public static interface SamReader.PrimitiveSamReader
SAMRecord
data source.
SamReader
itself is somewhat large and bulky, but the core functionality can be captured in
relatively few methods, which are included here. For documentation, see the corresponding methods
in SamReader
.
See also: SamReader.PrimitiveSamReaderToSamReaderAdapter
, SamReader.ReaderImplementation
Modifier and Type | Method and Description |
---|---|
void |
close() |
SAMFileHeader |
getFileHeader() |
SAMFileSpan |
getFilePointerSpanningReads() |
BAMIndex |
getIndex() |
CloseableIterator<SAMRecord> |
getIterator() |
CloseableIterator<SAMRecord> |
getIterator(SAMFileSpan fileSpan) |
ValidationStringency |
getValidationStringency() |
boolean |
hasIndex() |
CloseableIterator<SAMRecord> |
query(QueryInterval[] intervals,
boolean contained) |
CloseableIterator<SAMRecord> |
queryAlignmentStart(java.lang.String sequence,
int start) |
CloseableIterator<SAMRecord> |
queryUnmapped() |
SamReader.Type |
type() |
SamReader.Type type()
boolean hasIndex()
BAMIndex getIndex()
SAMFileHeader getFileHeader()
CloseableIterator<SAMRecord> getIterator()
CloseableIterator<SAMRecord> getIterator(SAMFileSpan fileSpan)
SAMFileSpan getFilePointerSpanningReads()
CloseableIterator<SAMRecord> query(QueryInterval[] intervals, boolean contained)
CloseableIterator<SAMRecord> queryAlignmentStart(java.lang.String sequence, int start)
CloseableIterator<SAMRecord> queryUnmapped()
void close()
ValidationStringency getValidationStringency()