Deprecated API

Contents

• Deprecated Interfaces
• Deprecated Classes
• Deprecated Fields
• Deprecated Methods
• Deprecated Constructors

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
htsjdk.variant.variantcontext.filter.FilteringIterator
htsjdk.samtools.SAMRecordUtil

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.

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)
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() use getContig() instead
htsjdk.samtools.util.RelativeIso8601Date.getDate()
htsjdk.samtools.util.RelativeIso8601Date.getDay()
htsjdk.samtools.util.RelativeIso8601Date.getHours()
htsjdk.variant.variantcontext.GenotypeLikelihoods.getLog10GQ(GenotypeType)
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.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.tribble.util.FTPHelper.openInputStreamForRange(long, long)
htsjdk.tribble.util.HTTPHelper.openInputStreamForRange(long, long)
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.variant.vcf.VCFEncoder.setAllowMissingFieldsInHeader(boolean)
htsjdk.samtools.AbstractSAMHeaderRecord.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)
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.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.