| 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.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, long)
Invoke htsjdk.samtools.Chunk#optimizeChunkList(java.util.List, long) directly.
|
| 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.util.RelativeIso8601Date.setSeconds(int) |
| htsjdk.samtools.util.RelativeIso8601Date.setTime(long) |
| 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) |