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() |
default boolean |
isQueryable() |
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()
default boolean isQueryable()
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()