Package picard.cmdline

Class StandardOptionDefinitions

java.lang.Object

picard.cmdline.StandardOptionDefinitions

public class StandardOptionDefinitions
extends 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	Description
static final String	ASSUME_SORT_ORDER_SHORT_NAME
static final String	ASSUME_SORTED_SHORT_NAME
static final String	EXPECTED_INSERT_SIZE_SHORT_NAME
static final String	INPUT_SHORT_NAME
static final String	LANE_SHORT_NAME
static final String	LIBRARY_NAME_SHORT_NAME
static final String	METRICS_FILE_SHORT_NAME
static final String	MINIMUM_LOD_SHORT_NAME
static final String	MINIMUM_MAPPING_QUALITY_SHORT_NAME
static final String	OUTPUT_SHORT_NAME
static final String	PF_READS_ONLY_SHORT_NAME
static final String	PROGRAM_RECORD_ID_SHORT_NAME
static final String	READ_GROUP_ID_SHORT_NAME
static final String	REFERENCE_SHORT_NAME
static final String	SAMPLE_ALIAS_SHORT_NAME
static final String	SEQUENCE_DICTIONARY_SHORT_NAME
static final String	SORT_ORDER_SHORT_NAME
static final String	USE_ORIGINAL_QUALITIES_SHORT_NAME

Constructor Summary

Constructors

Constructor	Description
StandardOptionDefinitions()

Method Summary

Methods inherited from class java.lang.Object

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

Field Details

INPUT_SHORT_NAME

public static final String INPUT_SHORT_NAME

See Also:

• Constant Field Values

OUTPUT_SHORT_NAME

public static final String OUTPUT_SHORT_NAME

See Also:

• Constant Field Values

REFERENCE_SHORT_NAME

public static final String REFERENCE_SHORT_NAME

See Also:

• Constant Field Values

SAMPLE_ALIAS_SHORT_NAME

public static final String SAMPLE_ALIAS_SHORT_NAME

See Also:

• Constant Field Values

LIBRARY_NAME_SHORT_NAME

public static final String LIBRARY_NAME_SHORT_NAME

See Also:

• Constant Field Values

EXPECTED_INSERT_SIZE_SHORT_NAME

public static final String EXPECTED_INSERT_SIZE_SHORT_NAME

See Also:

• Constant Field Values

LANE_SHORT_NAME

public static final String LANE_SHORT_NAME

See Also:

• Constant Field Values

SEQUENCE_DICTIONARY_SHORT_NAME

public static final String SEQUENCE_DICTIONARY_SHORT_NAME

See Also:

• Constant Field Values

METRICS_FILE_SHORT_NAME

public static final String METRICS_FILE_SHORT_NAME

See Also:

• Constant Field Values

ASSUME_SORTED_SHORT_NAME

public static final String ASSUME_SORTED_SHORT_NAME

See Also:

• Constant Field Values

ASSUME_SORT_ORDER_SHORT_NAME

public static final String ASSUME_SORT_ORDER_SHORT_NAME

See Also:

• Constant Field Values

PF_READS_ONLY_SHORT_NAME

public static final String PF_READS_ONLY_SHORT_NAME

See Also:

• Constant Field Values

MINIMUM_MAPPING_QUALITY_SHORT_NAME

public static final String MINIMUM_MAPPING_QUALITY_SHORT_NAME

See Also:

• Constant Field Values

READ_GROUP_ID_SHORT_NAME

public static final String READ_GROUP_ID_SHORT_NAME

See Also:

• Constant Field Values

PROGRAM_RECORD_ID_SHORT_NAME

public static final String PROGRAM_RECORD_ID_SHORT_NAME

See Also:

• Constant Field Values

MINIMUM_LOD_SHORT_NAME

public static final String MINIMUM_LOD_SHORT_NAME

See Also:

• Constant Field Values

SORT_ORDER_SHORT_NAME

public static final String SORT_ORDER_SHORT_NAME

See Also:

• Constant Field Values

USE_ORIGINAL_QUALITIES_SHORT_NAME

public static final String USE_ORIGINAL_QUALITIES_SHORT_NAME

See Also:

• Constant Field Values

Constructor Details

StandardOptionDefinitions

public StandardOptionDefinitions()