178 lines
7.9 KiB
Java
178 lines
7.9 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 org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.commandline.ArgumentException;
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import org.broadinstitute.sting.commandline.Tags;
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import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
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import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
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import org.broadinstitute.sting.gatk.walkers.Walker;
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import org.broadinstitute.sting.gatk.walkers.readutils.PrintReads;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.GenomeLocSortedSet;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
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import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
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import org.testng.Assert;
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import org.testng.annotations.DataProvider;
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import org.testng.annotations.Test;
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import java.io.File;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collection;
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import java.util.List;
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/**
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* Tests selected functionality in the GenomeAnalysisEngine class
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*/
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public class GenomeAnalysisEngineUnitTest extends BaseTest {
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@Test(expectedExceptions=ArgumentException.class)
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public void testDuplicateSamFileHandlingSingleDuplicate() throws Exception {
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GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
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Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
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samFiles.add(new SAMReaderID(new File("public/testdata/exampleBAM.bam"), new Tags()));
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samFiles.add(new SAMReaderID(new File("public/testdata/exampleBAM.bam"), new Tags()));
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testEngine.setSAMFileIDs(samFiles);
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testEngine.checkForDuplicateSamFiles();
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}
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@Test(expectedExceptions=ArgumentException.class)
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public void testDuplicateSamFileHandlingMultipleDuplicates() throws Exception {
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GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
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Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
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samFiles.add(new SAMReaderID(new File("public/testdata/exampleBAM.bam"), new Tags()));
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samFiles.add(new SAMReaderID(new File("public/testdata/exampleNORG.bam"), new Tags()));
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samFiles.add(new SAMReaderID(new File("public/testdata/exampleBAM.bam"), new Tags()));
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samFiles.add(new SAMReaderID(new File("public/testdata/exampleNORG.bam"), new Tags()));
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testEngine.setSAMFileIDs(samFiles);
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testEngine.checkForDuplicateSamFiles();
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}
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@Test
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public void testEmptyIntervalSetHandling() throws Exception {
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GenomeLocParser genomeLocParser = new GenomeLocParser(ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000).getSequenceDictionary());
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GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
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testEngine.setWalker(new PrintReads());
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testEngine.setIntervals(new GenomeLocSortedSet(genomeLocParser));
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testEngine.validateSuppliedIntervals();
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}
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///////////////////////////////////////////////////
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// Test the ReadTransformer ordering enforcement //
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///////////////////////////////////////////////////
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public static class TestReadTransformer extends ReadTransformer {
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private OrderingConstraint orderingConstraint = OrderingConstraint.DO_NOT_CARE;
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private boolean enabled;
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protected TestReadTransformer(final OrderingConstraint orderingConstraint) {
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this.orderingConstraint = orderingConstraint;
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enabled = true;
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}
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// need this because PackageUtils will pick up this class as a possible ReadTransformer
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protected TestReadTransformer() {
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enabled = false;
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}
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@Override
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public OrderingConstraint getOrderingConstraint() { return orderingConstraint; }
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@Override
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public ApplicationTime initializeSub(final GenomeAnalysisEngine engine, final Walker walker) { return ApplicationTime.HANDLED_IN_WALKER; }
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@Override
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public boolean enabled() { return enabled; }
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@Override
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public GATKSAMRecord apply(final GATKSAMRecord read) { return read; }
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}
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@DataProvider(name = "ReadTransformerData")
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public Object[][] makeReadTransformerData() {
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List<Object[]> tests = new ArrayList<Object[]>();
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for ( final ReadTransformer.OrderingConstraint orderingConstraint1 : ReadTransformer.OrderingConstraint.values() ) {
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for ( final ReadTransformer.OrderingConstraint orderingConstraint2 : ReadTransformer.OrderingConstraint.values() ) {
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for ( final ReadTransformer.OrderingConstraint orderingConstraint3 : ReadTransformer.OrderingConstraint.values() ) {
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tests.add(new Object[]{orderingConstraint1, orderingConstraint2, orderingConstraint3});
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}
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}
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}
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return tests.toArray(new Object[][]{});
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}
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@Test(dataProvider = "ReadTransformerData")
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public void testReadTransformer(final ReadTransformer.OrderingConstraint oc1, final ReadTransformer.OrderingConstraint oc2, final ReadTransformer.OrderingConstraint oc3) {
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final GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
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final List<ReadTransformer> readTransformers = new ArrayList<ReadTransformer>(3);
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readTransformers.add(new TestReadTransformer(oc1));
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readTransformers.add(new TestReadTransformer(oc2));
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readTransformers.add(new TestReadTransformer(oc3));
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final boolean shouldThrowException = numWithConstraint(ReadTransformer.OrderingConstraint.MUST_BE_FIRST, oc1, oc2, oc3) > 1 ||
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numWithConstraint(ReadTransformer.OrderingConstraint.MUST_BE_LAST, oc1, oc2, oc3) > 1;
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try {
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testEngine.setReadTransformers(readTransformers);
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Assert.assertFalse(shouldThrowException);
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Assert.assertEquals(testEngine.getReadTransformers().size(), 3);
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Assert.assertTrue(testEngine.getReadTransformers().get(1).getOrderingConstraint() != ReadTransformer.OrderingConstraint.MUST_BE_FIRST);
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Assert.assertTrue(testEngine.getReadTransformers().get(2).getOrderingConstraint() != ReadTransformer.OrderingConstraint.MUST_BE_FIRST);
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Assert.assertTrue(testEngine.getReadTransformers().get(0).getOrderingConstraint() != ReadTransformer.OrderingConstraint.MUST_BE_LAST);
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Assert.assertTrue(testEngine.getReadTransformers().get(1).getOrderingConstraint() != ReadTransformer.OrderingConstraint.MUST_BE_LAST);
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} catch (UserException.IncompatibleReadFiltersException e) {
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Assert.assertTrue(shouldThrowException);
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}
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}
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private int numWithConstraint(final ReadTransformer.OrderingConstraint target, final ReadTransformer.OrderingConstraint... constraints ) {
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int count = 0;
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for ( final ReadTransformer.OrderingConstraint constraint : constraints ) {
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if ( constraint == target )
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count++;
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}
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return count;
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}
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}
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