public class StandardOptionDefinitions
extends java.lang.Object
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 and Description |
---|
StandardOptionDefinitions() |
public static final java.lang.String INPUT_SHORT_NAME
public static final java.lang.String OUTPUT_SHORT_NAME
public static final java.lang.String REFERENCE_SHORT_NAME
public static final java.lang.String SAMPLE_ALIAS_SHORT_NAME
public static final java.lang.String LIBRARY_NAME_SHORT_NAME
public static final java.lang.String EXPECTED_INSERT_SIZE_SHORT_NAME
public static final java.lang.String LANE_SHORT_NAME
public static final java.lang.String SEQUENCE_DICTIONARY_SHORT_NAME
public static final java.lang.String METRICS_FILE_SHORT_NAME
public static final java.lang.String ASSUME_SORTED_SHORT_NAME
public static final java.lang.String ASSUME_SORT_ORDER_SHORT_NAME
public static final java.lang.String PF_READS_ONLY_SHORT_NAME
public static final java.lang.String MINIMUM_MAPPING_QUALITY_SHORT_NAME
public static final java.lang.String READ_GROUP_ID_SHORT_NAME
public static final java.lang.String PROGRAM_RECORD_ID_SHORT_NAME
public static final java.lang.String MINIMUM_LOD_SHORT_NAME
public static final java.lang.String SORT_ORDER_SHORT_NAME
public static final java.lang.String USE_ORIGINAL_QUALITIES_SHORT_NAME