Package | Description |
---|---|
htsjdk.samtools |
Modifier and Type | Method and Description |
---|---|
abstract SamReaderFactory |
SamReaderFactory.disable(SamReaderFactory.Option... options)
Disables the provided
SamReaderFactory.Option s, then returns itself. |
abstract SamReaderFactory |
SamReaderFactory.enable(SamReaderFactory.Option... options)
Enables the provided
SamReaderFactory.Option s, then returns itself. |
static SamReaderFactory |
SamReaderFactory.make()
Creates an "empty" factory with no enabled
SamReaderFactory.Option s, ValidationStringency.DEFAULT_STRINGENCY , and
DefaultSAMRecordFactory . |
static SamReaderFactory |
SamReaderFactory.makeDefault()
Creates a copy of the default
SamReaderFactory . |
abstract SamReaderFactory |
SamReaderFactory.referenceSequence(File referenceSequence)
Sets the specified reference sequence *
|
abstract SamReaderFactory |
SamReaderFactory.referenceSource(ReferenceSource referenceSequence)
Sets the specified reference sequence *
|
abstract SamReaderFactory |
SamReaderFactory.samRecordFactory(SAMRecordFactory samRecordFactory)
Set this factory's
SAMRecordFactory to the provided one, then returns itself. |
abstract SamReaderFactory |
SamReaderFactory.setOption(SamReaderFactory.Option option,
boolean value)
Sets a specific Option to a boolean value.
|
abstract SamReaderFactory |
SamReaderFactory.validationStringency(ValidationStringency validationStringency)
Set this factory's
ValidationStringency to the provided one, then returns itself. |