Class and Description |
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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 |
Enum and Description |
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htsjdk.tribble.gelitext.DiploidGenotype |
Field and Description |
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htsjdk.variant.vcf.VCFConstants.GENOTYPE_LIKELIHOODS_KEY |
htsjdk.samtools.util.IOUtil.STANDARD_BUFFER_SIZE
Use Defaults.NON_ZERO_BUFFER_SIZE instead.
|
Constructor and Description |
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htsjdk.samtools.CRAMIterator(SeekableStream, ReferenceSource, long[]) |
htsjdk.samtools.MergingSamRecordIterator(SamFileHeaderMerger, boolean)
replaced by (SamFileHeaderMerger, Collection
|
htsjdk.samtools.SamFileHeaderMerger(Collection<SamReader>, SAMFileHeader.SortOrder)
replaced by SamFileHeaderMerger(Collection
|
htsjdk.samtools.SamFileHeaderMerger(Collection<SamReader>, SAMFileHeader.SortOrder, boolean)
replaced by SamFileHeaderMerger(Collection
|
htsjdk.samtools.SAMSequenceRecord(String)
Use SAMSequenceRecord(final String name, final int sequenceLength) instead.
sequenceLength is required for the object to be considered valid.
|