Deprecated List (htsjdk 2.11.0 API)

Deprecated Interfaces
Interface and Description

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

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

Deprecated Classes
Class and Description
htsjdk.samtools.util.CollectionUtil.Partitioner use Collectors.groupingBy instead
htsjdk.samtools.filter.FilteringIterator use `FilteringSamIterator` instead
htsjdk.variant.variantcontext.filter.FilteringIterator since 2/29/16 use `FilteringVariantContextIterator` instead
htsjdk.samtools.SAMRecordUtil 10/27/2016 Use `SAMRecord` constants and functions
htsjdk.samtools.SAMTools since 07/2017. This class does not add anything to the HTSJDK library except an example of how to iterate over a SAM/BAM file. In addition, it is not tested.

Deprecated Fields
Field and Description
htsjdk.variant.vcf.VCFConstants.GENOTYPE_LIKELIHOODS_KEY
htsjdk.samtools.util.IOUtil.STANDARD_BUFFER_SIZE Use `Defaults.NON_ZERO_BUFFER_SIZE` instead.
htsjdk.samtools.SAMRecordUtil.TAGS_TO_REVERSE 6/5/2017 Use `SAMRecord.TAGS_TO_REVERSE`
htsjdk.samtools.SAMRecordUtil.TAGS_TO_REVERSE_COMPLEMENT 6/5/2017 Use `SAMRecord.TAGS_TO_REVERSE_COMPLEMENT`

Deprecated Methods
Method and Description
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.variant.variantcontext.GenotypeLikelihoods.fromGLField(String)
htsjdk.variant.variantcontext.GenotypeLikelihoods.getAllelePairUsingDeprecatedOrdering(int) since 2/5/13
htsjdk.variant.variantcontext.Genotype.getAttributeAsDouble(String, double)
htsjdk.variant.variantcontext.Genotype.getAttributeAsInt(String, int)
htsjdk.variant.variantcontext.Genotype.getAttributeAsString(String, String)
htsjdk.tribble.Feature.getChr() on 03/2015. Use getContig() instead.
htsjdk.samtools.util.RelativeIso8601Date.getDate()
htsjdk.samtools.util.RelativeIso8601Date.getDay()
htsjdk.samtools.util.RelativeIso8601Date.getHours()
htsjdk.tribble.index.AbstractIndex.getIndexedFile() on 03/2017. Use `AbstractIndex.getIndexedPath()` instead.
htsjdk.variant.variantcontext.GenotypeLikelihoods.getLog10GQ(GenotypeType) since 2/5/13 use `GenotypeLikelihoods.getLog10GQ(Genotype, VariantContext)` or `GenotypeLikelihoods.getLog10GQ(Genotype, List)`
htsjdk.variant.variantcontext.Genotype.getLog10PError()
htsjdk.samtools.SamFileHeaderMerger.getMergedSequenceIndex(SamReader, Integer) replaced by `SamFileHeaderMerger.getMergedSequenceIndex(SAMFileHeader, Integer)`
htsjdk.samtools.util.RelativeIso8601Date.getMinutes()
htsjdk.samtools.util.RelativeIso8601Date.getMonth()
htsjdk.variant.variantcontext.Genotype.getPhredScaledQual()
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.fastq.FastqRecord.getReadHeader() since 02/2017. Use `FastqRecord.getReadName()` instead
htsjdk.samtools.util.AbstractLocusInfo.getRecordAndPositions() since name of the method can be confusing, new implementation should be used `getRecordAndOffsets()`
htsjdk.samtools.util.RelativeIso8601Date.getSeconds()
htsjdk.samtools.util.Interval.getSequence() use getContig() instead
htsjdk.samtools.util.TestUtil.getTempDirecory(String, String) Use properly spelled method. `TestUtil.getTempDirectory(java.lang.String, java.lang.String)`
htsjdk.samtools.util.RelativeIso8601Date.getTimezoneOffset()
htsjdk.samtools.util.IntervalList.getUniqueIntervals() use `#uniqued()#getIntervals()` instead.
htsjdk.samtools.util.IntervalList.getUniqueIntervals(boolean) use `#uniqued(boolean)#getIntervals()` or `IntervalList.getUniqueIntervals(IntervalList, boolean)` instead.
htsjdk.samtools.util.RelativeIso8601Date.getYear()
htsjdk.variant.variantcontext.Genotype.hasLog10PError()
htsjdk.samtools.SAMRecord.isAllowedAttributeValue(Object) The attribute type and value checks have been moved directly into `SAMBinaryTagAndValue`.
htsjdk.samtools.sra.SRAAccession.isSupported() use `SRAAccession.checkIfInitialized()` instead
htsjdk.samtools.fastq.FastqRecord.length() since 02/2017. Use `FastqRecord.getReadLength()` instead
htsjdk.tribble.util.FTPHelper.openInputStreamForRange(long, long)
htsjdk.tribble.util.HTTPHelper.openInputStreamForRange(long, long) since 12/10/14 Will be removed in a future release, as is somewhat fragile and not used.
htsjdk.tribble.util.RemoteURLHelper.openInputStreamForRange(long, long)
htsjdk.tribble.util.URLHelper.openInputStreamForRange(long, long) Will be removed in a future release, as is somewhat fragile and not used.
htsjdk.samtools.AbstractBAMFileIndex.optimizeChunkList(List<Chunk>, long) Invoke `Chunk.optimizeChunkList(java.util.List<htsjdk.samtools.Chunk>, long)` directly.
htsjdk.samtools.util.CollectionUtil.partition(Collection<V>, CollectionUtil.Partitioner<V, K>) use java8 .stream().collect(Collectors.groupingBy(()-> function)) 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.samtools.SAMRecordUtil.reverseComplement(SAMRecord) 6/5/2017 Use `SAMRecord.reverseComplement()` but note that the default behavior there is different It will default to making a copy, not reverse-complementing in-place!
htsjdk.samtools.SAMRecordUtil.reverseComplement(SAMRecord, boolean) 6/5/2017 Use `SAMRecord.reverseComplement()`
htsjdk.samtools.SAMRecordUtil.reverseComplement(SAMRecord, Collection<String>, Collection<String>, boolean) 6/5/2017 Use `SAMRecord.reverseComplement()`
htsjdk.variant.vcf.VCFEncoder.setAllowMissingFieldsInHeader(boolean) since 10/24/13 use the constructor
htsjdk.samtools.AbstractSAMHeaderRecord.setAttribute(String, Object) Use {@link #setAttribute(String, String) instead
htsjdk.samtools.SAMFileHeader.setAttribute(String, Object) Use {@link #setAttribute(String, String) instead
htsjdk.samtools.util.RelativeIso8601Date.setDate(int)
htsjdk.samtools.util.RelativeIso8601Date.setHours(int)
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.util.RelativeIso8601Date.setMinutes(int)
htsjdk.samtools.util.RelativeIso8601Date.setMonth(int)
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.setReadUmappedFlag(boolean)
htsjdk.samtools.DuplicateSetIterator.setScoringStrategy(DuplicateScoringStrategy.ScoringStrategy)
htsjdk.samtools.util.RelativeIso8601Date.setSeconds(int)
htsjdk.samtools.util.RelativeIso8601Date.setTime(long)
htsjdk.samtools.SamFileValidator.setValidateIndex(boolean) use `SamFileValidator.setIndexValidationStringency(htsjdk.samtools.BamIndexValidator.IndexValidationStringency)` instead
htsjdk.variant.vcf.VCFEncoder.setVCFHeader(VCFHeader) since 10/24/13 use the constructor
htsjdk.samtools.util.RelativeIso8601Date.setYear(int)
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.tribble.index.IndexFactory.writeIndex(Index, File) use `Index.write(File)` instead

Deprecated Constructors
Constructor and Description
htsjdk.tribble.readers.AsciiLineReader(InputStream) 8/8/2017 use `AsciiLineReader.from(java.io.InputStream)`
htsjdk.tribble.readers.AsciiLineReader(PositionalBufferedStream) 8/8/2017 use `AsciiLineReader.from(java.io.InputStream)`
htsjdk.samtools.CRAMIterator(SeekableStream, CRAMReferenceSource, long[])
htsjdk.samtools.MergingSamRecordIterator(SamFileHeaderMerger, boolean) replaced by `MergingSamRecordIterator.MergingSamRecordIterator(SamFileHeaderMerger, Collection, boolean)`
htsjdk.samtools.SamFileHeaderMerger(Collection<SamReader>, SAMFileHeader.SortOrder) replaced by `SamFileHeaderMerger.SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection, boolean)`
htsjdk.samtools.SamFileHeaderMerger(Collection<SamReader>, SAMFileHeader.SortOrder, boolean) replaced by `SamFileHeaderMerger.SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection, boolean)`
htsjdk.samtools.SAMSequenceRecord(String) Use `SAMSequenceRecord.SAMSequenceRecord(String, int)` instead. sequenceLength is required for the object to be considered valid.

Deprecated API

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