64 lines
2.5 KiB
Java
64 lines
2.5 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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* 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 THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.utils.interval;
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import org.broadinstitute.sting.WalkerTest;
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import org.testng.annotations.Test;
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import java.util.Arrays;
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import java.util.Collections;
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/**
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* Test the GATK core interval parsing mechanism.
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*/
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public class IntervalIntegrationTest extends WalkerTest {
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@Test
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public void testAllImplicitIntervalParsing() {
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String md5 = "7821db9e14d4f8e07029ff1959cd5a99";
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T CountLoci" +
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" -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
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" -R " + hg18Reference +
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" -o %s",
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1, // just one output file
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Arrays.asList(md5));
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executeTest("testAllIntervalsImplicit",spec);
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}
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@Test
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public void testAllExplicitIntervalParsing() {
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String md5 = "7821db9e14d4f8e07029ff1959cd5a99";
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T CountLoci" +
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" -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
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" -R " + hg18Reference +
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" -L all" +
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" -o %s",
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1, // just one output file
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Arrays.asList(md5));
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executeTest("testAllIntervalsExplicit",spec);
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}
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}
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