Package picard.cmdline
Class StandardOptionDefinitions
- java.lang.Object
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- picard.cmdline.StandardOptionDefinitions
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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.
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Field Summary
Fields Modifier and Type Field Description static String
ASSUME_SORT_ORDER_SHORT_NAME
static String
ASSUME_SORTED_SHORT_NAME
static String
EXPECTED_INSERT_SIZE_SHORT_NAME
static String
INPUT_SHORT_NAME
static String
LANE_SHORT_NAME
static String
LIBRARY_NAME_SHORT_NAME
static String
METRICS_FILE_SHORT_NAME
static String
MINIMUM_LOD_SHORT_NAME
static String
MINIMUM_MAPPING_QUALITY_SHORT_NAME
static String
OUTPUT_SHORT_NAME
static String
PF_READS_ONLY_SHORT_NAME
static String
PROGRAM_RECORD_ID_SHORT_NAME
static String
READ_GROUP_ID_SHORT_NAME
static String
REFERENCE_SHORT_NAME
static String
SAMPLE_ALIAS_SHORT_NAME
static String
SEQUENCE_DICTIONARY_SHORT_NAME
static String
SORT_ORDER_SHORT_NAME
static String
USE_ORIGINAL_QUALITIES_SHORT_NAME
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Constructor Summary
Constructors Constructor Description StandardOptionDefinitions()
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Field Detail
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INPUT_SHORT_NAME
public static final String INPUT_SHORT_NAME
- See Also:
- Constant Field Values
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OUTPUT_SHORT_NAME
public static final String OUTPUT_SHORT_NAME
- See Also:
- Constant Field Values
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REFERENCE_SHORT_NAME
public static final String REFERENCE_SHORT_NAME
- See Also:
- Constant Field Values
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SAMPLE_ALIAS_SHORT_NAME
public static final String SAMPLE_ALIAS_SHORT_NAME
- See Also:
- Constant Field Values
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LIBRARY_NAME_SHORT_NAME
public static final String LIBRARY_NAME_SHORT_NAME
- See Also:
- Constant Field Values
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EXPECTED_INSERT_SIZE_SHORT_NAME
public static final String EXPECTED_INSERT_SIZE_SHORT_NAME
- See Also:
- Constant Field Values
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LANE_SHORT_NAME
public static final String LANE_SHORT_NAME
- See Also:
- Constant Field Values
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SEQUENCE_DICTIONARY_SHORT_NAME
public static final String SEQUENCE_DICTIONARY_SHORT_NAME
- See Also:
- Constant Field Values
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METRICS_FILE_SHORT_NAME
public static final String METRICS_FILE_SHORT_NAME
- See Also:
- Constant Field Values
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ASSUME_SORTED_SHORT_NAME
public static final String ASSUME_SORTED_SHORT_NAME
- See Also:
- Constant Field Values
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ASSUME_SORT_ORDER_SHORT_NAME
public static final String ASSUME_SORT_ORDER_SHORT_NAME
- See Also:
- Constant Field Values
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PF_READS_ONLY_SHORT_NAME
public static final String PF_READS_ONLY_SHORT_NAME
- See Also:
- Constant Field Values
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MINIMUM_MAPPING_QUALITY_SHORT_NAME
public static final String MINIMUM_MAPPING_QUALITY_SHORT_NAME
- See Also:
- Constant Field Values
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READ_GROUP_ID_SHORT_NAME
public static final String READ_GROUP_ID_SHORT_NAME
- See Also:
- Constant Field Values
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PROGRAM_RECORD_ID_SHORT_NAME
public static final String PROGRAM_RECORD_ID_SHORT_NAME
- See Also:
- Constant Field Values
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MINIMUM_LOD_SHORT_NAME
public static final String MINIMUM_LOD_SHORT_NAME
- See Also:
- Constant Field Values
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SORT_ORDER_SHORT_NAME
public static final String SORT_ORDER_SHORT_NAME
- See Also:
- Constant Field Values
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USE_ORIGINAL_QUALITIES_SHORT_NAME
public static final String USE_ORIGINAL_QUALITIES_SHORT_NAME
- See Also:
- Constant Field Values
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