Class and Description |
---|
htsjdk.samtools.util.CollectionUtil.Partitioner
use Collectors.groupingBy instead
|
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.tribble.readers.LineReaderUtil |
htsjdk.samtools.SAMRecordUtil |
htsjdk.variant.variantcontext.writer.VariantContextWriterFactory
Replaced by
VariantContextWriterBuilder |
Enum and Description |
---|
htsjdk.tribble.gelitext.DiploidGenotype |
htsjdk.tribble.readers.LineReaderUtil.LineReaderOption |
Field and Description |
---|
htsjdk.variant.vcf.VCFConstants.GENOTYPE_LIKELIHOODS_KEY |
htsjdk.samtools.util.IOUtil.STANDARD_BUFFER_SIZE
Use
Defaults.NON_ZERO_BUFFER_SIZE instead. |
Constructor and Description |
---|
htsjdk.samtools.CRAMIterator(SeekableStream, CRAMReferenceSource, long[]) |
htsjdk.samtools.MergingSamRecordIterator(SamFileHeaderMerger, boolean) |
htsjdk.samtools.SamFileHeaderMerger(Collection<SamReader>, SAMFileHeader.SortOrder) |
htsjdk.samtools.SamFileHeaderMerger(Collection<SamReader>, SAMFileHeader.SortOrder, boolean) |
htsjdk.samtools.SAMSequenceRecord(String)
Use
SAMSequenceRecord.SAMSequenceRecord(String, int) instead.
sequenceLength is required for the object to be considered valid. |