Package htsjdk.samtools.reference

Class ReferenceSequenceFileWalker

java.lang.Object

htsjdk.samtools.reference.ReferenceSequenceFileWalker

All Implemented Interfaces:

Closeable, AutoCloseable

public class ReferenceSequenceFileWalker
extends Object
implements Closeable

Manages a ReferenceSequenceFile. Loads the requested sequence, ensuring that access is in order, and confirming that sequence name and index agree.

Constructor Summary

Constructors

Constructor	Description
ReferenceSequenceFileWalker(ReferenceSequenceFile referenceSequenceFile)
ReferenceSequenceFileWalker(File file)
ReferenceSequenceFileWalker(Path path)

Method Summary

Modifier and Type	Method	Description
void	close()
ReferenceSequence	get(int sequenceIndex)	Get reference sequence without validating name or length.
ReferenceSequence	get(int sequenceIndex, String sequenceName, int length)	Ensure that the requested sequence is loaded.
SAMSequenceDictionary	getSequenceDictionary()

Methods inherited from class java.lang.Object

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

Constructor Details

ReferenceSequenceFileWalker

public ReferenceSequenceFileWalker(ReferenceSequenceFile referenceSequenceFile)

ReferenceSequenceFileWalker

public ReferenceSequenceFileWalker(Path path)

ReferenceSequenceFileWalker

public ReferenceSequenceFileWalker(File file)

Method Details

get

public ReferenceSequence get(int sequenceIndex,
 String sequenceName,
 int length)

Ensure that the requested sequence is loaded. Throws an exception if out-of-order request is made, or if there is a mismatch between the requested name and the name found in the ReferenceSequenceFile

get

public ReferenceSequence get(int sequenceIndex)

Get reference sequence without validating name or length. This is OK if the entire sequence dictionary was validated before reading sequences.

getSequenceDictionary

public SAMSequenceDictionary getSequenceDictionary()

close

public void close()
           throws IOException

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Throws:

IOException