htsjdk.samtools.cram.ref

Class ReferenceSource

java.lang.Object

htsjdk.samtools.cram.ref.ReferenceSource

All Implemented Interfaces:

CRAMReferenceSource

public class ReferenceSource
extends java.lang.Object
implements CRAMReferenceSource

Used to represent a CRAM reference, the backing source for which can either be a file or the EBI ENA reference service. NOTE: In a future release, this class will be renamed and the functionality it contains will be refactored and distributed into one or more separate reference source implementations, each corresponding to the type of resource backing the reference.

Constructor Summary

Constructors

Constructor and Description
ReferenceSource(java.io.File file)
ReferenceSource(java.nio.file.Path path)
ReferenceSource(ReferenceSequenceFile rsFile)

Method Summary

Modifier and Type	Method and Description
static CRAMReferenceSource	getDefaultCRAMReferenceSource() Attempts to construct a default CRAMReferenceSource for use with CRAM files when one has not been explicitly provided.
int	getDownloadTriesBeforeFailing()
byte[]	getReferenceBases(SAMSequenceRecord record, boolean tryNameVariants) Get the reference bases for an entire reference contig.
byte[]	getReferenceBasesByRegion(SAMSequenceRecord sequenceRecord, int zeroBasedStart, int requestedRegionLength) Get the reference bases for a region of a reference contig.
void	setDownloadTriesBeforeFailing(int downloadTriesBeforeFailing)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ReferenceSource

public ReferenceSource(java.io.File file)

ReferenceSource

public ReferenceSource(java.nio.file.Path path)

ReferenceSource

public ReferenceSource(ReferenceSequenceFile rsFile)

Method Detail

getDefaultCRAMReferenceSource

public static CRAMReferenceSource getDefaultCRAMReferenceSource()

Attempts to construct a default CRAMReferenceSource for use with CRAM files when one has not been explicitly provided.

Returns:

CRAMReferenceSource if one can be acquired. Guaranteed to not be null if none of the listed exceptions is thrown.

Throws:

java.lang.IllegalArgumentException - if the reference_fasta environment variable refers to a a file that doesn't exist

Construct a default reference source to use when an explicit reference has not been provided by checking for fallback sources in this order:

• Defaults.REFERENCE_FASTA - the value of the system property "reference_fasta". If set, must refer to a valid reference file.
• ENA Reference Service if it is enabled

getReferenceBases

public byte[] getReferenceBases(SAMSequenceRecord record,
                                boolean tryNameVariants)

Description copied from interface: CRAMReferenceSource

Get the reference bases for an entire reference contig.

Specified by:

getReferenceBases in interface CRAMReferenceSource

Parameters:

record - the SAMSequenceRecord identifying the reference being requested

tryNameVariants - if true, attempt to match the requested sequence name against the reference by using common name variations, such as adding or removing a leading "chr" prefix from the requested name. if false, use exact match

Returns:

the upper-cased, normalized (see Utils.normalizeBase(byte)) bases representing the requested sequence, or null if the sequence cannot be found

getReferenceBasesByRegion

public byte[] getReferenceBasesByRegion(SAMSequenceRecord sequenceRecord,
                                        int zeroBasedStart,
                                        int requestedRegionLength)

Description copied from interface: CRAMReferenceSource

Get the reference bases for a region of a reference contig. If the sequence can be retrieved, but is not long enough to satisfy the requested length, it is permissible to return fewer bases than the requestedRegionLength. It is the caller's responsibility to detect and handle this case.

Specified by:

getReferenceBasesByRegion in interface CRAMReferenceSource

Parameters:

sequenceRecord - the SAMSequenceRecord for the reference contig being requested

zeroBasedStart - the zero based offset of the starting reference base, must be >= 0

requestedRegionLength - the length of the requested reference region

Returns:

the bases for the reference region, or null if the sequence cannot be found.

getDownloadTriesBeforeFailing

public int getDownloadTriesBeforeFailing()

setDownloadTriesBeforeFailing

public void setDownloadTriesBeforeFailing(int downloadTriesBeforeFailing)