85 lines
3.9 KiB
Java
Executable File
85 lines
3.9 KiB
Java
Executable File
package org.broadinstitute.sting.utils;
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import net.sf.samtools.SAMFileHeader;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.pileup.PileupElement;
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import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
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import org.broadinstitute.sting.utils.sam.ReadUtils;
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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.BeforeTest;
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import org.testng.annotations.Test;
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public class ReadUtilsUnitTest extends BaseTest {
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SAMRecord read, reducedRead;
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final static String BASES = "ACTG";
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final static String QUALS = "!+5?";
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final private static int REDUCED_READ_QUAL = 20;
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@BeforeTest
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public void init() {
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SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1,1,1000);
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read = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 1, BASES.length());
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read.setReadUnmappedFlag(true);
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read.setReadBases(new String(BASES).getBytes());
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read.setBaseQualityString(new String(QUALS));
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reducedRead = ArtificialSAMUtils.createArtificialRead(header, "reducedRead", 0, 1, BASES.length());
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reducedRead.setReadBases(BASES.getBytes());
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reducedRead.setBaseQualityString(QUALS);
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reducedRead.setAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG, REDUCED_READ_QUAL);
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}
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private void testReadBasesAndQuals(SAMRecord read, int expectedStart, int expectedStop) {
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SAMRecord clipped = ReadUtils.hardClipBases(read, expectedStart, expectedStop - 1, null);
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String expectedBases = BASES.substring(expectedStart, expectedStop);
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String expectedQuals = QUALS.substring(expectedStart, expectedStop);
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Assert.assertEquals(clipped.getReadBases(), expectedBases.getBytes(), "Clipped bases not those expected");
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Assert.assertEquals(clipped.getBaseQualityString(), expectedQuals, "Clipped quals not those expected");
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}
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@Test public void testNoClip() { testReadBasesAndQuals(read, 0, 4); }
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@Test public void testClip1Front() { testReadBasesAndQuals(read, 1, 4); }
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@Test public void testClip2Front() { testReadBasesAndQuals(read, 2, 4); }
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@Test public void testClip1Back() { testReadBasesAndQuals(read, 0, 3); }
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@Test public void testClip2Back() { testReadBasesAndQuals(read, 0, 2); }
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@Test
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public void testReducedReads() {
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Assert.assertFalse(ReadUtils.isReducedRead(read), "isReducedRead is false for normal read");
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Assert.assertEquals(ReadUtils.getReducedReadQualityTagValue(read), null, "No reduced read tag in normal read");
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Assert.assertTrue(ReadUtils.isReducedRead(reducedRead), "isReducedRead is true for reduced read");
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Assert.assertEquals((int) ReadUtils.getReducedReadQualityTagValue(reducedRead), REDUCED_READ_QUAL, "Reduced read tag is set to expected value");
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}
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@Test
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public void testreducedReadWithReducedQualsWithReducedRead() {
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SAMRecord replacedRead = ReadUtils.reducedReadWithReducedQuals(reducedRead);
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Assert.assertEquals(replacedRead.getReadBases(), reducedRead.getReadBases());
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Assert.assertEquals(replacedRead.getBaseQualities().length, reducedRead.getBaseQualities().length);
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for ( int i = 0; i < replacedRead.getBaseQualities().length; i++)
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Assert.assertEquals(replacedRead.getBaseQualities()[i], REDUCED_READ_QUAL);
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}
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@Test(expectedExceptions = IllegalArgumentException.class)
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public void testreducedReadWithReducedQualsWithNormalRead() {
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ReadUtils.reducedReadWithReducedQuals(read);
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}
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@Test
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public void testReducedReadPileupElement() {
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PileupElement readp = new PileupElement(read,0);
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PileupElement reducedreadp = new PileupElement(reducedRead,0);
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Assert.assertFalse(readp.isReducedRead());
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Assert.assertTrue(reducedreadp.isReducedRead());
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Assert.assertEquals(reducedreadp.getReducedCount(), 0);
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Assert.assertEquals(reducedreadp.getReducedQual(), REDUCED_READ_QUAL);
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}
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}
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