org.broadinstitute.hellbender.tools.funcotator.vcfOutput

Class VcfOutputRenderer

java.lang.Object

org.broadinstitute.hellbender.tools.funcotator.OutputRenderer

org.broadinstitute.hellbender.tools.funcotator.vcfOutput.VcfOutputRenderer

All Implemented Interfaces:

java.lang.AutoCloseable

public class VcfOutputRenderer
extends OutputRenderer

A Funcotator output renderer for writing to VCF files. Created by jonn on 8/30/17.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	ALL_TRANSCRIPT_DELIMITER The delimiter to use when separating the information regarding a transcript.
static java.lang.String	DESCRIPTION_PREAMBLE_DELIMITER The delimiter used between the preamble and the actual fields in the description of the FUNCOTATOR_VCF_FIELD_NAME attribute i the header.
static java.lang.String	END_TRANSCRIPT_DELIMITER The delimiter to use when ending the information regarding a transcript.
static java.lang.String	FIELD_DELIMITER The delimiter for each field within the VCF Funcotation field.
static java.lang.String	FUNCOTATOR_VCF_FIELD_NAME The name of the field inside the VCF INFO field in which to put Funcotator results.
static java.lang.String	HEADER_LISTED_FIELD_DELIMITER The delimiter in the header for the list of fields that each funcotation has.
static java.lang.String	OTHER_TRANSCRIPT_DELIMITER The delimiter for the `Other Transcript` field within the Funcotation annotation in the VCF.
static java.lang.String	START_TRANSCRIPT_DELIMITER The delimiter to use when starting the information regarding a transcript.

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

dataSourceFactories, manualAnnotations, toolVersion

Constructor Summary

Constructors

Constructor and Description

VcfOutputRenderer(htsjdk.variant.variantcontext.writer.VariantContextWriter vcfWriter, java.util.List<DataSourceFuncotationFactory> dataSources, htsjdk.variant.vcf.VCFHeader existingHeader, java.util.LinkedHashMap<java.lang.String,java.lang.String> unaccountedForDefaultAnnotations, java.util.LinkedHashMap<java.lang.String,java.lang.String> unaccountedForOverrideAnnotations, java.util.Set<htsjdk.variant.vcf.VCFHeaderLine> defaultToolVcfHeaderLines, java.util.Set<java.lang.String> excludedOutputFields, java.lang.String toolVersion) Create a VcfOutputRenderer.

Method Summary

Modifier and Type	Method and Description
void	close() Close the OutputRenderer.
void	write(htsjdk.variant.variantcontext.VariantContext variant, FuncotationMap txToFuncotationMap) Write the given variant and txToFuncotationMap to the output file.

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

createFuncotationFromLinkedHashMap, getDataSourceInfoString, getToolVersion

Methods inherited from class java.lang.Object

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

Field Detail

FUNCOTATOR_VCF_FIELD_NAME

public static final java.lang.String FUNCOTATOR_VCF_FIELD_NAME

The name of the field inside the VCF INFO field in which to put Funcotator results.

See Also:

Constant Field Values

HEADER_LISTED_FIELD_DELIMITER

public static final java.lang.String HEADER_LISTED_FIELD_DELIMITER

The delimiter in the header for the list of fields that each funcotation has.

See Also:

Constant Field Values

FIELD_DELIMITER

public static final java.lang.String FIELD_DELIMITER

The delimiter for each field within the VCF Funcotation field.

See Also:

Constant Field Values

OTHER_TRANSCRIPT_DELIMITER

public static final java.lang.String OTHER_TRANSCRIPT_DELIMITER

The delimiter for the `Other Transcript` field within the Funcotation annotation in the VCF.

See Also:

Constant Field Values

ALL_TRANSCRIPT_DELIMITER

public static final java.lang.String ALL_TRANSCRIPT_DELIMITER

The delimiter to use when separating the information regarding a transcript.

See Also:

Constant Field Values

START_TRANSCRIPT_DELIMITER

public static final java.lang.String START_TRANSCRIPT_DELIMITER

The delimiter to use when starting the information regarding a transcript.

See Also:

Constant Field Values

END_TRANSCRIPT_DELIMITER

public static final java.lang.String END_TRANSCRIPT_DELIMITER

The delimiter to use when ending the information regarding a transcript.

See Also:

Constant Field Values

DESCRIPTION_PREAMBLE_DELIMITER

public static final java.lang.String DESCRIPTION_PREAMBLE_DELIMITER

The delimiter used between the preamble and the actual fields in the description of the FUNCOTATOR_VCF_FIELD_NAME attribute i the header.

See Also:

Constant Field Values

Constructor Detail

VcfOutputRenderer

public VcfOutputRenderer(htsjdk.variant.variantcontext.writer.VariantContextWriter vcfWriter,
                         java.util.List<DataSourceFuncotationFactory> dataSources,
                         htsjdk.variant.vcf.VCFHeader existingHeader,
                         java.util.LinkedHashMap<java.lang.String,java.lang.String> unaccountedForDefaultAnnotations,
                         java.util.LinkedHashMap<java.lang.String,java.lang.String> unaccountedForOverrideAnnotations,
                         java.util.Set<htsjdk.variant.vcf.VCFHeaderLine> defaultToolVcfHeaderLines,
                         java.util.Set<java.lang.String> excludedOutputFields,
                         java.lang.String toolVersion)

Create a VcfOutputRenderer.

Parameters:

vcfWriter - a pre-initialized VariantContextWriter used for writing the output (must not be null).

dataSources - List of DataSourceFuncotationFactory to back our annotations (must not be null).

existingHeader - VCFHeader of input VCF file to preserve (must not be null).

unaccountedForDefaultAnnotations - LinkedHashMap of default annotations that must be added (must not be null).

unaccountedForOverrideAnnotations - LinkedHashMap of override annotations that must be added (must not be null).

defaultToolVcfHeaderLines - Lines to add to the header with information about the tool (must not be null).

excludedOutputFields - Fields that should not be rendered in the final output. Only exact name matches will be excluded (must not be null).

toolVersion - The version number of the tool used to produce the VCF file (must not be null).

Method Detail

close

public void close()

Description copied from class: OutputRenderer

Close the OutputRenderer.

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in class OutputRenderer

write

public void write(htsjdk.variant.variantcontext.VariantContext variant,
                  FuncotationMap txToFuncotationMap)

Description copied from class: OutputRenderer

Write the given variant and txToFuncotationMap to the output file.

Specified by:

write in class OutputRenderer

Parameters:

variant - VariantContext to write to the file.

txToFuncotationMap - FuncotationMap to add to the given variant on output.