192 lines
10 KiB
Java
192 lines
10 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.utils;
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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.Test;
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import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
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import net.sf.samtools.SAMRecord;
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import net.sf.samtools.SAMFileHeader;
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import java.util.*;
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/**
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* Basic tests to prove the integrity of the reservoir downsampler.
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* At the moment, always run tests on SAM records as that's the task
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* for which the downsampler was conceived.
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*
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* @author mhanna
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* @version 0.1
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*/
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public class LegacyReservoirDownsamplerUnitTest {
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private static final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1,1,200);
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@Test
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public void testEmptyIterator() {
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LegacyReservoirDownsampler<SAMRecord> downsampler = new LegacyReservoirDownsampler<SAMRecord>(1);
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Assert.assertTrue(downsampler.isEmpty(),"Downsampler is not empty but should be.");
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}
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@Test
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public void testOneElementWithPoolSizeOne() {
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List<GATKSAMRecord> reads = Collections.singletonList(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76));
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LegacyReservoirDownsampler<SAMRecord> downsampler = new LegacyReservoirDownsampler<SAMRecord>(1);
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downsampler.addAll(reads);
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Assert.assertFalse(downsampler.isEmpty(),"Downsampler is empty but shouldn't be");
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Collection<SAMRecord> batchedReads = downsampler.getDownsampledContents();
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Assert.assertEquals(batchedReads.size(), 1, "Downsampler is returning the wrong number of reads");
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Assert.assertSame(batchedReads.iterator().next(), reads.get(0), "Downsampler is returning an incorrect read");
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}
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@Test
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public void testOneElementWithPoolSizeGreaterThanOne() {
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List<GATKSAMRecord> reads = Collections.singletonList(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76));
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LegacyReservoirDownsampler<SAMRecord> downsampler = new LegacyReservoirDownsampler<SAMRecord>(5);
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downsampler.addAll(reads);
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Assert.assertFalse(downsampler.isEmpty(),"Downsampler is empty but shouldn't be");
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Collection<SAMRecord> batchedReads = downsampler.getDownsampledContents();
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Assert.assertEquals(batchedReads.size(), 1, "Downsampler is returning the wrong number of reads");
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Assert.assertSame(batchedReads.iterator().next(), reads.get(0), "Downsampler is returning an incorrect read");
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}
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@Test
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public void testPoolFilledPartially() {
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List<SAMRecord> reads = new ArrayList<SAMRecord>();
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reads.add(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76));
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reads.add(ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,76));
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reads.add(ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,76));
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LegacyReservoirDownsampler<SAMRecord> downsampler = new LegacyReservoirDownsampler<SAMRecord>(5);
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downsampler.addAll(reads);
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Assert.assertFalse(downsampler.isEmpty(),"Downsampler is empty but shouldn't be");
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List<SAMRecord> batchedReads = new ArrayList<SAMRecord>(downsampler.getDownsampledContents());
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Assert.assertEquals(batchedReads.size(), 3, "Downsampler is returning the wrong number of reads");
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Assert.assertSame(batchedReads.get(0), reads.get(0), "Downsampler read 1 is incorrect");
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Assert.assertSame(batchedReads.get(1), reads.get(1), "Downsampler read 2 is incorrect");
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Assert.assertSame(batchedReads.get(2), reads.get(2), "Downsampler read 3 is incorrect");
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}
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@Test
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public void testPoolFilledExactly() {
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List<SAMRecord> reads = new ArrayList<SAMRecord>();
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reads.add(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76));
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reads.add(ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,76));
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reads.add(ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,76));
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reads.add(ArtificialSAMUtils.createArtificialRead(header,"read4",0,1,76));
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reads.add(ArtificialSAMUtils.createArtificialRead(header,"read5",0,1,76));
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LegacyReservoirDownsampler<SAMRecord> downsampler = new LegacyReservoirDownsampler<SAMRecord>(5);
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downsampler.addAll(reads);
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Assert.assertFalse(downsampler.isEmpty(),"Downsampler is empty but shouldn't be");
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List<SAMRecord> batchedReads = new ArrayList<SAMRecord>(downsampler.getDownsampledContents());
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Assert.assertEquals(batchedReads.size(), 5, "Downsampler is returning the wrong number of reads");
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Assert.assertSame(batchedReads.iterator().next(), reads.get(0), "Downsampler is returning an incorrect read");
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Assert.assertSame(batchedReads.get(0), reads.get(0), "Downsampler read 1 is incorrect");
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Assert.assertSame(batchedReads.get(1), reads.get(1), "Downsampler read 2 is incorrect");
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Assert.assertSame(batchedReads.get(2), reads.get(2), "Downsampler read 3 is incorrect");
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Assert.assertSame(batchedReads.get(3), reads.get(3), "Downsampler read 4 is incorrect");
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Assert.assertSame(batchedReads.get(4), reads.get(4), "Downsampler read 5 is incorrect");
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}
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@Test
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public void testLargerPileWithZeroElementPool() {
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List<SAMRecord> reads = new ArrayList<SAMRecord>();
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reads.add(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76));
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reads.add(ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,76));
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reads.add(ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,76));
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LegacyReservoirDownsampler<SAMRecord> downsampler = new LegacyReservoirDownsampler<SAMRecord>(0);
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downsampler.addAll(reads);
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Assert.assertTrue(downsampler.isEmpty(),"Downsampler isn't empty but should be");
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List<SAMRecord> batchedReads = new ArrayList<SAMRecord>(downsampler.getDownsampledContents());
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Assert.assertEquals(batchedReads.size(), 0, "Downsampler is returning the wrong number of reads");
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}
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@Test
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public void testLargerPileWithSingleElementPool() {
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List<SAMRecord> reads = new ArrayList<SAMRecord>();
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reads.add(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76));
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reads.add(ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,76));
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reads.add(ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,76));
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reads.add(ArtificialSAMUtils.createArtificialRead(header,"read4",0,1,76));
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reads.add(ArtificialSAMUtils.createArtificialRead(header,"read5",0,1,76));
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LegacyReservoirDownsampler<SAMRecord> downsampler = new LegacyReservoirDownsampler<SAMRecord>(1);
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downsampler.addAll(reads);
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Assert.assertFalse(downsampler.isEmpty(),"Downsampler is empty but shouldn't be");
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List<SAMRecord> batchedReads = new ArrayList<SAMRecord>(downsampler.getDownsampledContents());
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Assert.assertEquals(batchedReads.size(), 1, "Downsampler is returning the wrong number of reads");
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Assert.assertTrue(reads.contains(batchedReads.get(0)),"Downsampler is returning a bad read.");
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}
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@Test
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public void testFillingAcrossLoci() {
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List<SAMRecord> reads = new ArrayList<SAMRecord>();
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reads.add(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76));
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LegacyReservoirDownsampler<SAMRecord> downsampler = new LegacyReservoirDownsampler<SAMRecord>(5);
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downsampler.addAll(reads);
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Assert.assertFalse(downsampler.isEmpty(),"Downsampler is empty but shouldn't be");
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List<SAMRecord> batchedReads = new ArrayList<SAMRecord>(downsampler.getDownsampledContents());
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Assert.assertEquals(batchedReads.size(), 1, "Downsampler is returning the wrong number of reads");
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Assert.assertEquals(batchedReads.get(0), reads.get(0), "Downsampler is returning an incorrect read.");
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reads.clear();
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reads.add(ArtificialSAMUtils.createArtificialRead(header,"read2",0,2,76));
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reads.add(ArtificialSAMUtils.createArtificialRead(header,"read3",0,2,76));
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downsampler.clear();
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downsampler.addAll(reads);
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Assert.assertFalse(downsampler.isEmpty(),"Downsampler is empty but shouldn't be");
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batchedReads = new ArrayList<SAMRecord>(downsampler.getDownsampledContents());
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Assert.assertEquals(batchedReads.size(), 2, "Downsampler is returning the wrong number of reads");
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Assert.assertEquals(batchedReads.get(0), reads.get(0), "Downsampler is returning an incorrect read.");
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Assert.assertEquals(batchedReads.get(1), reads.get(1), "Downsampler is returning an incorrect read.");
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reads.clear();
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reads.add(ArtificialSAMUtils.createArtificialRead(header,"read4",0,3,76));
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reads.add(ArtificialSAMUtils.createArtificialRead(header,"read5",0,3,76));
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downsampler.clear();
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downsampler.addAll(reads);
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Assert.assertFalse(downsampler.isEmpty(),"Downsampler is empty but shouldn't be");
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batchedReads = new ArrayList<SAMRecord>(downsampler.getDownsampledContents());
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Assert.assertEquals(batchedReads.size(), 2, "Downsampler is returning the wrong number of reads");
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Assert.assertEquals(batchedReads.get(0), reads.get(0), "Downsampler is returning an incorrect read.");
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Assert.assertEquals(batchedReads.get(1), reads.get(1), "Downsampler is returning an incorrect read.");
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}
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}
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