htsjdk.samtools

Class CRAMFileReader

java.lang.Object

htsjdk.samtools.SamReader.ReaderImplementation

htsjdk.samtools.CRAMFileReader

All Implemented Interfaces:

SamReader.Indexing, SamReader.PrimitiveSamReader

public class CRAMFileReader
extends SamReader.ReaderImplementation
implements SamReader.Indexing

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

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CRAMFileReader.IntervalIterator

Constructor Summary

Constructors

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

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.
SAMRecordIterator	getIterator()
CloseableIterator<SAMRecord>	getIterator(SAMFileSpan fileSpan)
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(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

CRAMFileReader

public CRAMFileReader(java.io.File cramFile,
                      java.io.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:

java.lang.IllegalArgumentException - if the cramFile and the inputStream are both null

java.lang.IllegalStateException - if a default reference source cannot be acquired

CRAMFileReader

public CRAMFileReader(java.io.File cramFile,
                      java.io.InputStream inputStream,
                      ReferenceSource 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:

java.lang.IllegalArgumentException - if the cramFile and the inputStream are both null or if the ReferenceSource is null

CRAMFileReader

public CRAMFileReader(java.io.File cramFile,
                      java.io.File indexFile,
                      ReferenceSource 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:

java.lang.IllegalArgumentException - if the cramFile or the ReferenceSource is null

CRAMFileReader

public CRAMFileReader(java.io.File cramFile,
                      ReferenceSource 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:

java.lang.IllegalArgumentException - if the cramFile or the ReferenceSource is null

CRAMFileReader

public CRAMFileReader(java.io.InputStream inputStream,
                      SeekableStream indexInputStream,
                      ReferenceSource referenceSource,
                      ValidationStringency validationStringency)
               throws java.io.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:

java.lang.IllegalArgumentException - if the inputStream or the ReferenceSource is null

java.io.IOException

CRAMFileReader

public CRAMFileReader(java.io.InputStream stream,
                      java.io.File indexFile,
                      ReferenceSource referenceSource,
                      ValidationStringency validationStringency)
               throws java.io.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:

java.lang.IllegalArgumentException - if the inputStream or the ReferenceSource is null

java.io.IOException

CRAMFileReader

public CRAMFileReader(java.io.File cramFile,
                      java.io.File indexFile,
                      ReferenceSource referenceSource,
                      ValidationStringency validationStringency)
               throws java.io.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:

java.lang.IllegalArgumentException - if the cramFile or the ReferenceSource is null

java.io.IOException

Method Detail

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)

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(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

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