Package | Description |
---|---|
htsjdk.samtools | |
htsjdk.samtools.sra |
Modifier and Type | Method and Description |
---|---|
static SamInputResource |
SamInputResource.of(SRAAccession acc) |
Constructor and Description |
---|
SRAFileReader(SRAAccession acc) |
SRAIterator(SRAAccession accession,
ngs.ReadCollection run,
SAMFileHeader header,
ReferenceCache cachedReferences,
SRAIterator.RecordRangeInfo recordRangeInfo,
List<Chunk> chunks) |
Constructor and Description |
---|
SRAAlignmentIterator(SRAAccession accession,
ngs.ReadCollection run,
SAMFileHeader header,
ReferenceCache cachedReferences,
SRAIterator.RecordRangeInfo recordRangeInfo,
Chunk chunk) |
SRAIndexedSequenceFile(SRAAccession acc) |
SRALazyRecord(SAMFileHeader header,
SRAAccession accession,
ngs.ReadCollection run,
ngs.AlignmentIterator alignmentIterator,
String readId,
String alignmentId) |
SRALazyRecord(SAMFileHeader header,
SRAAccession accession,
ngs.ReadCollection run,
ngs.ReadIterator unalignmentIterator,
String readId,
int unalignedReadFragmentIndex) |
SRALazyRecord(SAMFileHeader header,
SRAAccession accession,
String readId,
int unalignedReadFragmentIndex) |
SRALazyRecord(SAMFileHeader header,
SRAAccession accession,
String readId,
String alignmentId) |
SRAUnalignmentIterator(SRAAccession accession,
ngs.ReadCollection run,
SAMFileHeader header,
SRAIterator.RecordRangeInfo recordRangeInfo,
Chunk chunk) |