Uses of Class
htsjdk.samtools.SamReaderFactory

Packages that use SamReaderFactory

Package	Description
htsjdk.samtools

Uses of SamReaderFactory in htsjdk.samtools

Methods in htsjdk.samtools that return SamReaderFactory

Modifier and Type	Method and Description
abstract SamReaderFactory	SamReaderFactory.disable(SamReaderFactory.Option... options) Disables the provided SamReaderFactory.Options, then returns itself.
abstract SamReaderFactory	SamReaderFactory.enable(SamReaderFactory.Option... options) Enables the provided SamReaderFactory.Options, then returns itself.
static SamReaderFactory	SamReaderFactory.make() Creates an "empty" factory with no enabled SamReaderFactory.Options, ValidationStringency.DEFAULT_STRINGENCY, and DefaultSAMRecordFactory.
static SamReaderFactory	SamReaderFactory.makeDefault() Creates a copy of the default SamReaderFactory.
abstract SamReaderFactory	SamReaderFactory.referenceSequence(java.io.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.