org.broadinstitute.hellbender.engine

Class ReferenceFileSource

java.lang.Object

org.broadinstitute.hellbender.engine.ReferenceFileSource

All Implemented Interfaces:

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

public final class ReferenceFileSource
extends java.lang.Object
implements ReferenceDataSource

Manages traversals and queries over reference data (for now, fasta files only) Supports targeted queries over the reference by interval, but does not yet support complete iteration over the entire reference.

Constructor Summary

Constructors

Constructor and Description
ReferenceFileSource(java.nio.file.Path fastaPath) Initialize this data source using a fasta file.
ReferenceFileSource(java.nio.file.Path fastaPath, boolean preserveFileBases) Initialize this data source using a fasta file.

Method Summary

Modifier and Type	Method and Description
void	close() Permanently close this data source
htsjdk.samtools.SAMSequenceDictionary	getSequenceDictionary() Get the sequence dictionary for this reference
java.util.Iterator<java.lang.Byte>	iterator() Start an iteration over the entire reference.
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 class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.broadinstitute.hellbender.engine.ReferenceDataSource

of, of, of, query, queryAndPrefetch

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

ReferenceFileSource

public ReferenceFileSource(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 file

ReferenceFileSource

public ReferenceFileSource(java.nio.file.Path fastaPath,
                           boolean preserveFileBases)

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 file

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

Method Detail

iterator

public java.util.Iterator<java.lang.Byte> iterator()

Start an iteration over the entire reference. Not yet supported! See the BaseUtils class for guidance on how to work with bases in this format.

Specified by:

iterator in interface java.lang.Iterable<java.lang.Byte>

Returns:

iterator over all bases in this reference

queryAndPrefetch

public 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.

Specified by:

queryAndPrefetch in interface ReferenceDataSource

Parameters:

contig - query interval contig

start - query interval start

stop - query interval stop

Returns:

a ReferenceSequence containing all bases spanning the query interval, prefetched

getSequenceDictionary

public htsjdk.samtools.SAMSequenceDictionary getSequenceDictionary()

Get the sequence dictionary for this reference

Specified by:

getSequenceDictionary in interface ReferenceDataSource

Returns:

SAMSequenceDictionary for this reference

close

public void close()

Permanently close this data source

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in interface ReferenceDataSource