66 lines
2.7 KiB
Java
66 lines
2.7 KiB
Java
/*
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* Copyright (c) 2010 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.arguments;
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import org.broadinstitute.sting.commandline.EnumerationArgumentDefault;
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import java.util.ArrayList;
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import java.util.List;
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public class ValidationExclusion {
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// our validation options
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public enum TYPE {
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ALLOW_UNINDEXED_BAM, // allow bam files that do not have an index; we'll traverse them using monolithic shard
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ALLOW_EMPTY_INTERVAL_LIST, // allow the user to pass in an empty interval list
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ALLOW_UNSET_BAM_SORT_ORDER, // assume that the bam is sorted, even if the SO (sort-order) flag is not set
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NO_READ_ORDER_VERIFICATION, // do not validate that the reads are in order as we take them from the bam file
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ALLOW_SEQ_DICT_INCOMPATIBILITY, // allow dangerous, but not fatal, sequence dictionary incompabilities
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@EnumerationArgumentDefault // set the ALL value to the default value, so if they specify just -U, we get the ALL
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ALL // do not check for all of the above conditions, DEFAULT
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}
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// a storage for the passed in exclusions
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List<TYPE> exclusions = new ArrayList<TYPE>();
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public ValidationExclusion(List<TYPE> exclusionsList) {
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exclusions.addAll(exclusionsList);
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}
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public ValidationExclusion() {}
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/**
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* do we contain the exclusion specified, or were we set to ALL
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* @param t the exclusion case to test for
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* @return true if we contain the exclusion or if we're set to ALL, false otherwise
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*/
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public boolean contains(TYPE t) {
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return (exclusions.contains(TYPE.ALL) || exclusions.contains(t));
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}
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}
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