org.broadinstitute.hellbender.engine

Interface ReferenceDataSource

All Superinterfaces:

java.lang.AutoCloseable, GATKDataSource<java.lang.Byte>, java.lang.Iterable<java.lang.Byte>

All Known Implementing Classes:

ReferenceFileSource, ReferenceMemorySource

public interface ReferenceDataSource
extends GATKDataSource<java.lang.Byte>, java.lang.AutoCloseable

Manages traversals and queries over reference data. Supports targeted queries over the reference by interval and over the entire reference.

Method Summary

Modifier and Type	Method and Description
default void	close() Permanently close this data source.
htsjdk.samtools.SAMSequenceDictionary	getSequenceDictionary() Get the sequence dictionary for this reference
static ReferenceDataSource	of(java.nio.file.Path fastaPath) Initialize this data source using a fasta file.
static ReferenceDataSource	of(java.nio.file.Path fastaPath, boolean preserveAmbiguityCodesAndCapitalization) Initialize this data source using a fasta file.
static ReferenceDataSource	of(ReferenceBases bases, htsjdk.samtools.SAMSequenceDictionary referenceSequenceDictionary) Initialize this data source using ReferenceBases and corresponding sequence dictionary.
default java.util.Iterator<java.lang.Byte>	query(SimpleInterval interval) Query a specific interval on this reference, and get back an iterator over the bases spanning that interval.
default htsjdk.samtools.reference.ReferenceSequence	queryAndPrefetch(SimpleInterval interval) Query a specific interval on this reference, and get back all bases spanning that interval at once.
htsjdk.samtools.reference.ReferenceSequence	queryAndPrefetch(java.lang.String contig, long start, long stop) Query a specific interval on this reference, and get back all bases spanning that interval at once.

Methods inherited from interface java.lang.Iterable

forEach, iterator, spliterator

Method Detail

of

static ReferenceDataSource of(java.nio.file.Path fastaPath)

Initialize this data source using a fasta file. The provided fasta file must have companion .fai and .dict files.

Parameters:

fastaPath - reference fasta Path

of

static ReferenceDataSource of(java.nio.file.Path fastaPath,
                              boolean preserveAmbiguityCodesAndCapitalization)

Initialize this data source using a fasta file. The provided fasta file must have companion .fai and .dict files. If preserveFileBases is true, will NOT convert IUPAC bases in the file to `N` and will NOT capitalize lower-case bases. NOTE: Most GATK tools do not support data created by setting preserveFileBases to true.

Parameters:

fastaPath - reference fasta Path

preserveAmbiguityCodesAndCapitalization - Whether to preserve the original bases in the given reference file path.

of

static ReferenceDataSource of(ReferenceBases bases,
                              htsjdk.samtools.SAMSequenceDictionary referenceSequenceDictionary)

Initialize this data source using ReferenceBases and corresponding sequence dictionary.

queryAndPrefetch

default htsjdk.samtools.reference.ReferenceSequence queryAndPrefetch(SimpleInterval interval)

Query a specific interval on this reference, and get back all bases spanning that interval at once. Call getBases() on the returned ReferenceSequence to get the actual reference bases. See the BaseUtils class for guidance on how to work with bases in this format. The default implementation calls #queryAndPrefetch(contig, start, stop).

Parameters:

interval - query interval

Returns:

a ReferenceSequence containing all bases spanning the query interval, prefetched

queryAndPrefetch

htsjdk.samtools.reference.ReferenceSequence queryAndPrefetch(java.lang.String contig,
                                                             long start,
                                                             long stop)

Query a specific interval on this reference, and get back all bases spanning that interval at once. Call getBases() on the returned ReferenceSequence to get the actual reference bases. See the BaseUtils class for guidance on how to work with bases in this format.

Parameters:

contig - query interval contig

start - query interval start

stop - query interval stop

Returns:

a ReferenceSequence containing all bases spanning the query interval, prefetched

query

default java.util.Iterator<java.lang.Byte> query(SimpleInterval interval)

Query a specific interval on this reference, and get back an iterator over the bases spanning that interval. See the BaseUtils class for guidance on how to work with bases in this format.

Specified by:

query in interface GATKDataSource<java.lang.Byte>

Parameters:

interval - query interval

Returns:

iterator over the bases spanning the query interval

getSequenceDictionary

htsjdk.samtools.SAMSequenceDictionary getSequenceDictionary()

Get the sequence dictionary for this reference

Returns:

SAMSequenceDictionary for this reference

close

default void close()

Permanently close this data source. The default implementation does nothing.

Specified by:

close in interface java.lang.AutoCloseable