org.broadinstitute.hellbender.tools.funcotator

Interface Funcotation

All Known Implementing Classes:

GencodeFuncotation, TableFuncotation

public interface Funcotation

Abstract class representing a Funcotator annotation. Created by jonn on 8/30/17.

Method Summary

Modifier and Type	Method and Description
htsjdk.variant.variantcontext.Allele	getAltAllele()
java.lang.String	getDataSourceName()
java.lang.String	getField(java.lang.String fieldName) Get the value of a field in this Funcotation.
java.util.LinkedHashSet<java.lang.String>	getFieldNames() Get the names of the fields in this Funcotation.
java.lang.String	serializeToVcfString() Converts this Funcotation to a string suitable for insertion into a VCF file.
default java.lang.String	serializeToVcfString(java.lang.String manualAnnotationString) TODO: This interface should have nothing specific to a VCF.
void	setFieldSerializationOverrideValue(java.lang.String fieldName, java.lang.String overrideValue) Override the given field with a given value for when it comes time to serialize and write this Funcotation.
default void	setFieldSerializationOverrideValues(java.util.Map<java.lang.String,java.lang.String> fieldSerializationOverrides) Override fields with values as specified by the input map (for when it comes time to serialize and write this Funcotation).

Method Detail

getAltAllele

htsjdk.variant.variantcontext.Allele getAltAllele()

Returns:

The alternate Allele that is associated with this Funcotation.

setFieldSerializationOverrideValue

void setFieldSerializationOverrideValue(java.lang.String fieldName,
                                        java.lang.String overrideValue)

Override the given field with a given value for when it comes time to serialize and write this Funcotation. If the given field is not contained in this Funcotation then a UserException will be thrown.

Parameters:

fieldName - A String comprising the name of the field to override.

overrideValue - The String value for the field to override.

serializeToVcfString

java.lang.String serializeToVcfString()

Converts this Funcotation to a string suitable for insertion into a VCF file.

Returns:

a String representing this Funcotation suitable for insertion into a VCF file.

getDataSourceName

java.lang.String getDataSourceName()

Returns:

The name of the data source behind the DataSourceFuncotationFactory used to create this Funcotation.

getFieldNames

java.util.LinkedHashSet<java.lang.String> getFieldNames()

Get the names of the fields in this Funcotation.

Returns:

The ordered set of fields in this Funcotation as a LinkedHashSet of Strings.

getField

java.lang.String getField(java.lang.String fieldName)

Get the value of a field in this Funcotation.

Returns:

The String value of a field in this Funcotation.

Throws:

{@link - org.broadinstitute.hellbender.exceptions.GATKException} if the given fieldName is not in this Funcotation.

setFieldSerializationOverrideValues

default void setFieldSerializationOverrideValues(java.util.Map<java.lang.String,java.lang.String> fieldSerializationOverrides)

Override fields with values as specified by the input map (for when it comes time to serialize and write this Funcotation). If the given overrides map is null, will not override any field. If the given overrides map is not null and if the given field is not contained in this Funcotation then a UserException will be thrown.

Parameters:

fieldSerializationOverrides - A Map containing fields to override in this Funcotation.

serializeToVcfString

default java.lang.String serializeToVcfString(java.lang.String manualAnnotationString)

TODO: This interface should have nothing specific to a VCF. That should be the job of the VCFOutputRenderer to sanitize any strings. https://github.com/broadinstitute/gatk/issues/4797 Converts this Funcotation to a string suitable for insertion into a VCF file. manualAnnotationString should be written first, followed by the inherent annotations in this Funcotation.

Parameters:

manualAnnotationString - A String of manually-provided annotations to add to this Funcotation.

Returns:

a String representing this Funcotation suitable for insertion into a VCF file.