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

All Methods Instance Methods Concrete Methods
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 Detail
  - 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 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)
```
    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 Detail

CRAMFileReader

CRAMFileReader

CRAMFileReader

CRAMFileReader

CRAMFileReader

CRAMFileReader

CRAMFileReader

Method Detail

hasIndex

getIndex

hasBrowseableIndex

getBrowseableIndex

iterator

getFileHeader

getIterator

getIterator

getFilePointerSpanningReads

queryAlignmentStart

queryUnmapped

close

getValidationStringency

query

type

createIndexIterator