67 lines
2.5 KiB
Java
67 lines
2.5 KiB
Java
/*
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* Copyright (c) 2012 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.commandline;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.WalkerTest;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.testng.annotations.Test;
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import org.testng.annotations.DataProvider;
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/**
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* Created by IntelliJ IDEA.
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* User: chartl
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* Date: 8/31/12
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* Time: 11:03 AM
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* To change this template use File | Settings | File Templates.
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*/
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public class InvalidArgumentIntegrationTest extends WalkerTest {
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private static final String callsB36 = BaseTest.validationDataLocation + "lowpass.N3.chr1.raw.vcf";
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private WalkerTest.WalkerTestSpec baseTest(String flag, String arg, Class exeption) {
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return new WalkerTest.WalkerTestSpec("-T VariantsToTable -M 10 --variant:vcf "
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+ callsB36 + " -F POS,CHROM -R "
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+ b36KGReference + " -o %s " + flag + " " + arg,
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1, exeption);
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}
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@Test
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public void testUnknownReadFilter() {
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executeTest("UnknownReadFilter",baseTest("-rf","TestUnknownReadFilter", UserException.MalformedReadFilterException.class));
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}
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@Test
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public void testMalformedWalkerArgs() {
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executeTest("MalformedWalkerArgs",
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new WalkerTest.WalkerTestSpec("-T UnknownWalkerName -M 10 --variant:vcf "
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+ callsB36 + " -F POS,CHROM -R "
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+ b36KGReference + " -o %s ",
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1, UserException.MalformedWalkerArgumentsException.class));
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}
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}
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