Deprecated API

Contents

• Interfaces
• Classes
• Fields
• Methods
• Constructors
• Enum Constants

Deprecated Interfaces

Interface	Description
htsjdk.samtools.util.Lazy.LazyInitializer	since 1/2017 use a Supplier instead

Deprecated Classes

Class	Description
htsjdk.samtools.apps.TimeChannel	This is deprecated with no replacement. 1/19
htsjdk.samtools.apps.TimeRandomAccessFile	This is deprecated with no replacement. 1/19
htsjdk.samtools.filter.FilteringIterator	use FilteringSamIterator instead
htsjdk.samtools.filter.NotPrimaryAlignmentFilter	use SecondaryAlignmentFilter instead.
htsjdk.samtools.NotPrimarySkippingIterator	use SecondaryAlignmentSkippingIterator instead.
htsjdk.samtools.SAMTagUtil	as of 11/2018, the functions in this class have been absorbed by the SAMTag enum.
htsjdk.samtools.SQTagUtil	since 11/2018. SQ is a reserved tag that shouldn't be used and this code untested.
htsjdk.samtools.util.CollectionUtil.Partitioner	use Collectors.groupingBy instead
htsjdk.samtools.util.StringLineReader	use BufferedLineReader.fromString(String).
htsjdk.variant.variantcontext.filter.FilteringIterator	since 2/29/16 use FilteringVariantContextIterator instead
htsjdk.variant.variantcontext.writer.SortingVariantContextWriter	9/2017, this class is completely untested and unsupported, there is no replacement at this time if you use this class please file an issue on github or it will be removed at some point in the future

Deprecated Fields

Field	Description
htsjdk.samtools.BamFileIoUtils.BAM_FILE_EXTENSION	since June 2019 Use FileExtensions.BAM instead.
htsjdk.samtools.BAMIndex.BAI_INDEX_SUFFIX	since June 2019 Use FileExtensions.BAI_INDEX instead.
htsjdk.samtools.BAMIndex.BAMIndexSuffix	since June 2019 Use FileExtensions.BAI_INDEX instead.
htsjdk.samtools.BAMIndex.CSI_INDEX_SUFFIX	since June 2019 Use FileExtensions.CSI instead.
htsjdk.samtools.cram.build.CramIO.CRAM_FILE_EXTENSION	since June 2019 Use FileExtensions.CRAM instead.
htsjdk.samtools.cram.CRAIIndex.CRAI_INDEX_SUFFIX	since June 2019 Use FileExtensions.CRAM_INDEX instead.
htsjdk.samtools.reference.ReferenceSequenceFileFactory.FASTA_EXTENSIONS	since June 2019 Use FileExtensions.FASTA instead.
htsjdk.samtools.reference.ReferenceSequenceFileFactory.FASTA_INDEX_EXTENSION	since June 2019 Use FileExtensions.FASTA_INDEX instead.
htsjdk.samtools.SAMSequenceRecord.RESERVED_MRNM_SEQUENCE_NAME
htsjdk.samtools.SAMTagUtil.AM	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.AS	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.BC	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.BQ	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.BZ	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.CB	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.CC	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.CG	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.CM	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.CO	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.CP	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.CQ	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.CR	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.CS	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.CT	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.CY	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.E2	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.FI	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.FS	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.FT	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.FZ	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.GC	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.GQ	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.GS	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.H0	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.H1	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.H2	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.HI	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.IH	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.LB	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.MC	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.MD	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.MF	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.MI	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.MQ	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.NH	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.NM	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.OC	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.OF	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.OP	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.OQ	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.OR	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.OX	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.PG	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.PQ	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.PT	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.PU	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.Q2	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.QT	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.QX	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.R2	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.RG	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.RT	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.RX	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.S2	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.SA	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.SM	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.SQ	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.TC	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.U2	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SAMTagUtil.UQ	use SAMTag.getBinaryTag() instead.
htsjdk.samtools.SBIIndex.FILE_EXTENSION	since June 2019 Use FileExtensions.SBI instead.
htsjdk.samtools.util.GZIIndex.DEFAULT_EXTENSION	since June 2019 Use FileExtensions.GZI instead.
htsjdk.samtools.util.IntervalList.INTERVAL_LIST_FILE_EXTENSION	since June 2019 Use FileExtensions.INTERVAL_LIST instead.
htsjdk.samtools.util.IOUtil.BCF_FILE_EXTENSION	since June 2019 Use FileExtensions.BCF instead.
htsjdk.samtools.util.IOUtil.BLOCK_COMPRESSED_EXTENSIONS	Use since June 2019 FileExtensions.BLOCK_COMPRESSED instead.
htsjdk.samtools.util.IOUtil.COMPRESSED_VCF_FILE_EXTENSION	since June 2019 Use FileExtensions.COMPRESSED_VCF instead.
htsjdk.samtools.util.IOUtil.COMPRESSED_VCF_INDEX_EXTENSION	since June 2019 Use FileExtensions.COMPRESSED_VCF_INDEX instead.
htsjdk.samtools.util.IOUtil.DICT_FILE_EXTENSION	since June 2019 Use FileExtensions.DICT instead.
htsjdk.samtools.util.IOUtil.INTERVAL_LIST_FILE_EXTENSION	since June 2019 Use FileExtensions.INTERVAL_LIST instead.
htsjdk.samtools.util.IOUtil.SAM_FILE_EXTENSION	since June 2019 Use FileExtensions.SAM instead.
htsjdk.samtools.util.IOUtil.STANDARD_BUFFER_SIZE	Use Defaults.NON_ZERO_BUFFER_SIZE instead.
htsjdk.samtools.util.IOUtil.VCF_EXTENSIONS	since June 2019 Use FileExtensions.VCF_LIST instead.
htsjdk.samtools.util.IOUtil.VCF_EXTENSIONS_LIST	since June 2019 Use FileExtensions.VCF_LIST instead.
htsjdk.samtools.util.IOUtil.VCF_FILE_EXTENSION	since June 2019 Use FileExtensions.VCF instead.
htsjdk.samtools.util.IOUtil.VCF_INDEX_EXTENSION	since June 2019 Use FileExtensions.VCF_INDEX instead.
htsjdk.tribble.AbstractFeatureReader.BLOCK_COMPRESSED_EXTENSIONS	since June 2019 use FileExtensions.BLOCK_COMPRESSED instead.
htsjdk.tribble.bed.BEDCodec.BED_EXTENSION	since June 2019 Use FileExtensions.BED instead.
htsjdk.tribble.Tribble.STANDARD_INDEX_EXTENSION	since June 2019 Use FileExtensions.TRIBBLE_INDEX instead.
htsjdk.tribble.util.TabixUtils.STANDARD_INDEX_EXTENSION	Use since June 2019 FileExtensions.TABIX_INDEX instead.
htsjdk.variant.vcf.VCFConstants.GENOTYPE_LIKELIHOODS_KEY

Deprecated Methods

Method	Description
htsjdk.samtools.AbstractBAMFileIndex.optimizeChunkList(List<Chunk>, long)	Invoke Chunk.optimizeChunkList(java.util.List<htsjdk.samtools.Chunk>, long) directly.
htsjdk.samtools.AbstractBAMFileIndex.regionToBins(int, int)	Use GenomicIndexUtil.regionToBins(int, int) instead. Get candidate bins for the specified region
htsjdk.samtools.AbstractSAMHeaderRecord.setAttribute(String, Object)	Use instead
htsjdk.samtools.DuplicateSetIterator.setScoringStrategy(DuplicateScoringStrategy.ScoringStrategy)
htsjdk.samtools.fastq.FastqRecord.getReadHeader()	since 02/2017. Use FastqRecord.getReadName() instead
htsjdk.samtools.fastq.FastqRecord.length()	since 02/2017. Use FastqRecord.getReadLength() instead
htsjdk.samtools.reference.IndexedFastaSequenceFile.canCreateIndexedFastaReader(File)	use ReferenceSequenceFileFactory.canCreateIndexedFastaReader(Path) instead.
htsjdk.samtools.reference.IndexedFastaSequenceFile.canCreateIndexedFastaReader(Path)	use ReferenceSequenceFileFactory.canCreateIndexedFastaReader(Path) instead.
htsjdk.samtools.SAMFileHeader.getTextHeader()	since May 1st 2019 - text version of header is no longer stored.
htsjdk.samtools.SAMFileHeader.setAttribute(String, Object)	Use instead
htsjdk.samtools.SAMFileHeader.setTextHeader(String)	since May 1st 2019 - text version of header is no longer stored.
htsjdk.samtools.SAMFileHeader.SortOrder.getComparator()	since 7/2018, use SAMFileHeader.SortOrder.getComparatorInstance() with Object.getClass() instead
htsjdk.samtools.SamFileHeaderMerger.getMergedSequenceIndex(SamReader, Integer)	replaced by SamFileHeaderMerger.getMergedSequenceIndex(SAMFileHeader, Integer)
htsjdk.samtools.SamFileHeaderMerger.getProgramGroupId(SamReader, String)	replaced by SamFileHeaderMerger.getProgramGroupId(SAMFileHeader, String)
htsjdk.samtools.SamFileHeaderMerger.getReaders()	replaced by SamFileHeaderMerger.getHeaders()
htsjdk.samtools.SamFileHeaderMerger.getReadGroupId(SamReader, String)	replaced by SamFileHeaderMerger.getReadGroupId(SAMFileHeader, String)
htsjdk.samtools.SamFileValidator.setValidateIndex(boolean)	use SamFileValidator.setIndexValidationStringency(htsjdk.samtools.BamIndexValidator.IndexValidationStringency) instead
htsjdk.samtools.SAMFileWriterFactory.makeCRAMWriter(SAMFileHeader, boolean, Path, File)	since 6/18, prefer SAMFileWriterFactory.makeWriter(SAMFileHeader, boolean, Path, Path) for creating bam/cram writers however SAMFileWriterFactory.makeCRAMWriter(SAMFileHeader, boolean, Path, Path) is the direct replacement for this method
htsjdk.samtools.SAMFileWriterFactory.makeCRAMWriter(SAMFileHeader, Path, File)	since 6/18, prefer SAMFileWriterFactory.makeWriter(SAMFileHeader, boolean, Path, Path) for creating bam/cram writers however SAMFileWriterFactory.makeCRAMWriter(SAMFileHeader, boolean, Path, Path) is the direct replacement for this method
htsjdk.samtools.SAMFileWriterFactory.makeWriter(SAMFileHeader, boolean, Path, File)	since 6/18, use SAMFileWriterFactory.makeWriter(SAMFileHeader, boolean, Path, Path) instead
htsjdk.samtools.SAMFileWriterImpl.writeHeader(String)	since 06/2018. SAMFileWriterImpl.writeHeader(SAMFileHeader) is preferred for avoid String construction if not need it.
htsjdk.samtools.SamPairUtil.setMateInfo(SAMRecord, SAMRecord, SAMFileHeader)	use SamPairUtil.setMateInfo(SAMRecord, SAMRecord) instead
htsjdk.samtools.SamPairUtil.setMateInfo(SAMRecord, SAMRecord, SAMFileHeader, boolean)	use SamPairUtil.setMateInfo(SAMRecord, SAMRecord, boolean) instead
htsjdk.samtools.SamPairUtil.setProperPairAndMateInfo(SAMRecord, SAMRecord, SAMFileHeader, List<SamPairUtil.PairOrientation>)	use SamPairUtil.setProperPairAndMateInfo(SAMRecord, SAMRecord, List) instead
htsjdk.samtools.SamPairUtil.setProperPairAndMateInfo(SAMRecord, SAMRecord, SAMFileHeader, List<SamPairUtil.PairOrientation>, boolean)	use SamPairUtil.setProperPairAndMateInfo(SAMRecord, SAMRecord, List, boolean)
htsjdk.samtools.SAMRecord.computeIndexingBinIfAbsent(SAMRecord)	Use computeIndexingBin() if accessible or GenomicIndexUtil.regionToBin() otherwise.
htsjdk.samtools.SAMRecord.format()	This method is not guaranteed to return a valid SAM text representation of the SAMRecord. To get standard SAM text representation, SAMRecord.getSAMString().
htsjdk.samtools.SAMRecord.getNotPrimaryAlignmentFlag()	use SAMRecord.isSecondaryAlignment() instead.
htsjdk.samtools.SAMRecord.isAllowedAttributeValue(Object)	The attribute type and value checks have been moved directly into SAMBinaryTagAndValue.
htsjdk.samtools.SAMRecord.setNotPrimaryAlignmentFlag(boolean)	use SAMRecord.setSecondaryAlignment(boolean) instead.
htsjdk.samtools.SAMRecord.setReadUmappedFlag(boolean)
htsjdk.samtools.SamStreams.isGzippedSAMFile(InputStream)	use IOUtil.isGZIPInputStream(InputStream) instead
htsjdk.samtools.SAMTagUtil.getSingleton()	use the static methods in SAMTag instead
htsjdk.samtools.SAMTagUtil.makeBinaryTag(String)	use instead
htsjdk.samtools.SAMTagUtil.makeStringTag(short)	use SAMTag.makeStringTag(short) instead
htsjdk.samtools.SAMUtils.isReferenceSequenceCompatibleWithBAI(SAMSequenceRecord)	because the method does the exact opposite of what it says. Use the correctly named isReferenceSequenceIncompatibleWithBAI() instead.
htsjdk.samtools.seekablestream.SeekableStreamFactory.isFilePath(String)	this method is simplistic and no longer particularly useful since IOPath allows similar access to various non-file data sources, internal use has been replaced with SeekableStreamFactory.isBeingHandledByLegacyUrlSupport(String)
htsjdk.samtools.sra.SRAAccession.isSupported()	use SRAAccession.checkIfInitialized() instead
htsjdk.samtools.util.AbstractLocusInfo.getRecordAndPositions()	since name of the method can be confusing, new implementation should be used getRecordAndOffsets()
htsjdk.samtools.util.BlockCompressedInputStream.assertNonDefectiveFile(File)
htsjdk.samtools.util.CollectionUtil.partition(Collection<V>, CollectionUtil.Partitioner<V, K>)	use java8 .stream().collect(Collectors.groupingBy(()-> function)) instead
htsjdk.samtools.util.Interval.getSequence()	use getContig() instead
htsjdk.samtools.util.IntervalList.getUniqueIntervals()	use {@link #uniqued()#getIntervals()} instead.
htsjdk.samtools.util.IntervalList.getUniqueIntervals(boolean)	use {@link #uniqued(boolean)#getIntervals()} or IntervalList.getUniqueIntervals(IntervalList, boolean) instead.
htsjdk.samtools.util.IntervalList.sort()	use IntervalList.sorted() instead.
htsjdk.samtools.util.IntervalList.unique()	use IntervalList.uniqued() instead.
htsjdk.samtools.util.IntervalList.unique(boolean)	use IntervalList.uniqued(boolean) instead.
htsjdk.samtools.util.IOUtil.createTempDir(String, String)	Use IOUtil.createTempDir(String) instead. It turns out the mechanism was not "good enough" and caused security issues, the new implementation combines the prefix/morePrefix into a single prefix. The security flaw is fixed but due to the now extraneous morePrefix argument it is recommended to use the 1 argument form.
htsjdk.samtools.util.RelativeIso8601Date.getDate()
htsjdk.samtools.util.RelativeIso8601Date.getDay()
htsjdk.samtools.util.RelativeIso8601Date.getHours()
htsjdk.samtools.util.RelativeIso8601Date.getMinutes()
htsjdk.samtools.util.RelativeIso8601Date.getMonth()
htsjdk.samtools.util.RelativeIso8601Date.getSeconds()
htsjdk.samtools.util.RelativeIso8601Date.getTimezoneOffset()
htsjdk.samtools.util.RelativeIso8601Date.getYear()
htsjdk.samtools.util.RelativeIso8601Date.setDate(int)
htsjdk.samtools.util.RelativeIso8601Date.setHours(int)
htsjdk.samtools.util.RelativeIso8601Date.setMinutes(int)
htsjdk.samtools.util.RelativeIso8601Date.setMonth(int)
htsjdk.samtools.util.RelativeIso8601Date.setSeconds(int)
htsjdk.samtools.util.RelativeIso8601Date.setTime(long)
htsjdk.samtools.util.RelativeIso8601Date.setYear(int)
htsjdk.samtools.util.SortingCollection.newInstance(Class<T>, SortingCollection.Codec<T>, Comparator<T>, int, File...)	since 2017-09. Use SortingCollection.newInstance(Class, Codec, Comparator, int, Path...) instead
htsjdk.samtools.util.SortingCollection.newInstance(Class<T>, SortingCollection.Codec<T>, Comparator<T>, int, Collection<File>)	since 2017-09. Use SortingCollection.newInstanceFromPaths(Class, Codec, Comparator, int, Collection) instead
htsjdk.samtools.util.TestUtil.getTempDirecory(String, String)	Use properly spelled method. TestUtil.getTempDirectory(java.lang.String, java.lang.String)
htsjdk.samtools.util.TestUtil.recursiveDelete(File)	Since 3/19, prefer IOUtil.recursiveDelete(Path)
htsjdk.tribble.AbstractFeatureReader.hasBlockCompressedExtension(File)	use IOUtil.hasBlockCompressedExtension(File).
htsjdk.tribble.AbstractFeatureReader.hasBlockCompressedExtension(String)	use IOUtil.hasBlockCompressedExtension(String).
htsjdk.tribble.AbstractFeatureReader.hasBlockCompressedExtension(URI)	use IOUtil.hasBlockCompressedExtension(URI).
htsjdk.tribble.annotation.Strand.toStrand(String)	please use Strand.decode(char) instead.
htsjdk.tribble.Feature.getChr()	on 03/2015. Use getContig() instead.
htsjdk.tribble.index.AbstractIndex.getIndexedFile()	on 03/2017. Use AbstractIndex.getIndexedPath() instead.
htsjdk.tribble.index.IndexFactory.writeIndex(Index, File)	use Index.write(File) instead
htsjdk.tribble.readers.AsciiLineReader.readLine(PositionalBufferedStream)	8/8/2017 use AsciiLineReader.from(java.io.InputStream) to create a new AsciiLineReader and AsciiLineReader.readLine()
htsjdk.variant.utils.SAMSequenceDictionaryExtractor.extractDictionary(File)	in favor of SAMSequenceDictionaryExtractor.extractDictionary(Path)
htsjdk.variant.variantcontext.Allele.wouldBeBreakpoint(byte[])
htsjdk.variant.variantcontext.Allele.wouldBeNoCallAllele(byte[])
htsjdk.variant.variantcontext.Allele.wouldBeNullAllele(byte[])
htsjdk.variant.variantcontext.Allele.wouldBeSingleBreakend(byte[])
htsjdk.variant.variantcontext.Allele.wouldBeStarAllele(byte[])
htsjdk.variant.variantcontext.Allele.wouldBeSymbolicAllele(byte[])
htsjdk.variant.variantcontext.Genotype.getAttributeAsDouble(String, double)
htsjdk.variant.variantcontext.Genotype.getAttributeAsInt(String, int)
htsjdk.variant.variantcontext.Genotype.getAttributeAsString(String, String)
htsjdk.variant.variantcontext.Genotype.getLog10PError()
htsjdk.variant.variantcontext.Genotype.getPhredScaledQual()
htsjdk.variant.variantcontext.Genotype.hasLog10PError()
htsjdk.variant.variantcontext.GenotypeLikelihoods.fromGLField(String)
htsjdk.variant.variantcontext.GenotypeLikelihoods.getAllelePairUsingDeprecatedOrdering(int)	since 2/5/13
htsjdk.variant.variantcontext.GenotypeLikelihoods.getLog10GQ(GenotypeType)	since 2/5/13 use GenotypeLikelihoods.getLog10GQ(Genotype, VariantContext) or GenotypeLikelihoods.getLog10GQ(Genotype, List)
htsjdk.variant.variantcontext.GenotypeLikelihoods.getPLIndecesOfAlleles(int, int)	7/18 use GenotypeLikelihoods.getPLIndicesOfAlleles(int, int) instead
htsjdk.variant.variantcontext.GenotypeLikelihoods.initializeAnyploidPLIndexToAlleleIndices(int, int)	as of sept 2020, this method is no longer necessary
htsjdk.variant.variantcontext.VariantContext.getGLIndecesOfAlternateAllele(Allele)	7/18 use VariantContext.getGLIndicesOfAlternateAllele(Allele) instead
htsjdk.variant.vcf.VCFEncoder.setAllowMissingFieldsInHeader(boolean)	since 10/24/13 use the constructor
htsjdk.variant.vcf.VCFEncoder.setVCFHeader(VCFHeader)	since 10/24/13 use the constructor
htsjdk.variant.vcf.VCFFileReader.fromVcf(VCFFileReader)	since July 2018 since use VCFFileReader.toIntervalList(VCFFileReader) instead
htsjdk.variant.vcf.VCFFileReader.fromVcf(VCFFileReader, boolean)	since July 2018 since use VCFFileReader.toIntervalList(VCFFileReader, boolean) instead
htsjdk.variant.vcf.VCFFileReader.fromVcf(File)	since July 2018 use VCFFileReader.toIntervalList(Path) instead
htsjdk.variant.vcf.VCFFileReader.fromVcf(File, boolean)	since July 2018 use VCFFileReader.toIntervalList(Path, boolean) instead

Deprecated Constructors

Constructor	Description
htsjdk.samtools.MergingSamRecordIterator(SamFileHeaderMerger, boolean)	replaced by MergingSamRecordIterator(SamFileHeaderMerger, Collection, boolean)
htsjdk.samtools.SamFileHeaderMerger(Collection<SamReader>, SAMFileHeader.SortOrder)	replaced by SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection, boolean)
htsjdk.samtools.SamFileHeaderMerger(Collection<SamReader>, SAMFileHeader.SortOrder, boolean)	replaced by SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection, boolean)
htsjdk.samtools.SAMRecordDuplicateComparator(List<SAMFileHeader>)
htsjdk.samtools.SAMSequenceRecord(String)	Use SAMSequenceRecord(String, int) instead. sequenceLength is required for the object to be considered valid.
htsjdk.tribble.readers.AsciiLineReader(PositionalBufferedStream)	8/8/2017 use AsciiLineReader.from(java.io.InputStream)
htsjdk.tribble.readers.AsciiLineReader(InputStream)	8/8/2017 use AsciiLineReader.from(java.io.InputStream)

Deprecated Enum Constants

Enum Constant	Description
htsjdk.samtools.SAMFlag.NOT_PRIMARY_ALIGNMENT	use SAMFlag.SECONDARY_ALIGNMENT instead.
htsjdk.samtools.SAMReadGroupRecord.PlatformValue.BGI	Use SAMReadGroupRecord.PlatformValue.DNBSEQ instead.
htsjdk.samtools.SAMReadGroupRecord.PlatformValue.OTHER	OTHER is not an official value. It is recommended to omit PL if it is not in this list or is unknown.
htsjdk.samtools.SAMTag.GC	for backwards compatibility only
htsjdk.samtools.SAMTag.GQ	for backwards compatibility only
htsjdk.samtools.SAMTag.GS	for backwards compatibility only
htsjdk.samtools.SAMTag.MF	for backwards compatibility only
htsjdk.samtools.SAMTag.RT	use BC instead, for backwards compatibilty only
htsjdk.samtools.SAMTag.S2	for backwards compatibility only
htsjdk.samtools.SAMTag.SQ	for backwards compatibility only