Package org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf

Class VcfFuncotationFactory

java.lang.Object

org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory

org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf.VcfFuncotationFactory

All Implemented Interfaces:

Closeable, AutoCloseable

public class VcfFuncotationFactory
extends DataSourceFuncotationFactory

A class to create annotations from VCF feature sources. Created by jonn on 3/23/18.

Field Summary

Fields

Modifier and Type	Field	Description
protected static final org.apache.logging.log4j.Logger	logger	Standard Logger.

Fields inherited from class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory

annotationOverrideMap, dataSourceIsB37, DEFAULT_VERSION_STRING, mainSourceFileAsFeatureInput, minBasesForValidSegment, version

Constructor Summary

Constructors

Constructor	Description
VcfFuncotationFactory(String name, String version, Path sourceFilePath, LinkedHashMap<String,String> annotationOverridesMap, FeatureInput<? extends htsjdk.tribble.Feature> mainSourceFileAsFeatureInput)	Create a VcfFuncotationFactory.
VcfFuncotationFactory(String name, String version, Path sourceFilePath, LinkedHashMap<String,String> annotationOverridesMap, FeatureInput<? extends htsjdk.tribble.Feature> mainSourceFileAsFeatureInput, boolean isDataSourceB37)	Create a VcfFuncotationFactory.
VcfFuncotationFactory(String name, String version, Path sourceFilePath, LinkedHashMap<String,String> annotationOverridesMap, FeatureInput<? extends htsjdk.tribble.Feature> mainSourceFileAsFeatureInput, boolean isDataSourceB37, int minBasesForValidSegment)	Create a VcfFuncotationFactory.

Method Summary

Modifier and Type	Method	Description
void	close()	Perform cleanup tasks for this DataSourceFuncotationFactory.
protected List<Funcotation>	createDefaultFuncotationsOnVariant(htsjdk.variant.variantcontext.VariantContext variant, ReferenceContext referenceContext)	Creates a List of Funcotation for the given variant and referenceContext.
protected List<Funcotation>	createFuncotationsOnVariant(htsjdk.variant.variantcontext.VariantContext variant, ReferenceContext referenceContext, List<htsjdk.tribble.Feature> featureList)	Creates a List of Funcotation for the given variant, referenceContext, and featureContext.
protected List<Funcotation>	createFuncotationsOnVariant(htsjdk.variant.variantcontext.VariantContext variant, ReferenceContext referenceContext, List<htsjdk.tribble.Feature> featureList, List<GencodeFuncotation> gencodeFuncotations)	Creates a List of Funcotation for the given variant, referenceContext, featureContext, and gencodeFuncotations.
Class<? extends htsjdk.tribble.Feature>	getAnnotationFeatureClass()
String	getName()
LinkedHashSet<String>	getSupportedFuncotationFields()
FuncotatorArgumentDefinitions.DataSourceType	getType()

Methods inherited from class org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory

createFuncotations, createFuncotations, createFuncotationsOnSegment, getInfoString, getMainSourceFileAsFeatureInput, getSupportedFuncotationFieldsForSegments, getVersion, initializeAnnotationOverrides, isSupportingSegmentFuncotation, requiresFeatures, setOverrideValuesInFuncotations, transformFeatureQueryInterval

Methods inherited from class java.lang.Object

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

Field Details

logger

protected static final org.apache.logging.log4j.Logger logger

Standard Logger.

Constructor Details

VcfFuncotationFactory

public VcfFuncotationFactory(String name,
 String version,
 Path sourceFilePath,
 LinkedHashMap<String,String> annotationOverridesMap,
 FeatureInput<? extends htsjdk.tribble.Feature> mainSourceFileAsFeatureInput)

Create a VcfFuncotationFactory.

Parameters:

name - A String containing the name of this VcfFuncotationFactory.

version - The version String of the backing data source from which Funcotations will be made.

sourceFilePath - Path to the VCF file from which VariantContexts will be read in and used as Features from which to create Funcotations.

annotationOverridesMap - A LinkedHashMap<String,String> containing user-specified overrides for specific Funcotations.

mainSourceFileAsFeatureInput - The backing FeatureInput for this VcfFuncotationFactory, from which all Funcotations will be created.

VcfFuncotationFactory

public VcfFuncotationFactory(String name,
 String version,
 Path sourceFilePath,
 LinkedHashMap<String,String> annotationOverridesMap,
 FeatureInput<? extends htsjdk.tribble.Feature> mainSourceFileAsFeatureInput,
 boolean isDataSourceB37)

Create a VcfFuncotationFactory.

Parameters:

name - A String containing the name of this VcfFuncotationFactory.

version - The version String of the backing data source from which Funcotations will be made.

sourceFilePath - Path to the VCF file from which VariantContexts will be read in and used as Features from which to create Funcotations.

annotationOverridesMap - A LinkedHashMap<String,String> containing user-specified overrides for specific Funcotations.

mainSourceFileAsFeatureInput - The backing FeatureInput for this VcfFuncotationFactory, from which all Funcotations will be created.

isDataSourceB37 - If true, indicates that the data source behind this GencodeFuncotationFactory contains B37 data.

VcfFuncotationFactory

public VcfFuncotationFactory(String name,
 String version,
 Path sourceFilePath,
 LinkedHashMap<String,String> annotationOverridesMap,
 FeatureInput<? extends htsjdk.tribble.Feature> mainSourceFileAsFeatureInput,
 boolean isDataSourceB37,
 int minBasesForValidSegment)

Create a VcfFuncotationFactory.

Parameters:

name - A String containing the name of this VcfFuncotationFactory.

version - The version String of the backing data source from which Funcotations will be made.

sourceFilePath - Path to the VCF file from which VariantContexts will be read in and used as Features from which to create Funcotations.

annotationOverridesMap - A LinkedHashMap<String,String> containing user-specified overrides for specific Funcotations.

mainSourceFileAsFeatureInput - The backing FeatureInput for this VcfFuncotationFactory, from which all Funcotations will be created.

isDataSourceB37 - If true, indicates that the data source behind this GencodeFuncotationFactory contains B37 data.

minBasesForValidSegment - The minimum number of bases for a segment to be considered valid.

Method Details

getAnnotationFeatureClass

public Class<? extends htsjdk.tribble.Feature> getAnnotationFeatureClass()

Specified by:

getAnnotationFeatureClass in class DataSourceFuncotationFactory

Returns:

Get the Class of the feature type that can be used to create annotations by this DataSourceFuncotationFactory.

getName

public String getName()

Specified by:

getName in class DataSourceFuncotationFactory

Returns:

The name of the data source corresponding to this DataSourceFuncotationFactory.

getType

public FuncotatorArgumentDefinitions.DataSourceType getType()

Specified by:

getType in class DataSourceFuncotationFactory

Returns:

The FuncotatorArgumentDefinitions.DataSourceType of this DataSourceFuncotationFactory.

getSupportedFuncotationFields

public LinkedHashSet<String> getSupportedFuncotationFields()

Specified by:

getSupportedFuncotationFields in class DataSourceFuncotationFactory

Returns:

An ordered LinkedHashSet of the names of annotations that this Data Source supports.

createDefaultFuncotationsOnVariant

protected List<Funcotation> createDefaultFuncotationsOnVariant(htsjdk.variant.variantcontext.VariantContext variant,
 ReferenceContext referenceContext)

Description copied from class: DataSourceFuncotationFactory

Creates a List of Funcotation for the given variant and referenceContext. These will be default funcotations that essentially have empty values.

Specified by:

createDefaultFuncotationsOnVariant in class DataSourceFuncotationFactory

Parameters:

variant - VariantContext to annotate.

referenceContext - ReferenceContext corresponding to the given variant.

Returns:

List of Funcotation given the variant, referenceContext, and featureContext. This should never be empty.

createFuncotationsOnVariant

protected List<Funcotation> createFuncotationsOnVariant(htsjdk.variant.variantcontext.VariantContext variant,
 ReferenceContext referenceContext,
 List<htsjdk.tribble.Feature> featureList)

Creates a List of Funcotation for the given variant, referenceContext, and featureContext. This is really the only entry point for the Vcf FuncotationFactory. VcfFuncotationFactory can be used with or without Gencode annotations.

Specified by:

createFuncotationsOnVariant in class DataSourceFuncotationFactory

Parameters:

variant - VariantContext to annotate.

referenceContext - ReferenceContext corresponding to the given variant.

featureList - List of Feature corresponding to the given variant.

Returns:

List of Funcotation given the variant, referenceContext, and featureContext. This should never be empty.

createFuncotationsOnVariant

protected List<Funcotation> createFuncotationsOnVariant(htsjdk.variant.variantcontext.VariantContext variant,
 ReferenceContext referenceContext,
 List<htsjdk.tribble.Feature> featureList,
 List<GencodeFuncotation> gencodeFuncotations)

Description copied from class: DataSourceFuncotationFactory

Creates a List of Funcotation for the given variant, referenceContext, featureContext, and gencodeFuncotations. For some Data Sources knowledge of Gene Name or Transcript ID is required for annotation.

Specified by:

createFuncotationsOnVariant in class DataSourceFuncotationFactory

Parameters:

variant - VariantContext to annotate.

referenceContext - ReferenceContext corresponding to the given variant.

featureList - List of Feature corresponding to the given variant.

gencodeFuncotations - List of GencodeFuncotation that have already been created for the given variant/referenceContext/featureContext.

Returns:

List of Funcotation given the variant, referenceContext, and featureContext. This should never be empty.

close

public void close()

Description copied from class: DataSourceFuncotationFactory

Perform cleanup tasks for this DataSourceFuncotationFactory.

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Overrides:

close in class DataSourceFuncotationFactory