastqWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqConstants.FastqExtensions.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqConstants.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqEncoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqReader.LineType.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqRecord.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqWriterFactory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/AbstractJavascriptFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/AggregateFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/AlignedFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/DuplicateReadFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/FailsVendorReadQualityFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/FilteringIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/FilteringSamIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/InsertSizeFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/IntervalFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/IntervalKeepPairFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/InvertFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/JavascriptSamRecordFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/MappingQualityFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/NotPrimaryAlignmentFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/OverclippedReadFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/ReadNameFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/SamRecordFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/SecondaryAlignmentFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/SecondaryOrSupplementaryFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/SolexaNoiseFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/TagFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/WholeReadClippedFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/LiftOver.PartialLiftover.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/LiftOver.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/Header.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/MetricBase.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/MetricsFile.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/StringHeader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/VersionHeader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaReferenceWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaReferenceWriterBuilder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceFile.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceIndex.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceIndexCreator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceIndexEntry.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/IndexedFastaSequenceFile.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequence.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFile.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFileFactory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFileWalker.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/SamLocusAndReferenceIterator.SAMLocusAndReference.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/SamLocusAndReferenceIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ByteArraySeekableStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ISeekableStreamFactory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ReadableSeekableStreamByteChannel.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableBufferedStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFTPStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFTPStreamHelper.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFileStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableHTTPStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableMemoryStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekablePathStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableStreamFactory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/UserPasswordInput.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/ReferenceCache.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAAccession.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAAlignmentIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAIndexedSequenceFile.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRALazyRecord.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAUnalignmentIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAUtils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractAsyncWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractLocusInfo.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractLocusIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractProgressLogger.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractRecordAndOffset.AlignmentType.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractRecordAndOffset.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AsciiWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AsyncBlockCompressedInputStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AsyncBufferedIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BinaryCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedFilePointerUtil.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedInputStream.DecompressedBlock.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedInputStream.FileTermination.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedInputStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedOutputStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedStreamConstants.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockGunzipper.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BufferedLineReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CigarUtil.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CloseableIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CloserUtil.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CodeUtil.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.DefaultingMap.Factory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.DefaultingMap.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.MultiMap.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.Partitioner.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ComparableTuple.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CoordMath.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CoordSpanInputSteam.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CustomGzipOutputStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DateParser.InvalidDateException.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DateParser.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DelegatingIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DiskBackedQueue.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/EdgeReadIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/EdgingRecordAndOffset.Type.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/EdgingRecordAndOffset.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FastLineReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FastqQualityFormat.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FileAppendStreamLRUCache.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FileExtensions.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FormatUtil.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/GZIIndex.GZIIndexer.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/GZIIndex.IndexEntry.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/GZIIndex.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Histogram.Bin.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Histogram.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/HttpUtils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IOUtil.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Interval.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalCoordinateComparator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalList.IntervalMergerIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalList.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalListReferenceSequenceMask.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalListWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.FwdIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.Node.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.OverlapIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.RevIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.ValuesIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTreeMap.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalUtil.IntervalCombiner.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalUtil.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Iso8601Date.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IterableAdapter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IterableOnceIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Iterables.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Lazy.LazyInitializer.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Lazy.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/LineReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ListMap.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Locatable.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/LocationAware.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Locus.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/LocusComparator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/LocusImpl.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Log.LogLevel.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Log.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Md5CalculatingInputStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Md5CalculatingOutputStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/MergingIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Murmur3.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/OverlapDetector.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/PeekIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/PeekableIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/PositionalOutputStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProcessExecutor.ExitStatusAndOutput.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProcessExecutor.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProgressLogger.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProgressLoggerInterface.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/QualityEncodingDetector.FileContext.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/QualityEncodingDetector.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/QualityUtil.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ReferenceSequenceMask.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/RelativeIso8601Date.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ResourceLimitedMap.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ResourceLimitedMapFunctor.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/RuntimeEOFException.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/RuntimeIOException.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/RuntimeScriptException.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SAMRecordPrefetchingIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamConstants.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamLocusIterator.LocusInfo.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamLocusIterator.RecordAndOffset.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamLocusIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamRecordIntervalIteratorFactory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamRecordTrackingBuffer.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamRecordWithOrdinal.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SequenceUtil.SequenceListsDifferException.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SequenceUtil.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SnappyLoader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SolexaQualityConverter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SortingCollection.Codec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SortingCollection.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SortingLongCollection.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/StopWatch.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/StringLineReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/StringUtil.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/TempStreamFactory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/TerminatorlessBlockCompressedOutputStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/TestUtil.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/TrimmingUtil.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Tuple.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/WholeGenomeReferenceSequenceMask.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/FTPClient.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/FTPReply.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/FTPStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/FTPUtils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetClass.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetErrorResponse.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetFormat.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetMalformedResponseException.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetPOSTRequest.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetRequest.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetRequestField.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetResponse.Block.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetResponse.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/nio/DeleteOnExitPathHook.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/nio/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/nio/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/DeflaterFactory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/InflaterFactory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AbstractFeatureCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AbstractFeatureReader.ComponentMethods.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AbstractFeatureReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AsciiFeatureCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/BinaryFeatureCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/CloseableTribbleIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/Feature.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/FeatureCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/FeatureCodecHeader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/FeatureReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/IntervalListCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/MutableFeature.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/NameAwareCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/NamedFeature.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/SimpleFeature.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TabixFeatureReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/Tribble.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.CorruptedIndexFile.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.FeatureFileDoesntExist.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.InternalCodecException.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.InvalidDecodeLine.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.InvalidHeader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.MalformedFeatureFile.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.TabixReaderFailure.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.UnableToCreateCorrectIndexType.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.UnableToReadIndexFile.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleIndexedFeatureReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/Strand.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDCodec.StartOffset.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDFeature.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.Exon.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.Exon2.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/SimpleBEDFeature.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/CountRecords.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/ExampleBinaryCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/IndexToTable.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/IndicesAreEqual.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/ProfileIndexReading.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/CodecLineParsingException.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/UnsortedFileException.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3BaseData.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.DecodeDepth.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.Gff3Directive.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Constants.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Feature.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3FeatureImpl.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Writer.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/SequenceRegion.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.BlockStats.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.IndexType.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/Block.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/ChrIndex.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/DynamicIndexCreator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/Index.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexCreator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.IndexBalanceApproach.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.IndexType.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/MutableIndex.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/TribbleIndexCreator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/Interval.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalIndexCreator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTreeIndex.ChrIndex.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTreeIndex.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/LinearIndex.ChrIndex.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/LinearIndex.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/LinearIndexCreator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/AllRefsTabixIndexCreator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/StreamBasedTabixIndexCreator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixFormat.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndex.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndexCreator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndexMerger.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/AsciiLineReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/AsciiLineReaderIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineIteratorImpl.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LongLineBufferedReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/Positional.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/PositionalBufferedStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/SynchronousLineReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixIteratorLineReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.Iterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.TIndex.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.TPair64.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/FTPHelper.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/HTTPHelper.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/LittleEndianInputStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/LittleEndianOutputStream.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/MathUtils.RunningStat.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/MathUtils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/ParsingUtils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/RemoteURLHelper.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TIndex.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TIntv.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TPair64.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/URLHelper.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/URLHelperFactory.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/HardyWeinbergCalculation.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/utils/ClassFinder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/utils/ValidationUtils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/utils/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/utils/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.LazyData.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.SitesInfoForDecoding.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Decoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.Decoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2LazyGenotypesDecoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Type.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Utils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCFVersion.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/example/PrintVariantsExample.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/example/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/example/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/BinomialCoefficientUtil.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/GeneralUtils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/SAMSequenceDictionaryExtractor.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/VCFHeaderReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/Allele.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/CommonInfo.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/FastGenotype.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/Genotype.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeBuilder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeJEXLContext.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeLikelihoods.GenotypeLikelihoodsAllelePair.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeLikelihoods.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeType.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypesContext.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/JexlMissingValueTreatment.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.LazyData.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.LazyParser.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/SimpleAllele.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/StructuralVariantType.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.Type.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.Validation.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextBuilder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextComparator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextUtils.JexlVCMatchExp.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextUtils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/CompoundFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/FilteringIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/FilteringVariantContextIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/GenotypeQualityFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/HeterozygosityFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/JavascriptVariantFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/PassingVariantFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/SnpFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/VariantContextFilter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/AsyncVariantContextWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2Encoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.AtomicInt.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.Flag.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.Float.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.GenericInts.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.IntArray.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.StringOrCharacter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.FTGenotypesWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GTWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GenericSiteWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GenotypesWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.IGFGenotypesWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.IntegerTypeGenotypesWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.SiteWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.StaticallyTypeGenotypesWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriterManager.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.ADAccessor.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.Accessor.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.DPAccessor.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.GQAccessor.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.PLAccessor.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/Options.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/SortingVariantContextWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriter.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.OutputType.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/package-tree.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/AbstractVCFCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCF3Codec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFAltHeaderLine.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCompoundHeaderLine.SupportedHeaderLineType.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCompoundHeaderLine.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFConstants.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFContigHeaderLine.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFEncoder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFileReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFilterHeaderLine.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFormatHeaderLine.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeader.HEADER_FIELDS.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLine.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineCount.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineTranslator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineType.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderVersion.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFIDHeaderLine.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFInfoHeaderLine.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFIterator.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFIteratorBuilder.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFMetaHeaderLine.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPassThruTextTransformer.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPedigreeHeaderLine.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPercentEncodedTextTransformer.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFReader.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFRecordCodec.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFSampleHeaderLine.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFSimpleHeaderLine.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFStandardHeaderLines.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFTextTransformer.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFUtils.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-summary.html /usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-tree.html /usr/share/doc/libhtsjdk-java/api/index-all.html /usr/share/doc/libhtsjdk-java/api/index.html /usr/share/doc/libhtsjdk-java/api/legal/ASSEMBLY_EXCEPTION /usr/share/doc/libhtsjdk-java/api/legal/jquery.md /usr/share/doc/libhtsjdk-java/api/legal/jqueryUI.md /usr/share/doc/libhtsjdk-java/api/link.svg /usr/share/doc/libhtsjdk-java/api/member-search-index.js /usr/share/doc/libhtsjdk-java/api/module-search-index.js /usr/share/doc/libhtsjdk-java/api/overview-summary.html /usr/share/doc/libhtsjdk-java/api/overview-tree.html /usr/share/doc/libhtsjdk-java/api/package-search-index.js /usr/share/doc/libhtsjdk-java/api/resources/glass.png /usr/share/doc/libhtsjdk-java/api/resources/x.png /usr/share/doc/libhtsjdk-java/api/script-dir/jquery-3.7.1.min.js /usr/share/doc/libhtsjdk-java/api/script-dir/jquery-ui.min.css /usr/share/doc/libhtsjdk-java/api/script-dir/jquery-ui.min.js /usr/share/doc/libhtsjdk-java/api/script.js /usr/share/doc/libhtsjdk-java/api/search-page.js /usr/share/doc/libhtsjdk-java/api/search.html /usr/share/doc/libhtsjdk-java/api/search.js /usr/share/doc/libhtsjdk-java/api/serialized-form.html /usr/share/doc/libhtsjdk-java/api/stylesheet.css /usr/share/doc/libhtsjdk-java/api/tag-search-index.js /usr/share/doc/libhtsjdk-java/api/type-search-index.js /usr/share/lintian/overrides/libhtsjdk-java-doc