picard.cmdline.StandardOptionDefinitions Maven / Gradle / Ivy
/*
* The MIT License
*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package picard.cmdline;
/**
* 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.
*/
public class StandardOptionDefinitions {
public static final String INPUT_SHORT_NAME = "I";
public static final String OUTPUT_SHORT_NAME = "O";
public static final String REFERENCE_SHORT_NAME = "R";
public static final String SAMPLE_ALIAS_SHORT_NAME = "ALIAS";
public static final String LIBRARY_NAME_SHORT_NAME = "LIB";
public static final String EXPECTED_INSERT_SIZE_SHORT_NAME = "INSERT";
public static final String LANE_SHORT_NAME = "L";
public static final String SEQUENCE_DICTIONARY_SHORT_NAME = "SD";
public static final String METRICS_FILE_SHORT_NAME = "M";
public static final String ASSUME_SORTED_SHORT_NAME = "AS";
public static final String ASSUME_SORT_ORDER_SHORT_NAME = "ASO";
public static final String PF_READS_ONLY_SHORT_NAME = "PF";
public static final String MINIMUM_MAPPING_QUALITY_SHORT_NAME = "MQ";
public static final String READ_GROUP_ID_SHORT_NAME = "RG";
public static final String PROGRAM_RECORD_ID_SHORT_NAME = "PG";
public static final String MINIMUM_LOD_SHORT_NAME = "LOD";
public static final String SORT_ORDER_SHORT_NAME = "SO";
public static final String USE_ORIGINAL_QUALITIES_SHORT_NAME = "OQ";
}