Deprecated API

Contents

• Deprecated Classes
• Deprecated Enums
• Deprecated Fields
• Deprecated Methods
• Deprecated Constructors

Deprecated Classes

Class and Description
htsjdk.samtools.util.CollectionUtil.Partitioner
htsjdk.samtools.filter.FilteringIterator
htsjdk.variant.variantcontext.filter.FilteringIterator
htsjdk.tribble.gelitext.GeliTextCodec This is deprecated and unsupported.
htsjdk.tribble.gelitext.GeliTextFeature this is deprecated and no longer supported
htsjdk.samtools.SAMFileReader
htsjdk.samtools.SAMFileTruncatedReader
htsjdk.variant.variantcontext.writer.VariantContextWriterFactory Replaced by VariantContextWriterBuilder

Deprecated Enums

Enum and Description
htsjdk.tribble.gelitext.DiploidGenotype

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.util.SequenceUtil.calculateSamNmTag(SAMRecord, char[], int)
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, use htsjdk.samtools.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.tribble.SimpleFeature.getChr()
htsjdk.tribble.bed.SimpleBEDFeature.getChr()
htsjdk.tribble.gelitext.GeliTextFeature.getChr()
htsjdk.variant.variantcontext.VariantContext.getChr()
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 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 getProgramGroupId(SAMFileHeader, String)
htsjdk.samtools.SamFileHeaderMerger.getReaders() replaced by getHeaders()
htsjdk.samtools.SamFileHeaderMerger.getReadGroupId(SamReader, String) replaced by getReadGroupId(SAMFileHeader, String)
htsjdk.samtools.util.RelativeIso8601Date.getSeconds()
htsjdk.samtools.util.Interval.getSequence() use getContig() instead
htsjdk.samtools.util.TestUtil.getTempDirecory(String, String) Use properly spelled method.
htsjdk.samtools.util.RelativeIso8601Date.getTimezoneOffset()
htsjdk.samtools.util.IntervalList.getUniqueIntervals()
htsjdk.samtools.util.IntervalList.getUniqueIntervals(boolean)
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.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 htsjdk.samtools.Chunk#optimizeChunkList(java.util.List, long) directly.
htsjdk.samtools.util.CollectionUtil.partition(Collection<V>, CollectionUtil.Partitioner<V, K>)
htsjdk.variant.vcf.VCFEncoder.setAllowMissingFieldsInHeader(boolean)
htsjdk.samtools.AbstractSAMHeaderRecord.setAttribute(String, Object) Use the version that takes a String value instead
htsjdk.samtools.util.RelativeIso8601Date.setDate(int)
htsjdk.samtools.util.RelativeIso8601Date.setHours(int)
htsjdk.samtools.SamPairUtil.setMateInfo(SAMRecord, SAMRecord, SAMFileHeader, boolean)
htsjdk.samtools.util.RelativeIso8601Date.setMinutes(int)
htsjdk.samtools.util.RelativeIso8601Date.setMonth(int)
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 setIndexValidationStringency instead
htsjdk.variant.vcf.VCFEncoder.setVCFHeader(VCFHeader)
htsjdk.samtools.util.RelativeIso8601Date.setYear(int)
htsjdk.samtools.util.IntervalList.sort()
htsjdk.samtools.util.SequenceUtil.sumQualitiesOfMismatches(SAMRecord, char[], int)
htsjdk.samtools.util.IntervalList.unique()
htsjdk.samtools.util.IntervalList.unique(boolean)

Deprecated Constructors

Constructor and Description
htsjdk.samtools.CRAMIterator(SeekableStream, ReferenceSource, long[])
htsjdk.samtools.MergingSamRecordIterator(SamFileHeaderMerger, boolean) replaced by (SamFileHeaderMerger, Collection, boolean)
htsjdk.samtools.SamFileHeaderMerger(Collection<SamReader>, SAMFileHeader.SortOrder) replaced by SamFileHeaderMerger(Collection, SAMFileHeader.SortOrder, boolean)
htsjdk.samtools.SamFileHeaderMerger(Collection<SamReader>, SAMFileHeader.SortOrder, boolean) replaced by SamFileHeaderMerger(Collection, SAMFileHeader.SortOrder, boolean)
htsjdk.samtools.SAMSequenceRecord(String) Use SAMSequenceRecord(final String name, final int sequenceLength) instead. sequenceLength is required for the object to be considered valid.