htsjdk.samtools.cram.ref

Class ReferenceSource

java.lang.Object

htsjdk.samtools.cram.ref.ReferenceSource

public class ReferenceSource
extends java.lang.Object

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
void	clearCache()
int	getDownloadTriesBeforeFailing()
byte[]	getReferenceBases(SAMSequenceRecord record, boolean tryNameVariants)
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()

ReferenceSource

public ReferenceSource(java.io.File file)

ReferenceSource

public ReferenceSource(ReferenceSequenceFile rsFile)

Method Detail

clearCache

public void clearCache()

getReferenceBases

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

getDownloadTriesBeforeFailing

public int getDownloadTriesBeforeFailing()

setDownloadTriesBeforeFailing

public void setDownloadTriesBeforeFailing(int downloadTriesBeforeFailing)