Class GenomeRegionSequenceExtractor
- java.lang.Object
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- de.charite.compbio.jannovar.htsjdk.GenomeRegionSequenceExtractor
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public class GenomeRegionSequenceExtractor extends Object
Extract sequence for aGenomeInterval
from aIndexedFastaSequenceFile
.- Author:
- Manuel Holtgrewe
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Constructor Summary
Constructors Constructor Description GenomeRegionSequenceExtractor(de.charite.compbio.jannovar.data.JannovarData jannovarData, htsjdk.samtools.reference.IndexedFastaSequenceFile indexedFile)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description String
load(de.charite.compbio.jannovar.reference.GenomeInterval region)
Load sequence from the givenregion
fromindexedFile
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Method Detail
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load
public String load(de.charite.compbio.jannovar.reference.GenomeInterval region)
Load sequence from the givenregion
fromindexedFile
- Parameters:
region
-GenomeInterval
to load sequence for- Returns:
- String with the selected sequenced loaded from
indexedFile
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