gatk-3.8/java/test/org/broadinstitute/sting/utils/GenomeLocUnitTest.java

// our package
package org.broadinstitute.sting.utils;


// the imports for unit testing.


import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
import org.broadinstitute.sting.utils.interval.IntervalUtils;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;

import java.io.File;
import java.io.FileNotFoundException;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;

import net.sf.picard.reference.ReferenceSequenceFile;
import net.sf.picard.reference.IndexedFastaSequenceFile;

/**
 * Basic unit test for GenomeLoc
 */
public class GenomeLocUnitTest extends BaseTest {
    private static ReferenceSequenceFile seq;
    private GenomeLocParser genomeLocParser;

    @BeforeClass
    public void init() throws FileNotFoundException {
        // sequence
        seq = new CachingIndexedFastaSequenceFile(new File(hg18Reference));
        genomeLocParser = new GenomeLocParser(seq);
    }

    /**
     * Tests that we got a string parameter in correctly
     */
    @Test
    public void testIsBetween() {
        logger.warn("Executing testIsBetween");

        GenomeLoc locMiddle = genomeLocParser.createGenomeLoc("chr1", 3, 3);

        GenomeLoc locLeft = genomeLocParser.createGenomeLoc("chr1", 1, 1);
        GenomeLoc locRight = genomeLocParser.createGenomeLoc("chr1", 5, 5);

        Assert.assertTrue(locMiddle.isBetween(locLeft, locRight));
        Assert.assertFalse(locLeft.isBetween(locMiddle, locRight));
        Assert.assertFalse(locRight.isBetween(locLeft, locMiddle));

    }
    @Test
    public void testContigIndex() {
        logger.warn("Executing testContigIndex");
        GenomeLoc locOne = genomeLocParser.createGenomeLoc("chr1",1,1);
        Assert.assertEquals(1, locOne.getContigIndex());
        Assert.assertEquals("chr1", locOne.getContig());

        GenomeLoc locX = genomeLocParser.createGenomeLoc("chrX",1,1);
        Assert.assertEquals(23, locX.getContigIndex());
        Assert.assertEquals("chrX", locX.getContig());

        GenomeLoc locNumber = genomeLocParser.createGenomeLoc(seq.getSequenceDictionary().getSequence(1).getSequenceName(),1,1);
        Assert.assertEquals(1, locNumber.getContigIndex());
        Assert.assertEquals("chr1", locNumber.getContig());
        Assert.assertEquals(0, locOne.compareTo(locNumber));

    }

    @Test
    public void testCompareTo() {
        logger.warn("Executing testCompareTo");
        GenomeLoc twoOne = genomeLocParser.createGenomeLoc("chr2", 1);
        GenomeLoc twoFive = genomeLocParser.createGenomeLoc("chr2", 5);
        GenomeLoc twoOtherFive = genomeLocParser.createGenomeLoc("chr2", 5);
        Assert.assertEquals(twoFive.compareTo(twoOtherFive), 0);

        Assert.assertEquals(twoOne.compareTo(twoFive), -1);
        Assert.assertEquals(twoFive.compareTo(twoOne), 1);

        GenomeLoc oneOne = genomeLocParser.createGenomeLoc("chr1", 5);
        Assert.assertEquals(oneOne.compareTo(twoOne), -1);
        Assert.assertEquals(twoOne.compareTo(oneOne), 1);
    }


    @Test
    public void testUnmappedSort() {
        GenomeLoc chr1 = genomeLocParser.createGenomeLoc("chr1",1,10000000);
        GenomeLoc chr2 = genomeLocParser.createGenomeLoc("chr2",1,10000000);
        GenomeLoc unmapped = GenomeLoc.UNMAPPED;

        List<GenomeLoc> unmappedOnly = Arrays.asList(unmapped);
        Collections.sort(unmappedOnly);
        Assert.assertEquals(unmappedOnly.size(),1,"Wrong number of elements in unmapped-only list.");
        Assert.assertEquals(unmappedOnly.get(0),unmapped,"List sorted in wrong order");

        List<GenomeLoc> chr1Presorted = Arrays.asList(chr1,unmapped);
        Collections.sort(chr1Presorted);
        Assert.assertEquals(chr1Presorted.size(),2,"Wrong number of elements in chr1,unmapped list.");
        Assert.assertEquals(chr1Presorted,Arrays.asList(chr1,unmapped),"List sorted in wrong order");

        List<GenomeLoc> chr1Inverted = Arrays.asList(unmapped,chr1);
        Collections.sort(chr1Inverted);
        Assert.assertEquals(chr1Inverted.size(),2,"Wrong number of elements in chr1,unmapped list.");
        Assert.assertEquals(chr1Inverted,Arrays.asList(chr1,unmapped),"List sorted in wrong order");

        List<GenomeLoc> chr1and2Presorted = Arrays.asList(chr1,chr2,unmapped);
        Collections.sort(chr1and2Presorted);
        Assert.assertEquals(chr1and2Presorted.size(),3,"Wrong number of elements in chr1,chr2,unmapped list.");
        Assert.assertEquals(chr1and2Presorted,Arrays.asList(chr1,chr2,unmapped),"List sorted in wrong order");

        List<GenomeLoc> chr1and2UnmappedInFront = Arrays.asList(unmapped,chr1,chr2);
        Collections.sort(chr1and2UnmappedInFront);
        Assert.assertEquals(chr1and2UnmappedInFront.size(),3,"Wrong number of elements in unmapped,chr1,chr2 list.");
        Assert.assertEquals(chr1and2UnmappedInFront,Arrays.asList(chr1,chr2,unmapped),"List sorted in wrong order");

        List<GenomeLoc> chr1and2UnmappedSandwiched = Arrays.asList(chr1,unmapped,chr2);
        Collections.sort(chr1and2UnmappedSandwiched);
        Assert.assertEquals(chr1and2UnmappedSandwiched.size(),3,"Wrong number of elements in chr1,unmapped,chr2 list.");
        Assert.assertEquals(chr1and2UnmappedSandwiched,Arrays.asList(chr1,chr2,unmapped),"List sorted in wrong order");
    }

    @Test
    public void testUnmappedMerge() {
        GenomeLoc chr1 = genomeLocParser.createGenomeLoc("chr1",1,10000000);
        GenomeLoc unmapped = GenomeLoc.UNMAPPED;

        List<GenomeLoc> oneUnmappedOnly = Arrays.asList(unmapped);
        oneUnmappedOnly = IntervalUtils.sortAndMergeIntervals(genomeLocParser,oneUnmappedOnly, IntervalMergingRule.OVERLAPPING_ONLY).toList();
        Assert.assertEquals(oneUnmappedOnly.size(),1,"Wrong number of elements in list.");
        Assert.assertEquals(oneUnmappedOnly.get(0),unmapped,"List sorted in wrong order");

        List<GenomeLoc> twoUnmapped = Arrays.asList(unmapped,unmapped);
        twoUnmapped = IntervalUtils.sortAndMergeIntervals(genomeLocParser,twoUnmapped,IntervalMergingRule.OVERLAPPING_ONLY).toList();
        Assert.assertEquals(twoUnmapped.size(),1,"Wrong number of elements in list.");
        Assert.assertEquals(twoUnmapped.get(0),unmapped,"List sorted in wrong order");

        List<GenomeLoc> twoUnmappedAtEnd = Arrays.asList(chr1,unmapped,unmapped);
        twoUnmappedAtEnd = IntervalUtils.sortAndMergeIntervals(genomeLocParser,twoUnmappedAtEnd,IntervalMergingRule.OVERLAPPING_ONLY).toList();
        Assert.assertEquals(twoUnmappedAtEnd.size(),2,"Wrong number of elements in list.");
        Assert.assertEquals(twoUnmappedAtEnd,Arrays.asList(chr1,unmapped),"List sorted in wrong order");

        List<GenomeLoc> twoUnmappedMixed = Arrays.asList(unmapped,chr1,unmapped);
        twoUnmappedMixed = IntervalUtils.sortAndMergeIntervals(genomeLocParser,twoUnmappedMixed,IntervalMergingRule.OVERLAPPING_ONLY).toList();
        Assert.assertEquals(twoUnmappedMixed.size(),2,"Wrong number of elements in list.");
        Assert.assertEquals(twoUnmappedMixed,Arrays.asList(chr1,unmapped),"List sorted in wrong order");
    }
}