htsjdk.samtools

Class SRAFileReader

java.lang.Object

htsjdk.samtools.SamReader.ReaderImplementation

htsjdk.samtools.SRAFileReader

All Implemented Interfaces:

SamReader.Indexing, SamReader.PrimitiveSamReader

public class SRAFileReader
extends SamReader.ReaderImplementation
implements SamReader.Indexing

Constructor Summary

Constructors

Constructor and Description
SRAFileReader(SRAAccession acc)

Method Summary

Modifier and Type	Method and Description
void	close()
BrowseableBAMIndex	getBrowseableIndex() Gets an index tagged with the BrowseableBAMIndex interface.
SAMFileHeader	getFileHeader()
SAMFileSpan	getFilePointerSpanningReads() Gets a pointer spanning all reads in the BAM file.
BAMIndex	getIndex() Retrieves the index for the given file type.
CloseableIterator<SAMRecord>	getIterator()
CloseableIterator<SAMRecord>	getIterator(SAMFileSpan chunks)
protected SRAIterator.RecordRangeInfo	getRecordsRangeInfo()
ValidationStringency	getValidationStringency()
boolean	hasBrowseableIndex() Returns true if the supported index is browseable, meaning the bins in it can be traversed and chunk data inspected and retrieved.
boolean	hasIndex()
SAMRecordIterator	iterator(SAMFileSpan chunks) Iterate through the given chunks in the file.
CloseableIterator<SAMRecord>	query(QueryInterval[] intervals, boolean contained)
CloseableIterator<SAMRecord>	queryAlignmentStart(java.lang.String sequence, int start)
CloseableIterator<SAMRecord>	queryUnmapped()
SamReader.Type	type()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SRAFileReader

public SRAFileReader(SRAAccession acc)

Method Detail

type

public SamReader.Type type()

Specified by:

type in interface SamReader.PrimitiveSamReader

hasIndex

public boolean hasIndex()

Specified by:

hasIndex in interface SamReader.PrimitiveSamReader

getIndex

public BAMIndex getIndex()

Description copied from interface: SamReader.Indexing

Retrieves the index for the given file type. Ensure that the index is of the specified type.

Specified by:

getIndex in interface SamReader.Indexing

Specified by:

getIndex in interface SamReader.PrimitiveSamReader

Returns:

An index of the given type.

getFileHeader

public SAMFileHeader getFileHeader()

Specified by:

getFileHeader in interface SamReader.PrimitiveSamReader

getIterator

public CloseableIterator<SAMRecord> getIterator()

Specified by:

getIterator in interface SamReader.PrimitiveSamReader

getIterator

public CloseableIterator<SAMRecord> getIterator(SAMFileSpan chunks)

Specified by:

getIterator in interface SamReader.PrimitiveSamReader

getFilePointerSpanningReads

public SAMFileSpan getFilePointerSpanningReads()

Description copied from interface: SamReader.Indexing

Gets a pointer spanning all reads in the BAM file.

Specified by:

getFilePointerSpanningReads in interface SamReader.Indexing

Specified by:

getFilePointerSpanningReads in interface SamReader.PrimitiveSamReader

Returns:

Unbounded pointer to the first record, in chunk format.

query

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

Specified by:

query in interface SamReader.PrimitiveSamReader

queryAlignmentStart

public CloseableIterator<SAMRecord> queryAlignmentStart(java.lang.String sequence,
                                                        int start)

Specified by:

queryAlignmentStart in interface SamReader.PrimitiveSamReader

queryUnmapped

public CloseableIterator<SAMRecord> queryUnmapped()

Specified by:

queryUnmapped in interface SamReader.PrimitiveSamReader

close

public void close()

Specified by:

close in interface SamReader.PrimitiveSamReader

getValidationStringency

public ValidationStringency getValidationStringency()

Specified by:

getValidationStringency in interface SamReader.PrimitiveSamReader

hasBrowseableIndex

public boolean hasBrowseableIndex()

Returns true if the supported index is browseable, meaning the bins in it can be traversed and chunk data inspected and retrieved.

Specified by:

hasBrowseableIndex in interface SamReader.Indexing

Returns:

True if the index supports the BrowseableBAMIndex interface. False otherwise.

getBrowseableIndex

public BrowseableBAMIndex getBrowseableIndex()

Gets an index tagged with the BrowseableBAMIndex interface. Throws an exception if no such index is available.

Specified by:

getBrowseableIndex in interface SamReader.Indexing

Returns:

An index with a browseable interface, if possible.

Throws:

SAMException - if no such index is available.

iterator

public SAMRecordIterator iterator(SAMFileSpan chunks)

Iterate through the given chunks in the file.

Specified by:

iterator in interface SamReader.Indexing

Parameters:

chunks - List of chunks for which to retrieve data.

Returns:

An iterator over the given chunks.

getRecordsRangeInfo

protected SRAIterator.RecordRangeInfo getRecordsRangeInfo()