107 lines
4.5 KiB
Java
107 lines
4.5 KiB
Java
/*
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* Copyright (c) 2011, 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.gatk;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.commandline.ParsingEngine;
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import org.broadinstitute.sting.commandline.Tags;
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import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
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import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
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import org.testng.Assert;
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import org.testng.annotations.BeforeClass;
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import org.testng.annotations.Test;
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import java.io.File;
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import java.io.PrintWriter;
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import java.util.ArrayList;
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import java.util.List;
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/**
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* Tests selected functionality in the CommandLineExecutable class
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*/
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public class CommandLineExecutableUnitTest extends BaseTest {
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@Test
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public void testIgnoreBlankLinesInBAMListFiles() throws Exception {
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File tempListFile = createTempListFile("testIgnoreBlankLines",
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"",
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"testdata/exampleBAM.bam",
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" "
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);
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List<SAMReaderID> expectedBAMFileListAfterUnpacking = new ArrayList<SAMReaderID>();
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expectedBAMFileListAfterUnpacking.add(new SAMReaderID(new File("testdata/exampleBAM.bam"), new Tags()));
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performBAMListFileUnpackingTest(tempListFile, expectedBAMFileListAfterUnpacking);
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}
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@Test
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public void testCommentSupportInBAMListFiles() throws Exception {
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File tempListFile = createTempListFile("testCommentSupport",
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"#",
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"testdata/exampleBAM.bam",
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"#testdata/foo.bam",
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" # testdata/bar.bam"
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);
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List<SAMReaderID> expectedBAMFileListAfterUnpacking = new ArrayList<SAMReaderID>();
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expectedBAMFileListAfterUnpacking.add(new SAMReaderID(new File("testdata/exampleBAM.bam"), new Tags()));
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performBAMListFileUnpackingTest(tempListFile, expectedBAMFileListAfterUnpacking);
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}
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private File createTempListFile( String tempFilePrefix, String... lines ) throws Exception {
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File tempListFile = File.createTempFile(tempFilePrefix, ".list");
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tempListFile.deleteOnExit();
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PrintWriter out = new PrintWriter(tempListFile);
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for ( String line : lines ) {
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out.println(line);
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}
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out.close();
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return tempListFile;
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}
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private void performBAMListFileUnpackingTest( File tempListFile, List<SAMReaderID> expectedUnpackedFileList ) throws Exception {
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List<String> bamFiles = new ArrayList<String>();
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bamFiles.add(tempListFile.getAbsolutePath());
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GATKArgumentCollection argCollection = new GATKArgumentCollection();
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argCollection.samFiles = bamFiles;
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CommandLineGATK testInstance = new CommandLineGATK();
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testInstance.setParser(new ParsingEngine(testInstance));
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List<SAMReaderID> unpackedBAMFileList = testInstance.unpackBAMFileList(argCollection);
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Assert.assertEquals(unpackedBAMFileList.size(), expectedUnpackedFileList.size(),
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"Unpacked BAM file list contains extraneous lines");
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Assert.assertEquals(unpackedBAMFileList, expectedUnpackedFileList,
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"Unpacked BAM file list does not contain correct BAM file names");
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}
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}
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