org.broadinstitute.hellbender.tools.funcotator

Class FuncotatorArgumentDefinitions

java.lang.Object

org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions

public class FuncotatorArgumentDefinitions
extends java.lang.Object

Class to store argument definitions specific to Funcotator. Created by jonn on 11/17/17.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	FuncotatorArgumentDefinitions.DataSourceType An enum to handle the different types of input files for data sources.
static class	FuncotatorArgumentDefinitions.OutputFormatType The file format of the output file.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	ALLOW_HG19_GENCODE_B37_CONTIG_MATCHING_LONG_NAME
static java.util.List<java.lang.String>	ANNOTATION_DEFAULTS_DEFAULT_VALUE
static java.lang.String	ANNOTATION_DEFAULTS_LONG_NAME
static java.util.List<java.lang.String>	ANNOTATION_OVERRIDES_DEFAULT_VALUE
static java.lang.String	ANNOTATION_OVERRIDES_LONG_NAME
static java.lang.String	DATA_SOURCES_PATH_LONG_NAME
static java.lang.String	HG19_REFERENCE_VERSION_STRING
static java.lang.String	HG38_REFERENCE_VERSION_STRING
static int	LOOKAHEAD_CACHE_IN_BP_DEFAULT_VALUE
static java.lang.String	LOOKAHEAD_CACHE_IN_BP_NAME
static char	MAP_NAME_VALUE_DELIMITER
static java.lang.String	OUTPUT_FORMAT_LONG_NAME
static java.lang.String	REFERENCE_VERSION_LONG_NAME
static java.lang.String	REMOVE_FILTERED_VARIANTS_LONG_NAME
static java.util.Set<java.lang.String>	TRANSCRIPT_LIST_DEFAULT_VALUE
static java.lang.String	TRANSCRIPT_LIST_LONG_NAME
static TranscriptSelectionMode	TRANSCRIPT_SELECTION_MODE_DEFAULT_VALUE
static java.lang.String	TRANSCRIPT_SELECTION_MODE_LONG_NAME

Constructor Summary

Constructors

Constructor and Description
FuncotatorArgumentDefinitions()

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

MAP_NAME_VALUE_DELIMITER

public static final char MAP_NAME_VALUE_DELIMITER

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Constant Field Values

REFERENCE_VERSION_LONG_NAME

public static final java.lang.String REFERENCE_VERSION_LONG_NAME

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Constant Field Values

DATA_SOURCES_PATH_LONG_NAME

public static final java.lang.String DATA_SOURCES_PATH_LONG_NAME

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Constant Field Values

OUTPUT_FORMAT_LONG_NAME

public static final java.lang.String OUTPUT_FORMAT_LONG_NAME

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Constant Field Values

REMOVE_FILTERED_VARIANTS_LONG_NAME

public static final java.lang.String REMOVE_FILTERED_VARIANTS_LONG_NAME

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Constant Field Values

TRANSCRIPT_SELECTION_MODE_LONG_NAME

public static final java.lang.String TRANSCRIPT_SELECTION_MODE_LONG_NAME

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Constant Field Values

TRANSCRIPT_SELECTION_MODE_DEFAULT_VALUE

public static final TranscriptSelectionMode TRANSCRIPT_SELECTION_MODE_DEFAULT_VALUE

TRANSCRIPT_LIST_LONG_NAME

public static final java.lang.String TRANSCRIPT_LIST_LONG_NAME

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Constant Field Values

TRANSCRIPT_LIST_DEFAULT_VALUE

public static final java.util.Set<java.lang.String> TRANSCRIPT_LIST_DEFAULT_VALUE

ANNOTATION_DEFAULTS_LONG_NAME

public static final java.lang.String ANNOTATION_DEFAULTS_LONG_NAME

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Constant Field Values

ANNOTATION_DEFAULTS_DEFAULT_VALUE

public static final java.util.List<java.lang.String> ANNOTATION_DEFAULTS_DEFAULT_VALUE

ANNOTATION_OVERRIDES_LONG_NAME

public static final java.lang.String ANNOTATION_OVERRIDES_LONG_NAME

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Constant Field Values

ANNOTATION_OVERRIDES_DEFAULT_VALUE

public static final java.util.List<java.lang.String> ANNOTATION_OVERRIDES_DEFAULT_VALUE

ALLOW_HG19_GENCODE_B37_CONTIG_MATCHING_LONG_NAME

public static final java.lang.String ALLOW_HG19_GENCODE_B37_CONTIG_MATCHING_LONG_NAME

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Constant Field Values

HG19_REFERENCE_VERSION_STRING

public static final java.lang.String HG19_REFERENCE_VERSION_STRING

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Constant Field Values

HG38_REFERENCE_VERSION_STRING

public static final java.lang.String HG38_REFERENCE_VERSION_STRING

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Constant Field Values

LOOKAHEAD_CACHE_IN_BP_NAME

public static final java.lang.String LOOKAHEAD_CACHE_IN_BP_NAME

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Constant Field Values

LOOKAHEAD_CACHE_IN_BP_DEFAULT_VALUE

public static final int LOOKAHEAD_CACHE_IN_BP_DEFAULT_VALUE

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Constant Field Values

Constructor Detail

FuncotatorArgumentDefinitions

public FuncotatorArgumentDefinitions()