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Deprecated Methods |
htsjdk.samtools.cram.encoding.huffman.HuffmanCode.buildTreeUsingPriorityQueue(int[], T[])
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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)
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htsjdk.variant.variantcontext.GenotypeLikelihoods.getAllelePairUsingDeprecatedOrdering(int)
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htsjdk.variant.variantcontext.Genotype.getAttributeAsDouble(String, double)
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htsjdk.variant.variantcontext.Genotype.getAttributeAsInt(String, int)
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htsjdk.variant.variantcontext.Genotype.getAttributeAsString(String, String)
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htsjdk.samtools.util.RelativeIso8601Date.getDate()
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htsjdk.samtools.util.RelativeIso8601Date.getDay()
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htsjdk.samtools.util.RelativeIso8601Date.getHours()
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htsjdk.variant.variantcontext.GenotypeLikelihoods.getLog10GQ(GenotypeType)
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htsjdk.variant.variantcontext.Genotype.getLog10PError()
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htsjdk.samtools.SamFileHeaderMerger.getMergedSequenceIndex(SamReader, Integer)
replaced by getMergedSequenceIndex(SAMFileHeader, Integer) |
htsjdk.samtools.util.RelativeIso8601Date.getMinutes()
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htsjdk.samtools.util.RelativeIso8601Date.getMonth()
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htsjdk.variant.variantcontext.Genotype.getPhredScaledQual()
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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()
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htsjdk.samtools.util.TestUtil.getTempDirecory(String, String)
Use properly spelled method. |
htsjdk.samtools.util.RelativeIso8601Date.getTimezoneOffset()
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htsjdk.samtools.util.IntervalList.getUniqueIntervals()
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htsjdk.samtools.util.IntervalList.getUniqueIntervals(boolean)
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htsjdk.samtools.util.RelativeIso8601Date.getYear()
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htsjdk.variant.variantcontext.Genotype.hasLog10PError()
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htsjdk.variant.variantcontext.GenotypeBuilder.log10PError(double)
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htsjdk.tribble.util.FTPHelper.openInputStreamForRange(long, long)
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htsjdk.tribble.util.HTTPHelper.openInputStreamForRange(long, long)
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htsjdk.tribble.util.RemoteURLHelper.openInputStreamForRange(long, long)
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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, long)
Invoke htsjdk.samtools.Chunk#optimizeChunkList(java.util.List, long) directly. |
htsjdk.variant.vcf.VCFEncoder.setAllowMissingFieldsInHeader(boolean)
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htsjdk.samtools.AbstractSAMHeaderRecord.setAttribute(String, Object)
Use the version that takes a String value instead |
htsjdk.samtools.util.RelativeIso8601Date.setDate(int)
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htsjdk.samtools.util.RelativeIso8601Date.setHours(int)
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htsjdk.samtools.SamPairUtil.setMateInfo(SAMRecord, SAMRecord, SAMFileHeader, boolean)
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htsjdk.samtools.util.RelativeIso8601Date.setMinutes(int)
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htsjdk.samtools.util.RelativeIso8601Date.setMonth(int)
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htsjdk.samtools.SAMRecord.setReadUmappedFlag(boolean)
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htsjdk.samtools.util.RelativeIso8601Date.setSeconds(int)
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htsjdk.samtools.util.RelativeIso8601Date.setTime(long)
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htsjdk.variant.vcf.VCFEncoder.setVCFHeader(VCFHeader)
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htsjdk.samtools.util.RelativeIso8601Date.setYear(int)
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htsjdk.samtools.util.IntervalList.sort()
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htsjdk.samtools.util.IntervalList.unique()
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htsjdk.samtools.util.IntervalList.unique(boolean)
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