Uses of Interface
htsjdk.samtools.reference.ReferenceSequenceFile

Packages that use ReferenceSequenceFile

Package	Description
htsjdk.samtools
htsjdk.samtools.cram.ref
htsjdk.samtools.reference
htsjdk.samtools.sra

Uses of ReferenceSequenceFile in htsjdk.samtools

Methods in htsjdk.samtools with parameters of type ReferenceSequenceFile

Modifier and Type	Method and Description
boolean	SamFileValidator.validateSamFileSummary(SamReader samReader, ReferenceSequenceFile reference) Outputs validation summary report to out.
boolean	SamFileValidator.validateSamFileVerbose(SamReader samReader, ReferenceSequenceFile reference) Outputs validation error details to out.

Uses of ReferenceSequenceFile in htsjdk.samtools.cram.ref

Constructors in htsjdk.samtools.cram.ref with parameters of type ReferenceSequenceFile

Constructor and Description
ReferenceSource(ReferenceSequenceFile rsFile)

Uses of ReferenceSequenceFile in htsjdk.samtools.reference

Classes in htsjdk.samtools.reference that implement ReferenceSequenceFile

Modifier and Type	Class and Description
class	FastaSequenceFile Implementation of ReferenceSequenceFile for reading from FASTA files.
class	IndexedFastaSequenceFile A fasta file driven by an index for fast, concurrent lookups.

Methods in htsjdk.samtools.reference that return ReferenceSequenceFile

Modifier and Type	Method and Description
static ReferenceSequenceFile	ReferenceSequenceFileFactory.getReferenceSequenceFile(java.io.File file) Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.
static ReferenceSequenceFile	ReferenceSequenceFileFactory.getReferenceSequenceFile(java.io.File file, boolean truncateNamesAtWhitespace) Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.
static ReferenceSequenceFile	ReferenceSequenceFileFactory.getReferenceSequenceFile(java.io.File file, boolean truncateNamesAtWhitespace, boolean preferIndexed) Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.
static ReferenceSequenceFile	ReferenceSequenceFileFactory.getReferenceSequenceFile(java.nio.file.Path path) Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.
static ReferenceSequenceFile	ReferenceSequenceFileFactory.getReferenceSequenceFile(java.nio.file.Path path, boolean truncateNamesAtWhitespace) Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.
static ReferenceSequenceFile	ReferenceSequenceFileFactory.getReferenceSequenceFile(java.nio.file.Path path, boolean truncateNamesAtWhitespace, boolean preferIndexed) Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.

Constructors in htsjdk.samtools.reference with parameters of type ReferenceSequenceFile

Constructor and Description
ReferenceSequenceFileWalker(ReferenceSequenceFile referenceSequenceFile)

Uses of ReferenceSequenceFile in htsjdk.samtools.sra

Classes in htsjdk.samtools.sra that implement ReferenceSequenceFile

Modifier and Type	Class and Description
class	SRAIndexedSequenceFile Allows reading Reference data from SRA