122 lines
4.5 KiB
Java
122 lines
4.5 KiB
Java
package org.broadinstitute.sting.gatk.walkers;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.gatk.datasources.shards.Shard;
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import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.utils.sam.ArtificialReadsTraversal;
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import org.broadinstitute.sting.utils.sam.ArtificialSAMFileWriter;
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import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
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import org.junit.Before;
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import org.junit.Test;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertTrue;
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import net.sf.samtools.SAMRecord;
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import net.sf.samtools.SAMFileHeader;
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import net.sf.samtools.SAMFileWriterFactory;
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/*
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* Copyright (c) 2009 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 THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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/**
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* @author aaron
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* <p/>
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* Class PrintReadsWalkerUnitTest
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* <p/>
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* This tests the print reads walker, using the artificial reads traversal
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*/
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public class PrintReadsWalkerUnitTest extends BaseTest {
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/**
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* our private fake reads traversal. This traversal seeds the
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* the walker with a specified number of fake reads, which are named sequentially
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*/
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private ArtificialReadsTraversal trav;
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private int readTotal = 0;
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//private char bases[] = {'a', 't'};
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private ReferenceContext bases = null;
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//private ReferenceContext ref = new ReferenceContext()
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@Before
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public void before() {
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trav = new ArtificialReadsTraversal();
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readTotal = ( ( trav.endingChr - trav.startingChr ) + 1 ) * trav.readsPerChr + trav.unMappedReads;
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}
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/** test that we get out the same number of reads we put in */
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@Test
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public void testReadCount() {
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PrintReadsWalker walker = new PrintReadsWalker();
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ArtificialSAMFileWriter writer = new ArtificialSAMFileWriter();
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walker.out = writer;
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trav.traverse(walker, null, writer);
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assertEquals(readTotal, writer.getRecords().size());
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}
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/** test that we're ok with a null read */
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@Test
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public void testNullRead() {
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PrintReadsWalker walker = new PrintReadsWalker();
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ArtificialSAMFileWriter writer = new ArtificialSAMFileWriter();
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walker.out = writer;
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SAMRecord rec = walker.map(bases, null, null);
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assertTrue(rec == null);
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}
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/** tes that we get the read we put into the map function */
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@Test
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public void testReturnRead() {
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PrintReadsWalker walker = new PrintReadsWalker();
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ArtificialSAMFileWriter writer = new ArtificialSAMFileWriter();
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walker.out = writer;
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SAMFileHeader head = ArtificialSAMUtils.createArtificialSamHeader(3,1,1000);
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SAMRecord rec = ArtificialSAMUtils.createArtificialRead(head, "FakeRead", 1, 1, 50);
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SAMRecord ret = walker.map(bases, rec,null);
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assertTrue(ret == rec);
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assertTrue(ret.getReadName().equals(rec.getReadName()));
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}
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/** test that the read makes it to the output source */
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@Test
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public void testReducingRead() {
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PrintReadsWalker walker = new PrintReadsWalker();
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ArtificialSAMFileWriter writer = new ArtificialSAMFileWriter();
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walker.out = writer;
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SAMFileHeader head = ArtificialSAMUtils.createArtificialSamHeader(3,1,1000);
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SAMRecord rec = ArtificialSAMUtils.createArtificialRead(head, "FakeRead", 1, 1, 50);
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SAMRecord ret = walker.map(bases, null,null);
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walker.reduce(ret,writer);
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assertTrue(writer.getRecords().size() == 1);
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}
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}
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