215 lines
9.8 KiB
Java
215 lines
9.8 KiB
Java
// our package
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package org.broadinstitute.sting.utils;
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// the imports for unit testing.
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import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
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import org.broadinstitute.sting.utils.interval.IntervalUtils;
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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.DataProvider;
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import org.testng.annotations.Test;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.List;
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import net.sf.picard.reference.ReferenceSequenceFile;
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import net.sf.picard.reference.IndexedFastaSequenceFile;
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/**
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* Basic unit test for GenomeLoc
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*/
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public class GenomeLocUnitTest extends BaseTest {
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private static ReferenceSequenceFile seq;
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private GenomeLocParser genomeLocParser;
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@BeforeClass
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public void init() throws FileNotFoundException {
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// sequence
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seq = new CachingIndexedFastaSequenceFile(new File(hg18Reference));
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genomeLocParser = new GenomeLocParser(seq);
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}
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/**
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* Tests that we got a string parameter in correctly
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*/
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@Test
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public void testIsBetween() {
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logger.warn("Executing testIsBetween");
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GenomeLoc locMiddle = genomeLocParser.createGenomeLoc("chr1", 3, 3);
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GenomeLoc locLeft = genomeLocParser.createGenomeLoc("chr1", 1, 1);
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GenomeLoc locRight = genomeLocParser.createGenomeLoc("chr1", 5, 5);
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Assert.assertTrue(locMiddle.isBetween(locLeft, locRight));
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Assert.assertFalse(locLeft.isBetween(locMiddle, locRight));
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Assert.assertFalse(locRight.isBetween(locLeft, locMiddle));
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}
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@Test
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public void testContigIndex() {
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logger.warn("Executing testContigIndex");
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GenomeLoc locOne = genomeLocParser.createGenomeLoc("chr1",1,1);
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Assert.assertEquals(1, locOne.getContigIndex());
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Assert.assertEquals("chr1", locOne.getContig());
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GenomeLoc locX = genomeLocParser.createGenomeLoc("chrX",1,1);
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Assert.assertEquals(23, locX.getContigIndex());
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Assert.assertEquals("chrX", locX.getContig());
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GenomeLoc locNumber = genomeLocParser.createGenomeLoc(seq.getSequenceDictionary().getSequence(1).getSequenceName(),1,1);
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Assert.assertEquals(1, locNumber.getContigIndex());
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Assert.assertEquals("chr1", locNumber.getContig());
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Assert.assertEquals(0, locOne.compareTo(locNumber));
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}
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@Test
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public void testCompareTo() {
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logger.warn("Executing testCompareTo");
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GenomeLoc twoOne = genomeLocParser.createGenomeLoc("chr2", 1);
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GenomeLoc twoFive = genomeLocParser.createGenomeLoc("chr2", 5);
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GenomeLoc twoOtherFive = genomeLocParser.createGenomeLoc("chr2", 5);
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Assert.assertEquals(twoFive.compareTo(twoOtherFive), 0);
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Assert.assertEquals(twoOne.compareTo(twoFive), -1);
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Assert.assertEquals(twoFive.compareTo(twoOne), 1);
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GenomeLoc oneOne = genomeLocParser.createGenomeLoc("chr1", 5);
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Assert.assertEquals(oneOne.compareTo(twoOne), -1);
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Assert.assertEquals(twoOne.compareTo(oneOne), 1);
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}
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@Test
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public void testUnmappedSort() {
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GenomeLoc chr1 = genomeLocParser.createGenomeLoc("chr1",1,10000000);
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GenomeLoc chr2 = genomeLocParser.createGenomeLoc("chr2",1,10000000);
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GenomeLoc unmapped = GenomeLoc.UNMAPPED;
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List<GenomeLoc> unmappedOnly = Arrays.asList(unmapped);
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Collections.sort(unmappedOnly);
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Assert.assertEquals(unmappedOnly.size(),1,"Wrong number of elements in unmapped-only list.");
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Assert.assertEquals(unmappedOnly.get(0),unmapped,"List sorted in wrong order");
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List<GenomeLoc> chr1Presorted = Arrays.asList(chr1,unmapped);
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Collections.sort(chr1Presorted);
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Assert.assertEquals(chr1Presorted.size(),2,"Wrong number of elements in chr1,unmapped list.");
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Assert.assertEquals(chr1Presorted,Arrays.asList(chr1,unmapped),"List sorted in wrong order");
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List<GenomeLoc> chr1Inverted = Arrays.asList(unmapped,chr1);
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Collections.sort(chr1Inverted);
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Assert.assertEquals(chr1Inverted.size(),2,"Wrong number of elements in chr1,unmapped list.");
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Assert.assertEquals(chr1Inverted,Arrays.asList(chr1,unmapped),"List sorted in wrong order");
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List<GenomeLoc> chr1and2Presorted = Arrays.asList(chr1,chr2,unmapped);
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Collections.sort(chr1and2Presorted);
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Assert.assertEquals(chr1and2Presorted.size(),3,"Wrong number of elements in chr1,chr2,unmapped list.");
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Assert.assertEquals(chr1and2Presorted,Arrays.asList(chr1,chr2,unmapped),"List sorted in wrong order");
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List<GenomeLoc> chr1and2UnmappedInFront = Arrays.asList(unmapped,chr1,chr2);
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Collections.sort(chr1and2UnmappedInFront);
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Assert.assertEquals(chr1and2UnmappedInFront.size(),3,"Wrong number of elements in unmapped,chr1,chr2 list.");
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Assert.assertEquals(chr1and2UnmappedInFront,Arrays.asList(chr1,chr2,unmapped),"List sorted in wrong order");
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List<GenomeLoc> chr1and2UnmappedSandwiched = Arrays.asList(chr1,unmapped,chr2);
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Collections.sort(chr1and2UnmappedSandwiched);
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Assert.assertEquals(chr1and2UnmappedSandwiched.size(),3,"Wrong number of elements in chr1,unmapped,chr2 list.");
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Assert.assertEquals(chr1and2UnmappedSandwiched,Arrays.asList(chr1,chr2,unmapped),"List sorted in wrong order");
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}
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@Test
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public void testUnmappedMerge() {
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GenomeLoc chr1 = genomeLocParser.createGenomeLoc("chr1",1,10000000);
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GenomeLoc unmapped = GenomeLoc.UNMAPPED;
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List<GenomeLoc> oneUnmappedOnly = Arrays.asList(unmapped);
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oneUnmappedOnly = IntervalUtils.sortAndMergeIntervals(genomeLocParser,oneUnmappedOnly, IntervalMergingRule.OVERLAPPING_ONLY).toList();
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Assert.assertEquals(oneUnmappedOnly.size(),1,"Wrong number of elements in list.");
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Assert.assertEquals(oneUnmappedOnly.get(0),unmapped,"List sorted in wrong order");
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List<GenomeLoc> twoUnmapped = Arrays.asList(unmapped,unmapped);
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twoUnmapped = IntervalUtils.sortAndMergeIntervals(genomeLocParser,twoUnmapped,IntervalMergingRule.OVERLAPPING_ONLY).toList();
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Assert.assertEquals(twoUnmapped.size(),1,"Wrong number of elements in list.");
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Assert.assertEquals(twoUnmapped.get(0),unmapped,"List sorted in wrong order");
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List<GenomeLoc> twoUnmappedAtEnd = Arrays.asList(chr1,unmapped,unmapped);
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twoUnmappedAtEnd = IntervalUtils.sortAndMergeIntervals(genomeLocParser,twoUnmappedAtEnd,IntervalMergingRule.OVERLAPPING_ONLY).toList();
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Assert.assertEquals(twoUnmappedAtEnd.size(),2,"Wrong number of elements in list.");
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Assert.assertEquals(twoUnmappedAtEnd,Arrays.asList(chr1,unmapped),"List sorted in wrong order");
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List<GenomeLoc> twoUnmappedMixed = Arrays.asList(unmapped,chr1,unmapped);
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twoUnmappedMixed = IntervalUtils.sortAndMergeIntervals(genomeLocParser,twoUnmappedMixed,IntervalMergingRule.OVERLAPPING_ONLY).toList();
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Assert.assertEquals(twoUnmappedMixed.size(),2,"Wrong number of elements in list.");
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Assert.assertEquals(twoUnmappedMixed,Arrays.asList(chr1,unmapped),"List sorted in wrong order");
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}
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// -------------------------------------------------------------------------------------
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//
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// testing overlap detection
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//
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// -------------------------------------------------------------------------------------
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private class ReciprocalOverlapProvider extends TestDataProvider {
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GenomeLoc gl1, gl2;
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int overlapSize;
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double overlapFraction;
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private ReciprocalOverlapProvider(int start1, int stop1, int start2, int stop2) {
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super(ReciprocalOverlapProvider.class);
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gl1 = genomeLocParser.createGenomeLoc("chr1", start1, stop1);
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gl2 = genomeLocParser.createGenomeLoc("chr1", start2, stop2);
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int shared = 0;
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for ( int i = start1; i <= stop1; i++ ) {
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if ( i >= start2 && i <= stop2 )
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shared++;
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}
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this.overlapSize = shared;
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this.overlapFraction = Math.min((1.0*shared)/gl1.size(), (1.0*shared)/gl2.size());
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super.setName(String.format("%d-%d / %d-%d overlap=%d / %.2f", start1, stop1, start2, stop2, overlapSize, overlapFraction));
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}
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}
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@DataProvider(name = "ReciprocalOverlapProvider")
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public Object[][] makeReciprocalOverlapProvider() {
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for ( int start1 = 1; start1 <= 10; start1++ ) {
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for ( int stop1 = start1; stop1 <= 10; stop1++ ) {
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new ReciprocalOverlapProvider(start1, stop1, 1, 10);
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new ReciprocalOverlapProvider(start1, stop1, 5, 10);
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new ReciprocalOverlapProvider(start1, stop1, 5, 7);
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new ReciprocalOverlapProvider(start1, stop1, 5, 15);
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new ReciprocalOverlapProvider(start1, stop1, 11, 20);
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new ReciprocalOverlapProvider(1, 10, start1, stop1);
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new ReciprocalOverlapProvider(5, 10, start1, stop1);
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new ReciprocalOverlapProvider(5, 7, start1, stop1);
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new ReciprocalOverlapProvider(5, 15, start1, stop1);
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new ReciprocalOverlapProvider(11, 20, start1, stop1);
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}
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}
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return ReciprocalOverlapProvider.getTests(ReciprocalOverlapProvider.class);
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}
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@Test(dataProvider = "ReciprocalOverlapProvider")
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public void testReciprocalOverlapProvider(ReciprocalOverlapProvider cfg) {
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if ( cfg.overlapSize == 0 ) {
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Assert.assertFalse(cfg.gl1.overlapsP(cfg.gl2));
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} else {
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Assert.assertTrue(cfg.gl1.overlapsP(cfg.gl2));
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Assert.assertEquals(cfg.gl1.intersect(cfg.gl2).size(), cfg.overlapSize);
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Assert.assertEquals(cfg.gl1.reciprocialOverlapFraction(cfg.gl2), cfg.overlapFraction);
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}
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}
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}
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