picard.cmdline

Class StandardOptionDefinitions

java.lang.Object

picard.cmdline.StandardOptionDefinitions

public class StandardOptionDefinitions
extends java.lang.Object

A set of String constants in which the name of the constant (minus the _SHORT_NAME suffix) is the standard long Option name, and the value of the constant is the standard shortName.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	ASSUME_SORT_ORDER_SHORT_NAME
static java.lang.String	ASSUME_SORTED_SHORT_NAME
static java.lang.String	EXPECTED_INSERT_SIZE_SHORT_NAME
static java.lang.String	INPUT_SHORT_NAME
static java.lang.String	LANE_SHORT_NAME
static java.lang.String	LIBRARY_NAME_SHORT_NAME
static java.lang.String	METRICS_FILE_SHORT_NAME
static java.lang.String	MINIMUM_LOD_SHORT_NAME
static java.lang.String	MINIMUM_MAPPING_QUALITY_SHORT_NAME
static java.lang.String	OUTPUT_SHORT_NAME
static java.lang.String	PF_READS_ONLY_SHORT_NAME
static java.lang.String	PROGRAM_RECORD_ID_SHORT_NAME
static java.lang.String	READ_GROUP_ID_SHORT_NAME
static java.lang.String	REFERENCE_SHORT_NAME
static java.lang.String	SAMPLE_ALIAS_SHORT_NAME
static java.lang.String	SEQUENCE_DICTIONARY_SHORT_NAME
static java.lang.String	SORT_ORDER_SHORT_NAME
static java.lang.String	USE_ORIGINAL_QUALITIES_SHORT_NAME

Constructor Summary

Constructors

Constructor and Description
StandardOptionDefinitions()

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

INPUT_SHORT_NAME

public static final java.lang.String INPUT_SHORT_NAME

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Constant Field Values

OUTPUT_SHORT_NAME

public static final java.lang.String OUTPUT_SHORT_NAME

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Constant Field Values

REFERENCE_SHORT_NAME

public static final java.lang.String REFERENCE_SHORT_NAME

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Constant Field Values

SAMPLE_ALIAS_SHORT_NAME

public static final java.lang.String SAMPLE_ALIAS_SHORT_NAME

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Constant Field Values

LIBRARY_NAME_SHORT_NAME

public static final java.lang.String LIBRARY_NAME_SHORT_NAME

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Constant Field Values

EXPECTED_INSERT_SIZE_SHORT_NAME

public static final java.lang.String EXPECTED_INSERT_SIZE_SHORT_NAME

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Constant Field Values

LANE_SHORT_NAME

public static final java.lang.String LANE_SHORT_NAME

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Constant Field Values

SEQUENCE_DICTIONARY_SHORT_NAME

public static final java.lang.String SEQUENCE_DICTIONARY_SHORT_NAME

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Constant Field Values

METRICS_FILE_SHORT_NAME

public static final java.lang.String METRICS_FILE_SHORT_NAME

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Constant Field Values

ASSUME_SORTED_SHORT_NAME

public static final java.lang.String ASSUME_SORTED_SHORT_NAME

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Constant Field Values

ASSUME_SORT_ORDER_SHORT_NAME

public static final java.lang.String ASSUME_SORT_ORDER_SHORT_NAME

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Constant Field Values

PF_READS_ONLY_SHORT_NAME

public static final java.lang.String PF_READS_ONLY_SHORT_NAME

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Constant Field Values

MINIMUM_MAPPING_QUALITY_SHORT_NAME

public static final java.lang.String MINIMUM_MAPPING_QUALITY_SHORT_NAME

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Constant Field Values

READ_GROUP_ID_SHORT_NAME

public static final java.lang.String READ_GROUP_ID_SHORT_NAME

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Constant Field Values

PROGRAM_RECORD_ID_SHORT_NAME

public static final java.lang.String PROGRAM_RECORD_ID_SHORT_NAME

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Constant Field Values

MINIMUM_LOD_SHORT_NAME

public static final java.lang.String MINIMUM_LOD_SHORT_NAME

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Constant Field Values

SORT_ORDER_SHORT_NAME

public static final java.lang.String SORT_ORDER_SHORT_NAME

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Constant Field Values

USE_ORIGINAL_QUALITIES_SHORT_NAME

public static final java.lang.String USE_ORIGINAL_QUALITIES_SHORT_NAME

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Constant Field Values

Constructor Detail

StandardOptionDefinitions

public StandardOptionDefinitions()