Package htsjdk.samtools

Class CRAMFileReader

java.lang.Object

htsjdk.samtools.SamReader.ReaderImplementation

htsjdk.samtools.CRAMFileReader

All Implemented Interfaces:

SamReader.Indexing, SamReader.PrimitiveSamReader, AutoCloseable

public class CRAMFileReader
extends SamReader.ReaderImplementation
implements SamReader.Indexing, AutoCloseable

BAMFileReader analogue for CRAM files. Supports random access using BAI index file formats.

Constructor Summary

Constructors

Constructor	Description
CRAMFileReader(File cramFile, CRAMReferenceSource referenceSource)	Create a CRAMFileReader from a file using the supplied reference source.
CRAMFileReader(File cramFile, File indexFile, CRAMReferenceSource referenceSource)	Create a CRAMFileReader from a file and optional index file using the supplied reference source.
CRAMFileReader(File cramFile, File indexFile, CRAMReferenceSource referenceSource, ValidationStringency validationStringency)	Create a CRAMFileReader from a CRAM file and optional index file using the supplied reference source and validation stringency.
CRAMFileReader(File cramFile, InputStream inputStream)	Create a CRAMFileReader from either a file or input stream using the reference source returned by getDefaultCRAMReferenceSource.
CRAMFileReader(File cramFile, InputStream inputStream, CRAMReferenceSource referenceSource)	Create a CRAMFileReader from either a file or input stream using the supplied reference source.
CRAMFileReader(InputStream inputStream, SeekableStream indexInputStream, CRAMReferenceSource referenceSource, ValidationStringency validationStringency)	Create a CRAMFileReader from an input stream and optional index stream using the supplied reference source and validation stringency.
CRAMFileReader(InputStream stream, File indexFile, CRAMReferenceSource referenceSource, ValidationStringency validationStringency)	Create a CRAMFileReader from an input stream and optional index file using the supplied reference source and validation stringency.

Method Summary

Modifier and Type	Method	Description
void	close()
CloseableIterator<SAMRecord>	createIndexIterator(QueryInterval[] intervals, boolean contained, long[] filePointers)	Prepare to iterate through SAMRecords that match the intersection of the given intervals and chunk boundaries.
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.
SAMRecordIterator	getIterator()
CloseableIterator<SAMRecord>	getIterator(SAMFileSpan fileSpan)	Note: the resolution of this iterator is the Slice, so the records returned are all of the records in all the slices that overlap these spans.
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 fileSpan)	Iterate through the given chunks in the file.
CloseableIterator<SAMRecord>	query(QueryInterval[] intervals, boolean contained)
CloseableIterator<SAMRecord>	queryAlignmentStart(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

Methods inherited from interface htsjdk.samtools.SamReader.PrimitiveSamReader

isQueryable

Constructor Details

CRAMFileReader

public CRAMFileReader(File cramFile,
 InputStream inputStream)

Create a CRAMFileReader from either a file or input stream using the reference source returned by getDefaultCRAMReferenceSource.

Parameters:

cramFile - CRAM file to open

inputStream - CRAM stream to read

Throws:

IllegalArgumentException - if the cramFile and the inputStream are both null

IllegalStateException - if a default reference source cannot be acquired

CRAMFileReader

public CRAMFileReader(File cramFile,
 InputStream inputStream,
 CRAMReferenceSource referenceSource)

Create a CRAMFileReader from either a file or input stream using the supplied reference source.

Parameters:

cramFile - CRAM file to read

inputStream - CRAM stream to read

referenceSource - a source of reference sequences. May not be null.

Throws:

IllegalArgumentException - if the cramFile and the inputStream are both null or if the CRAMReferenceSource is null

CRAMFileReader

public CRAMFileReader(File cramFile,
 File indexFile,
 CRAMReferenceSource referenceSource)

Create a CRAMFileReader from a file and optional index file using the supplied reference source. If index file is supplied then random access will be available.

Parameters:

cramFile - CRAM file to read. May not be null.

indexFile - index file to be used for random access. May be null.

referenceSource - a source of reference sequences. May not be null.

Throws:

IllegalArgumentException - if the cramFile or the CRAMReferenceSource is null

CRAMFileReader

public CRAMFileReader(File cramFile,
 CRAMReferenceSource referenceSource)

Create a CRAMFileReader from a file using the supplied reference source.

Parameters:

cramFile - CRAM file to read. Can not be null.

referenceSource - a source of reference sequences. May not be null.

Throws:

IllegalArgumentException - if the cramFile or the CRAMReferenceSource is null

CRAMFileReader

public CRAMFileReader(InputStream inputStream,
 SeekableStream indexInputStream,
 CRAMReferenceSource referenceSource,
 ValidationStringency validationStringency)
               throws IOException

Create a CRAMFileReader from an input stream and optional index stream using the supplied reference source and validation stringency.

Parameters:

inputStream - CRAM stream to read. May not be null.

indexInputStream - index stream to be used for random access. May be null.

referenceSource - a source of reference sequences. May not be null.

validationStringency - Validation stringency to be used when reading

Throws:

IllegalArgumentException - if the inputStream or the CRAMReferenceSource is null

IOException

CRAMFileReader

public CRAMFileReader(InputStream stream,
 File indexFile,
 CRAMReferenceSource referenceSource,
 ValidationStringency validationStringency)
               throws IOException

Create a CRAMFileReader from an input stream and optional index file using the supplied reference source and validation stringency.

Parameters:

stream - CRAM stream to read. May not be null.

indexFile - index file to be used for random access. May be null.

referenceSource - a source of reference sequences. May not be null.

validationStringency - Validation stringency to be used when reading

Throws:

IllegalArgumentException - if the inputStream or the CRAMReferenceSource is null

IOException

CRAMFileReader

public CRAMFileReader(File cramFile,
 File indexFile,
 CRAMReferenceSource referenceSource,
 ValidationStringency validationStringency)
               throws IOException

Create a CRAMFileReader from a CRAM file and optional index file using the supplied reference source and validation stringency.

Parameters:

cramFile - CRAM stream to read. May not be null.

indexFile - index file to be used for random access. May be null.

referenceSource - a source of reference sequences. May not be null.

validationStringency - Validation stringency to be used when reading

Throws:

IllegalArgumentException - if the cramFile or the CRAMReferenceSource is null

IOException

Method Details

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.

hasBrowseableIndex

public boolean hasBrowseableIndex()

Description copied from interface: SamReader.Indexing

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()

Description copied from interface: SamReader.Indexing

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.

iterator

public SAMRecordIterator iterator(SAMFileSpan fileSpan)

Description copied from interface: SamReader.Indexing

Iterate through the given chunks in the file.

Specified by:

iterator in interface SamReader.Indexing

Parameters:

fileSpan - List of chunks for which to retrieve data.

Returns:

An iterator over the given chunks.

getFileHeader

public SAMFileHeader getFileHeader()

Specified by:

getFileHeader in interface SamReader.PrimitiveSamReader

getIterator

public SAMRecordIterator getIterator()

Specified by:

getIterator in interface SamReader.PrimitiveSamReader

getIterator

public CloseableIterator<SAMRecord> getIterator(SAMFileSpan fileSpan)

Note: the resolution of this iterator is the Slice, so the records returned are all of the records in all the slices that overlap these spans.

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.

queryAlignmentStart

public CloseableIterator<SAMRecord> queryAlignmentStart(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 AutoCloseable

Specified by:

close in interface SamReader.PrimitiveSamReader

getValidationStringency

public ValidationStringency getValidationStringency()

Specified by:

getValidationStringency in interface SamReader.PrimitiveSamReader

query

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

Specified by:

query in interface SamReader.PrimitiveSamReader

type

public SamReader.Type type()

Specified by:

type in interface SamReader.PrimitiveSamReader

createIndexIterator

public CloseableIterator<SAMRecord> createIndexIterator(QueryInterval[] intervals,
 boolean contained,
 long[] filePointers)

Prepare to iterate through SAMRecords that match the intersection of the given intervals and chunk boundaries.

Parameters:

intervals - the intervals to restrict reads to

contained - if true, return records that are strictly contained in the intervals, otherwise return records that overlap

filePointers - file pointer pairs corresponding to chunk boundaries for the intervals