org.broadinstitute.hellbender.cmdline

Class ExomeStandardArgumentDefinitions

java.lang.Object

org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions

public final class ExomeStandardArgumentDefinitions
extends java.lang.Object

Created by davidben on 11/30/15.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	AF_PARAMETER_FILE_LONG_NAME
static java.lang.String	AF_PARAMETER_FILE_SHORT_NAME
static java.lang.String	ALLELIC_COUNTS_FILE_LONG_NAME
static java.lang.String	ALLELIC_COUNTS_FILE_SHORT_NAME
static java.lang.String	ALLELIC_PON_FILE_LONG_NAME
static java.lang.String	ALLELIC_PON_FILE_SHORT_NAME
static java.lang.String	BAITS_FILE_LONG_NAME
static java.lang.String	BAITS_FILE_SHORT_NAME
static java.lang.String	LEGACY_SEG_FILE_LONG_NAME
static java.lang.String	LEGACY_SEG_FILE_SHORT_NAME
static java.lang.String	LOG2_LONG_NAME
static java.lang.String	LOG2_SHORT_NAME
static java.lang.String	NORMAL_ALLELIC_COUNTS_FILE_LONG_NAME
static java.lang.String	NORMAL_ALLELIC_COUNTS_FILE_SHORT_NAME
static java.lang.String	NORMAL_BAM_FILE_LONG_NAME
static java.lang.String	NORMAL_BAM_FILE_SHORT_NAME
static java.lang.String	PON_FILE_LONG_NAME
static java.lang.String	PON_FILE_SHORT_NAME
static java.lang.String	PRE_TANGENT_NORMALIZED_COUNTS_FILE_LONG_NAME
static java.lang.String	PRE_TANGENT_NORMALIZED_COUNTS_FILE_SHORT_NAME
static java.lang.String	SEGMENT_FILE_LONG_NAME
static java.lang.String	SEGMENT_FILE_SHORT_NAME
static java.lang.String	SITES_FILE_LONG_NAME
static java.lang.String	SITES_FILE_SHORT_NAME
static java.lang.String	SNP_FILE_LONG_NAME
static java.lang.String	SNP_FILE_SHORT_NAME
static java.lang.String	TANGENT_NORMALIZED_COUNTS_FILE_LONG_NAME
static java.lang.String	TANGENT_NORMALIZED_COUNTS_FILE_SHORT_NAME
static java.lang.String	TARGET_FILE_LONG_NAME
static java.lang.String	TARGET_FILE_SHORT_NAME
static java.lang.String	TUMOR_ALLELIC_COUNTS_FILE_LONG_NAME
static java.lang.String	TUMOR_ALLELIC_COUNTS_FILE_SHORT_NAME
static java.lang.String	TUMOR_BAM_FILE_LONG_NAME
static java.lang.String	TUMOR_BAM_FILE_SHORT_NAME

Constructor Summary

Constructors

Constructor and Description
ExomeStandardArgumentDefinitions()

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

SEGMENT_FILE_LONG_NAME

public static final java.lang.String SEGMENT_FILE_LONG_NAME

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Constant Field Values

SEGMENT_FILE_SHORT_NAME

public static final java.lang.String SEGMENT_FILE_SHORT_NAME

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Constant Field Values

TARGET_FILE_LONG_NAME

public static final java.lang.String TARGET_FILE_LONG_NAME

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Constant Field Values

TARGET_FILE_SHORT_NAME

public static final java.lang.String TARGET_FILE_SHORT_NAME

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Constant Field Values

BAITS_FILE_LONG_NAME

public static final java.lang.String BAITS_FILE_LONG_NAME

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Constant Field Values

BAITS_FILE_SHORT_NAME

public static final java.lang.String BAITS_FILE_SHORT_NAME

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Constant Field Values

LEGACY_SEG_FILE_LONG_NAME

public static final java.lang.String LEGACY_SEG_FILE_LONG_NAME

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Constant Field Values

LEGACY_SEG_FILE_SHORT_NAME

public static final java.lang.String LEGACY_SEG_FILE_SHORT_NAME

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Constant Field Values

NORMAL_BAM_FILE_LONG_NAME

public static final java.lang.String NORMAL_BAM_FILE_LONG_NAME

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Constant Field Values

NORMAL_BAM_FILE_SHORT_NAME

public static final java.lang.String NORMAL_BAM_FILE_SHORT_NAME

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Constant Field Values

TUMOR_BAM_FILE_LONG_NAME

public static final java.lang.String TUMOR_BAM_FILE_LONG_NAME

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Constant Field Values

TUMOR_BAM_FILE_SHORT_NAME

public static final java.lang.String TUMOR_BAM_FILE_SHORT_NAME

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Constant Field Values

SNP_FILE_LONG_NAME

public static final java.lang.String SNP_FILE_LONG_NAME

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Constant Field Values

SNP_FILE_SHORT_NAME

public static final java.lang.String SNP_FILE_SHORT_NAME

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Constant Field Values

SITES_FILE_LONG_NAME

public static final java.lang.String SITES_FILE_LONG_NAME

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Constant Field Values

SITES_FILE_SHORT_NAME

public static final java.lang.String SITES_FILE_SHORT_NAME

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Constant Field Values

ALLELIC_COUNTS_FILE_LONG_NAME

public static final java.lang.String ALLELIC_COUNTS_FILE_LONG_NAME

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Constant Field Values

ALLELIC_COUNTS_FILE_SHORT_NAME

public static final java.lang.String ALLELIC_COUNTS_FILE_SHORT_NAME

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Constant Field Values

NORMAL_ALLELIC_COUNTS_FILE_LONG_NAME

public static final java.lang.String NORMAL_ALLELIC_COUNTS_FILE_LONG_NAME

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Constant Field Values

NORMAL_ALLELIC_COUNTS_FILE_SHORT_NAME

public static final java.lang.String NORMAL_ALLELIC_COUNTS_FILE_SHORT_NAME

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Constant Field Values

TUMOR_ALLELIC_COUNTS_FILE_LONG_NAME

public static final java.lang.String TUMOR_ALLELIC_COUNTS_FILE_LONG_NAME

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Constant Field Values

TUMOR_ALLELIC_COUNTS_FILE_SHORT_NAME

public static final java.lang.String TUMOR_ALLELIC_COUNTS_FILE_SHORT_NAME

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Constant Field Values

PON_FILE_LONG_NAME

public static final java.lang.String PON_FILE_LONG_NAME

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Constant Field Values

PON_FILE_SHORT_NAME

public static final java.lang.String PON_FILE_SHORT_NAME

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Constant Field Values

ALLELIC_PON_FILE_LONG_NAME

public static final java.lang.String ALLELIC_PON_FILE_LONG_NAME

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Constant Field Values

ALLELIC_PON_FILE_SHORT_NAME

public static final java.lang.String ALLELIC_PON_FILE_SHORT_NAME

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Constant Field Values

AF_PARAMETER_FILE_LONG_NAME

public static final java.lang.String AF_PARAMETER_FILE_LONG_NAME

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Constant Field Values

AF_PARAMETER_FILE_SHORT_NAME

public static final java.lang.String AF_PARAMETER_FILE_SHORT_NAME

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Constant Field Values

LOG2_LONG_NAME

public static final java.lang.String LOG2_LONG_NAME

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Constant Field Values

LOG2_SHORT_NAME

public static final java.lang.String LOG2_SHORT_NAME

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Constant Field Values

PRE_TANGENT_NORMALIZED_COUNTS_FILE_LONG_NAME

public static final java.lang.String PRE_TANGENT_NORMALIZED_COUNTS_FILE_LONG_NAME

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Constant Field Values

PRE_TANGENT_NORMALIZED_COUNTS_FILE_SHORT_NAME

public static final java.lang.String PRE_TANGENT_NORMALIZED_COUNTS_FILE_SHORT_NAME

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Constant Field Values

TANGENT_NORMALIZED_COUNTS_FILE_LONG_NAME

public static final java.lang.String TANGENT_NORMALIZED_COUNTS_FILE_LONG_NAME

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Constant Field Values

TANGENT_NORMALIZED_COUNTS_FILE_SHORT_NAME

public static final java.lang.String TANGENT_NORMALIZED_COUNTS_FILE_SHORT_NAME

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Constant Field Values

Constructor Detail

ExomeStandardArgumentDefinitions

public ExomeStandardArgumentDefinitions()