org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic

Class CosmicFuncotationFactory

java.lang.Object

org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory

org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.CosmicFuncotationFactory

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable

public class CosmicFuncotationFactory
extends DataSourceFuncotationFactory

Factory for creating Funcotations by handling a SQLite database containing information from COSMIC. The raw datasource (http://cancer.sanger.ac.uk/cosmic/download - CosmicCompleteTargetedScreensMutantExport.tsv.gz) must be unzipped and preprocessed with the script `createSqliteCosmicDb.sh`. This is a high-level object that interfaces with the internals of Funcotator. Created by jonn on 12/16/17.

Field Summary

Fields

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

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

annotationOverrideMap, DEFAULT_VERSION_STRING, version

Constructor Summary

Constructors

Constructor and Description
CosmicFuncotationFactory(java.nio.file.Path pathToCosmicDb)
CosmicFuncotationFactory(java.nio.file.Path pathToCosmicDb, java.util.LinkedHashMap<java.lang.String,java.lang.String> annotationOverridesMap, java.lang.String version)

Method Summary

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

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

createFuncotations, createFuncotations, getInfoString, getVersion, initializeAnnotationOverrides, setOverrideValuesInFuncotations

Methods inherited from class java.lang.Object

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

Field Detail

logger

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

Standard Logger.

Constructor Detail

CosmicFuncotationFactory

public CosmicFuncotationFactory(java.nio.file.Path pathToCosmicDb)

CosmicFuncotationFactory

public CosmicFuncotationFactory(java.nio.file.Path pathToCosmicDb,
                                java.util.LinkedHashMap<java.lang.String,java.lang.String> annotationOverridesMap,
                                java.lang.String version)

Method Detail

getAnnotationFeatureClass

protected java.lang.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.

close

public void close()

Description copied from class: DataSourceFuncotationFactory

Perform cleanup tasks for this DataSourceFuncotationFactory.

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Overrides:

close in class DataSourceFuncotationFactory

getName

public java.lang.String getName()

Specified by:

getName in class DataSourceFuncotationFactory

Returns:

The name of the data source corresponding to this DataSourceFuncotationFactory.

getSupportedFuncotationFields

public java.util.LinkedHashSet<java.lang.String> getSupportedFuncotationFields()

Specified by:

getSupportedFuncotationFields in class DataSourceFuncotationFactory

Returns:

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

createDefaultFuncotationsOnVariant

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

Description copied from class: DataSourceFuncotationFactory

Creates a List of Funcotation for the given variant, referenceContext, and featureContext.

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

getType

public FuncotatorArgumentDefinitions.DataSourceType getType()

Specified by:

getType in class DataSourceFuncotationFactory

Returns:

The FuncotatorArgumentDefinitions.DataSourceType of this DataSourceFuncotationFactory.