org.broadinstitute.hellbender.tools.funcotator.mafOutput

Class MafOutputRenderer

java.lang.Object

org.broadinstitute.hellbender.tools.funcotator.OutputRenderer

org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRenderer

All Implemented Interfaces:

java.lang.AutoCloseable

public class MafOutputRenderer
extends OutputRenderer

A Funcotator output renderer for writing to MAF files. Complies with version 2.4 of the MAF standard found here: https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+%28MAF%29+Specification+-+v2.4 Created by jonn on 12/5/17.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	VERSION Version of the MAF standard that this MafOutputRenderer writes.

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

dataSourceFactories, manualAnnotations, toolVersion

Constructor Summary

Constructors

Constructor and Description

MafOutputRenderer(java.nio.file.Path outputFilePath, java.util.List<DataSourceFuncotationFactory> dataSources, htsjdk.variant.vcf.VCFHeader inputFileHeader, java.util.LinkedHashMap<java.lang.String,java.lang.String> unaccountedForDefaultAnnotations, java.util.LinkedHashMap<java.lang.String,java.lang.String> unaccountedForOverrideAnnotations, java.util.Set<java.lang.String> toolHeaderLines, java.lang.String referenceVersion, java.util.Set<java.lang.String> excludedOutputFields, java.lang.String toolVersion) Create a MafOutputRenderer.

Method Summary

Modifier and Type	Method and Description
void	close() Close the OutputRenderer.
com.google.common.collect.ImmutableMap<java.lang.String,java.util.Set<java.lang.String>>	getReverseOutputFieldNameMap() No field ordering is preserved in the output of this method.
protected void	initializeDefaultMapWithKeys() Initializes defaultMap with the default keys for the columns in a MAF file.
static java.lang.String	mafTransform(java.lang.String key, java.lang.String value, java.lang.String referenceVersion) Transforms a given value to the equivalent MAF-valid value based on the given key.
static java.lang.String	mafTransformInvert(java.lang.String key, java.lang.String value, java.lang.String referenceVersion) Transforms a given value from a MAF-valid value to a general-purpose value based on the given key.
void	write(htsjdk.variant.variantcontext.VariantContext variant, FuncotationMap txToFuncotationMap) Write the given variant and txToFuncotationMap to the output file.
protected void	writeHeader(java.util.List<java.lang.String> outputFields) Write the header 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

VERSION

public static java.lang.String VERSION

Version of the MAF standard that this MafOutputRenderer writes.

Constructor Detail

MafOutputRenderer

public MafOutputRenderer(java.nio.file.Path outputFilePath,
                         java.util.List<DataSourceFuncotationFactory> dataSources,
                         htsjdk.variant.vcf.VCFHeader inputFileHeader,
                         java.util.LinkedHashMap<java.lang.String,java.lang.String> unaccountedForDefaultAnnotations,
                         java.util.LinkedHashMap<java.lang.String,java.lang.String> unaccountedForOverrideAnnotations,
                         java.util.Set<java.lang.String> toolHeaderLines,
                         java.lang.String referenceVersion,
                         java.util.Set<java.lang.String> excludedOutputFields,
                         java.lang.String toolVersion)

Create a MafOutputRenderer. Usage for germline use cases is unsupported.

Parameters:

outputFilePath - Path to output file (must not be null).

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

inputFileHeader - 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).

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

referenceVersion - Version of the reference we're using (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 MAF 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.

mafTransform

public static java.lang.String mafTransform(java.lang.String key,
                                            java.lang.String value,
                                            java.lang.String referenceVersion)

Transforms a given value to the equivalent MAF-valid value based on the given key.

Parameters:

key - The key off of which to base the transformation. This key is the final (transformed) key for output (i.e. the column name in the MAF file).

value - The value to transform into a MAF-valid value.

referenceVersion - The version of the reference used to create these annotations.

Returns:

The MAF-valid equivalent of the given value.

mafTransformInvert

public static java.lang.String mafTransformInvert(java.lang.String key,
                                                  java.lang.String value,
                                                  java.lang.String referenceVersion)

Transforms a given value from a MAF-valid value to a general-purpose value based on the given key.

Parameters:

key - The key off of which to base the transformation. This key is the transformed key for output (i.e. the column name in the MAF file).

value - The value to transform from a MAF-valid value into a general-purpose value.

referenceVersion - The version of the reference used to create these annotations.

Returns:

The general-purpose equivalent of the given MAF-valid value.

writeHeader

protected void writeHeader(java.util.List<java.lang.String> outputFields)

Write the header to the output file.

Parameters:

outputFields - Ordered list of the header columns. These will be written as presented.

getReverseOutputFieldNameMap

public com.google.common.collect.ImmutableMap<java.lang.String,java.util.Set<java.lang.String>> getReverseOutputFieldNameMap()

No field ordering is preserved in the output of this method.

Returns:

Immutable copy of the reverse output field map used by this MafOutputRenderer. In other words, return a mapping for the input field name to the MAF column this will produce. Never null

initializeDefaultMapWithKeys

protected void initializeDefaultMapWithKeys()

Initializes defaultMap with the default keys for the columns in a MAF file.