de.charite.compbio.jannovar.vardbs.base

Class AbstractDBAnnotationDriver<RecordType>

java.lang.Object

de.charite.compbio.jannovar.vardbs.base.AbstractDBAnnotationDriver<RecordType>

All Implemented Interfaces:

DBAnnotationDriver

Direct Known Subclasses:

DBSNPAnnotationDriver, ExacAnnotationDriver, UK10KAnnotationDriver

public abstract class AbstractDBAnnotationDriver<RecordType>
extends Object
implements DBAnnotationDriver

Abstract base class for annotation based on VCF files.

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor and Description
AbstractDBAnnotationDriver(String vcfPath, String fastaPath, DBAnnotationOptions options, VariantContextToRecordConverter<RecordType> vcToRecord) Create annotation driver for a coordinate-sorted, bgzip-compressed, VCF file

Method Summary

Modifier and Type	Method and Description
htsjdk.variant.variantcontext.VariantContext	annotateVariantContext(htsjdk.variant.variantcontext.VariantContext obsVC) Annotate the VariantContext object using the information in the database.

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.charite.compbio.jannovar.vardbs.base.DBAnnotationDriver

constructVCFHeaderExtender

Constructor Detail

AbstractDBAnnotationDriver

public AbstractDBAnnotationDriver(String vcfPath,
                                  String fastaPath,
                                  DBAnnotationOptions options,
                                  VariantContextToRecordConverter<RecordType> vcToRecord)
                           throws JannovarVarDBException

Create annotation driver for a coordinate-sorted, bgzip-compressed, VCF file

Parameters:

fastaPath - FAI-indexed FASTA file with reference

vcfPath - Path to VCF file with dbSNP.

options - configuration

vcToRecord - converter from VariantContext to record type

Throws:

JannovarVarDBException - on problems loading the reference FASTA/FAI file or incompatible dbSNP version

Method Detail

annotateVariantContext

public htsjdk.variant.variantcontext.VariantContext annotateVariantContext(htsjdk.variant.variantcontext.VariantContext obsVC)

Description copied from interface: DBAnnotationDriver

Annotate the VariantContext object using the information in the database. Note that the annotation in jannovar-vardbs makes a distinction between variants that are in the database and variants that are only at the same position or overlap.

Specified by:

annotateVariantContext in interface DBAnnotationDriver

Parameters:

obsVC - VariantContext to annotate

Returns:

Updated VariantContext object