Constructor and Description |
---|
SRAAlignmentIterator(SRAAccession accession,
ngs.ReadCollection run,
SAMFileHeader header,
ReferenceCache cachedReferences,
SRAIterator.RecordRangeInfo recordRangeInfo,
Chunk chunk) |
Modifier and Type | Method and Description |
---|---|
boolean |
hasNext() |
SAMRecord |
next() |
void |
remove() |
void |
setValidationStringency(ValidationStringency validationStringency) |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
forEachRemaining
public SRAAlignmentIterator(SRAAccession accession, ngs.ReadCollection run, SAMFileHeader header, ReferenceCache cachedReferences, SRAIterator.RecordRangeInfo recordRangeInfo, Chunk chunk)
run
- opened read collectionheader
- sam headercachedReferences
- list of cached references shared among all iterators from a single SRAFileReaderrecordRangeInfo
- info about record ranges withing SRA archivechunk
- used to determine which alignments the iterator should returnpublic void setValidationStringency(ValidationStringency validationStringency)