public class ReferenceSource extends java.lang.Object implements CRAMReferenceSource
| Constructor and Description |
|---|
ReferenceSource(java.io.File file) |
ReferenceSource(java.nio.file.Path path) |
ReferenceSource(ReferenceSequenceFile rsFile) |
| Modifier and Type | Method and Description |
|---|---|
void |
clearCache() |
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)
getReferenceBases
|
void |
setDownloadTriesBeforeFailing(int downloadTriesBeforeFailing) |
public ReferenceSource(java.io.File file)
public ReferenceSource(java.nio.file.Path path)
public ReferenceSource(ReferenceSequenceFile rsFile)
public static CRAMReferenceSource getDefaultCRAMReferenceSource()
java.lang.IllegalStateException - if no default reference source can be acquiredjava.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:
public void clearCache()
public byte[] getReferenceBases(SAMSequenceRecord record, boolean tryNameVariants)
CRAMReferenceSourcegetReferenceBases in interface CRAMReferenceSourcerecord - the SAMSequenceRecord identifying the reference
being requestedtryNameVariants - 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 matchUtils.normalizeBase(byte))
bases representing the requested sequence, or null if the sequence cannot be foundpublic int getDownloadTriesBeforeFailing()
public void setDownloadTriesBeforeFailing(int downloadTriesBeforeFailing)