public class CRAMFileReader extends SamReader.ReaderImplementation implements SamReader.Indexing
BAMFileReader
analogue for CRAM files.
Supports random access using BAI index file formats.Modifier and Type | Class and Description |
---|---|
static class |
CRAMFileReader.IntervalIterator |
Constructor and Description |
---|
CRAMFileReader(java.io.File cramFile,
java.io.File indexFile,
ReferenceSource referenceSource)
Open CRAM file for reading.
|
CRAMFileReader(java.io.File cramFile,
java.io.File indexFile,
ReferenceSource referenceSource,
ValidationStringency validationStringency) |
CRAMFileReader(java.io.File cramFile,
java.io.InputStream inputStream)
Open CRAM data for reading using either the file or the input stream
supplied in the arguments.
|
CRAMFileReader(java.io.File cramFile,
java.io.InputStream inputStream,
ReferenceSource referenceSource)
Open CRAM data for reading using either the file or the input stream
supplied in the arguments.
|
CRAMFileReader(java.io.File cramFile,
ReferenceSource referenceSource) |
CRAMFileReader(java.io.InputStream stream,
java.io.File indexFile,
ReferenceSource referenceSource,
ValidationStringency validationStringency) |
CRAMFileReader(java.io.InputStream inputStream,
SeekableStream indexInputStream,
ReferenceSource referenceSource,
ValidationStringency validationStringency) |
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() |
public CRAMFileReader(java.io.File cramFile, java.io.InputStream inputStream)
default
reference fasta
file will be used.cramFile
- CRAM file to openinputStream
- CRAM stream to readpublic CRAMFileReader(java.io.File cramFile, java.io.InputStream inputStream, ReferenceSource referenceSource)
cramFile
- CRAM file to readinputStream
- index file to be used for random accessreferenceSource
- a source
of
reference sequencespublic CRAMFileReader(java.io.File cramFile, java.io.File indexFile, ReferenceSource referenceSource)
cramFile
- CRAM file to readindexFile
- index file to be used for random accessreferenceSource
- a source
of
reference sequencespublic CRAMFileReader(java.io.File cramFile, ReferenceSource referenceSource)
public CRAMFileReader(java.io.InputStream inputStream, SeekableStream indexInputStream, ReferenceSource referenceSource, ValidationStringency validationStringency) throws java.io.IOException
java.io.IOException
public CRAMFileReader(java.io.InputStream stream, java.io.File indexFile, ReferenceSource referenceSource, ValidationStringency validationStringency) throws java.io.IOException
java.io.IOException
public CRAMFileReader(java.io.File cramFile, java.io.File indexFile, ReferenceSource referenceSource, ValidationStringency validationStringency) throws java.io.IOException
java.io.IOException
public boolean hasIndex()
hasIndex
in interface SamReader.PrimitiveSamReader
public BAMIndex getIndex()
SamReader.Indexing
getIndex
in interface SamReader.Indexing
getIndex
in interface SamReader.PrimitiveSamReader
public boolean hasBrowseableIndex()
SamReader.Indexing
hasBrowseableIndex
in interface SamReader.Indexing
public BrowseableBAMIndex getBrowseableIndex()
SamReader.Indexing
getBrowseableIndex
in interface SamReader.Indexing
public SAMRecordIterator iterator(SAMFileSpan fileSpan)
SamReader.Indexing
iterator
in interface SamReader.Indexing
fileSpan
- List of chunks for which to retrieve data.public SAMFileHeader getFileHeader()
getFileHeader
in interface SamReader.PrimitiveSamReader
public SAMRecordIterator getIterator()
getIterator
in interface SamReader.PrimitiveSamReader
public CloseableIterator<SAMRecord> getIterator(SAMFileSpan fileSpan)
getIterator
in interface SamReader.PrimitiveSamReader
public SAMFileSpan getFilePointerSpanningReads()
SamReader.Indexing
getFilePointerSpanningReads
in interface SamReader.Indexing
getFilePointerSpanningReads
in interface SamReader.PrimitiveSamReader
public CloseableIterator<SAMRecord> queryAlignmentStart(java.lang.String sequence, int start)
queryAlignmentStart
in interface SamReader.PrimitiveSamReader
public CloseableIterator<SAMRecord> queryUnmapped()
queryUnmapped
in interface SamReader.PrimitiveSamReader
public void close()
close
in interface SamReader.PrimitiveSamReader
public ValidationStringency getValidationStringency()
getValidationStringency
in interface SamReader.PrimitiveSamReader
public CloseableIterator<SAMRecord> query(QueryInterval[] intervals, boolean contained)
query
in interface SamReader.PrimitiveSamReader
public SamReader.Type type()
type
in interface SamReader.PrimitiveSamReader