40 lines
1.6 KiB
Java
40 lines
1.6 KiB
Java
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/*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*/
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package edu.mit.broad.picard.aligner.maq;
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/**
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* Utility class to hold Maq-related constants (program name, location, switches, etc)
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*/
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public class MaqConstants {
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// General Maq constants
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public static final String PROGRAM_NAME = "Maq";
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public static final String PROGRAM_VERSION = "0.7.1";
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public static final String MAQ_HOME = "/seq/dirseq/maq-0.7.1/";
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// Command-related constants
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public static final String MAQ_COMMAND = "maq";
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public static final String MAP_COMMAND = "map";
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public static final String MERGE_COMMAND = "mapmerge";
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// Constants related to Maq map switches
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public static final String SWITCH_SUM_MISMATCHES = "-e";
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public static final int HIGH_STRINGENCY_SUM_MISMATCHES = 100;
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public static final int LOW_STRINGENCY_QUALITY_FOR_MISMATCHES = 30;
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public static final String SWITCH_MAX_OUTER_DISTANCE = "-a";
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public static final int LOW_STRINGENCY_MAX_OUTER_DISTANCE = 1500;
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public static final double HIGH_STRINGENCY_MAX_OUTER_DISTANCE_MULTIPLIER = 1.5d;
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public static final String SWITCH_RANDOM_SEED = "-s";
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public static final int DEFAULT_RANDOM_SEED = 0;
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public static String getProgramVersion() { return PROGRAM_VERSION; }
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}
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