69 lines
2.6 KiB
Java
69 lines
2.6 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.gatk;
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import net.sf.samtools.SAMFileReader;
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import org.broadinstitute.sting.BaseTest;
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import org.testng.Assert;
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import org.testng.annotations.Test;
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import java.io.File;
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/**
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* @author Eric Banks
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* @since 7/18/12
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*/
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public class CommandLineGATKUnitTest extends BaseTest {
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@Test(enabled = true)
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public void testSamTextFileError1() {
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final File samFile = new File(publicTestDir + "testfile.sam");
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final File indexFile = new File(publicTestDir + "HiSeq.1mb.1RG.bai");
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try {
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final SAMFileReader reader = new SAMFileReader(samFile, indexFile, false);
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// we shouldn't get here
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Assert.fail("We should have exceptioned out when trying to create a reader with an index for a textual SAM file");
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} catch (RuntimeException e) {
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Assert.assertTrue(e.getMessage().indexOf(CommandLineGATK.PICARD_TEXT_SAM_FILE_ERROR_1) != -1);
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}
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}
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@Test(enabled = true)
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public void testSamTextFileError2() {
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File samFile = new File(publicTestDir + "testfile.sam");
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try {
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final SAMFileReader reader = new SAMFileReader(samFile);
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reader.getFilePointerSpanningReads();
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// we shouldn't get here
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Assert.fail("We should have exceptioned out when trying to call getFilePointerSpanningReads() for a textual SAM file");
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} catch (RuntimeException e) {
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Assert.assertTrue(e.getMessage().indexOf(CommandLineGATK.PICARD_TEXT_SAM_FILE_ERROR_2) != -1);
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}
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}
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}
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