Package de.charite.compbio.jannovar.htsjdk

Class GenomeRegionSequenceExtractor

java.lang.Object

de.charite.compbio.jannovar.htsjdk.GenomeRegionSequenceExtractor

public class GenomeRegionSequenceExtractor
extends Object

Extract sequence for a GenomeInterval from a IndexedFastaSequenceFile.

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor	Description
GenomeRegionSequenceExtractor(de.charite.compbio.jannovar.data.JannovarData jannovarData, htsjdk.samtools.reference.IndexedFastaSequenceFile indexedFile)

Method Summary

Modifier and Type	Method	Description
String	load(de.charite.compbio.jannovar.reference.GenomeInterval region)	Load sequence from the given region from indexedFile

Methods inherited from class java.lang.Object

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

Constructor Detail

GenomeRegionSequenceExtractor

public GenomeRegionSequenceExtractor(de.charite.compbio.jannovar.data.JannovarData jannovarData,
                                     htsjdk.samtools.reference.IndexedFastaSequenceFile indexedFile)

Method Detail

load

public String load(de.charite.compbio.jannovar.reference.GenomeInterval region)

Load sequence from the given region from indexedFile

Parameters:

region - GenomeInterval to load sequence for

Returns:

String with the selected sequenced loaded from indexedFile.