public class ReferenceSource extends Object
Constructor and Description |
---|
ReferenceSource() |
ReferenceSource(File file) |
ReferenceSource(Path path) |
ReferenceSource(ReferenceSequenceFile rsFile) |
Modifier and Type | Method and Description |
---|---|
void |
clearCache() |
static ReferenceSource |
getDefaultCRAMReferenceSource()
Attempts to construct a default ReferenceSource for use with CRAM files when
one has not been explicitly provided.
|
int |
getDownloadTriesBeforeFailing() |
byte[] |
getReferenceBases(SAMSequenceRecord record,
boolean tryNameVariants) |
void |
setDownloadTriesBeforeFailing(int downloadTriesBeforeFailing) |
public ReferenceSource()
public ReferenceSource(File file)
public ReferenceSource(Path path)
public ReferenceSource(ReferenceSequenceFile rsFile)
public static ReferenceSource getDefaultCRAMReferenceSource()
IllegalStateException
- if no default reference source can be acquiredIllegalArgumentException
- 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)
public int getDownloadTriesBeforeFailing()
public void setDownloadTriesBeforeFailing(int downloadTriesBeforeFailing)