Package htsjdk.samtools

Interface SamReader.PrimitiveSamReader

All Known Implementing Classes:

BAMFileReader, CRAMFileReader, HtsgetBAMFileReader, SamReader.ReaderImplementation, SRAFileReader

Enclosing interface:

SamReader

public static interface SamReader.PrimitiveSamReader

The minimal subset of functionality needed for a 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

Method Summary

Modifier and Type	Method	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(String sequence, int start)
CloseableIterator<SAMRecord>	queryUnmapped()
SamReader.Type	type()

Method Details

type

SamReader.Type type()

isQueryable

default boolean isQueryable()

hasIndex

boolean hasIndex()

getIndex

BAMIndex getIndex()

getFileHeader

SAMFileHeader getFileHeader()

getIterator

CloseableIterator<SAMRecord> getIterator()

getIterator

CloseableIterator<SAMRecord> getIterator(SAMFileSpan fileSpan)

getFilePointerSpanningReads

SAMFileSpan getFilePointerSpanningReads()

query

CloseableIterator<SAMRecord> query(QueryInterval[] intervals,
 boolean contained)

queryAlignmentStart

CloseableIterator<SAMRecord> queryAlignmentStart(String sequence,
 int start)

queryUnmapped

CloseableIterator<SAMRecord> queryUnmapped()

close

void close()

getValidationStringency

ValidationStringency getValidationStringency()