gatk-3.8/java/src/org/broadinstitute/sting/gatk/arguments/ValidationExclusion.java

/*
 * Copyright (c) 2010 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,
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 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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package org.broadinstitute.sting.gatk.arguments;

import org.broadinstitute.sting.commandline.EnumerationArgumentDefault;

import java.util.ArrayList;
import java.util.List;


public class ValidationExclusion {

    // our validation options

    public enum TYPE {
        ALLOW_UNINDEXED_BAM,        // allow bam files that do not have an index; we'll traverse them using monolithic shard
        ALLOW_EMPTY_INTERVAL_LIST,  // allow the user to pass in an empty interval list
        ALLOW_UNSET_BAM_SORT_ORDER, // assume that the bam is sorted, even if the SO (sort-order) flag is not set
        NO_READ_ORDER_VERIFICATION, // do not validate that the reads are in order as we take them from the bam file
        ALLOW_SEQ_DICT_INCOMPATIBILITY, // allow dangerous, but not fatal, sequence dictionary incompabilities
        @EnumerationArgumentDefault // set the ALL value to the default value, so if they specify just -U, we get the ALL
        ALL                         // do not check for all of the above conditions, DEFAULT
    }

    // a storage for the passed in exclusions
    List<TYPE> exclusions = new ArrayList<TYPE>();

    public ValidationExclusion(List<TYPE> exclusionsList) {
        exclusions.addAll(exclusionsList);
    }

    public ValidationExclusion() {}
    
    /**
     * do we contain the exclusion specified, or were we set to ALL
     * @param t the exclusion case to test for
     * @return true if we contain the exclusion or if we're set to ALL, false otherwise
     */
    public boolean contains(TYPE t) {
        return (exclusions.contains(TYPE.ALL) || exclusions.contains(t));
    }
}