public class DBVariantContextAnnotatorFactory extends Object
DBVariantContextAnnotator
objectsConstructor and Description |
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DBVariantContextAnnotatorFactory() |
Modifier and Type | Method and Description |
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DBVariantContextAnnotator |
constructDBSNP(String vcfDBPath,
String fastaRefPath,
DBAnnotationOptions options)
Construct dbSNP
VariantContext annotator factory. |
DBVariantContextAnnotator |
constructExac(String vcfDBPath,
String fastaRefPath,
DBAnnotationOptions options)
Construct ExAC
VariantContext annotator factory. |
DBVariantContextAnnotator |
constructUK10K(String vcfDBPath,
String fastaRefPath,
DBAnnotationOptions options)
Construct UK10K
VariantContext annotator factory. |
public DBVariantContextAnnotator constructDBSNP(String vcfDBPath, String fastaRefPath, DBAnnotationOptions options) throws JannovarVarDBException
VariantContext
annotator factory.vcfDBPath
- Path to gzip-compressed, normalized and tbi-indexed dbSNP file to use for the annotationfastaRefPath
- Path to reference FASTA fileoptions
- Configuration for the variant context annotaitonDBVariantContextAnnotator
objectJannovarVarDBException
- on problems loading the resourcespublic DBVariantContextAnnotator constructExac(String vcfDBPath, String fastaRefPath, DBAnnotationOptions options) throws JannovarVarDBException
VariantContext
annotator factory.vcfDBPath
- Path to gzip-compressed, normalized and tbi-indexed ExAC file to use for the annotationfastaRefPath
- Path to reference FASTA fileoptions
- Configuration for the variant context annotaitonDBVariantContextAnnotator
objectJannovarVarDBException
- on problems loading the resourcespublic DBVariantContextAnnotator constructUK10K(String vcfDBPath, String fastaRefPath, DBAnnotationOptions options) throws JannovarVarDBException
VariantContext
annotator factory.vcfDBPath
- Path to gzip-compressed, normalized and tbi-indexed ExAC file to use for the annotationfastaRefPath
- Path to reference FASTA fileoptions
- Configuration for the variant context annotaitonDBVariantContextAnnotator
objectJannovarVarDBException
- on problems loading the resourcesCopyright © 2016. All rights reserved.