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

Class CRAMFileReader

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface htsjdk.samtools.SamReader.PrimitiveSamReader

Constructor Details

CRAMFileReader

CRAMFileReader

CRAMFileReader

CRAMFileReader

CRAMFileReader

CRAMFileReader

CRAMFileReader

Method Details

hasIndex

getIndex

hasBrowseableIndex

getBrowseableIndex

iterator

getFileHeader

getIterator

getIterator

getFilePointerSpanningReads

queryAlignmentStart

queryUnmapped

close

getValidationStringency

query

type

createIndexIterator