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Unit tests for GATKSAMRecord class 

* new unit tests for the alignment shift properties of reduce reads
   * moved unit tests from ReadUtils that were actually testing GATKSAMRecord, not any of the ReadUtils to it.
   * cleaned up ReadUtilsUnitTest
This commit is contained in:
Mauricio Carneiro 2012-01-26 16:59:08 -05:00
parent 0d4027104f
commit 246e085ec9
2 changed files with 83 additions and 46 deletions
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83
public/java/test/org/broadinstitute/sting/utils/sam/GATKSAMRecordUnitTest.java 100755
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package org.broadinstitute.sting.utils.sam;
import net.sf.samtools.SAMFileHeader;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class GATKSAMRecordUnitTest extends BaseTest {
GATKSAMRecord read, reducedRead;
final static String BASES = "ACTG";
final static String QUALS = "!+5?";
final private static byte[] REDUCED_READ_COUNTS = new byte[]{10, 20, 30, 40, 1};
final private static byte[] REDUCED_READ_COUNTS_TAG = new byte[]{10, 10, 20, 30, -9}; // just the offsets
@BeforeClass
public void init() {
SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
read = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 1, BASES.length());
read.setReadUnmappedFlag(true);
read.setReadBases(new String(BASES).getBytes());
read.setBaseQualityString(new String(QUALS));
reducedRead = ArtificialSAMUtils.createArtificialRead(header, "reducedRead", 0, 1, BASES.length());
reducedRead.setReadBases(BASES.getBytes());
reducedRead.setBaseQualityString(QUALS);
reducedRead.setAttribute(GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, REDUCED_READ_COUNTS_TAG);
}
@Test
public void testReducedReads() {
Assert.assertFalse(read.isReducedRead(), "isReducedRead is false for normal read");
Assert.assertEquals(read.getReducedReadCounts(), null, "No reduced read tag in normal read");
Assert.assertTrue(reducedRead.isReducedRead(), "isReducedRead is true for reduced read");
for (int i = 0; i < reducedRead.getReadLength(); i++) {
Assert.assertEquals(reducedRead.getReducedCount(i), REDUCED_READ_COUNTS[i], "Reduced read count not set to the expected value at " + i);
}
}
@Test
public void testReducedReadPileupElement() {
PileupElement readp = new PileupElement(read, 0, false);
PileupElement reducedreadp = new PileupElement(reducedRead, 0, false);
Assert.assertFalse(readp.getRead().isReducedRead());
Assert.assertTrue(reducedreadp.getRead().isReducedRead());
Assert.assertEquals(reducedreadp.getRepresentativeCount(), REDUCED_READ_COUNTS[0]);
Assert.assertEquals(reducedreadp.getQual(), readp.getQual());
}
@Test
public void testGetOriginalAlignments() {
final byte [] bases = {'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A'};
final byte [] quals = {20 , 20 , 20 , 20 , 20 , 20 , 20 , 20 };
GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bases, quals, "6M");
// A regular read with all matches
Assert.assertEquals(read.getAlignmentStart(), read.getOriginalAlignmentStart());
Assert.assertEquals(read.getAlignmentEnd(), read.getOriginalAlignmentEnd());
// Alignment start shifted
int alignmentShift = 2;
read.setAttribute(GATKSAMRecord.REDUCED_READ_ORIGINAL_ALIGNMENT_START_SHIFT, alignmentShift);
Assert.assertEquals(read.getAlignmentStart() + alignmentShift, read.getOriginalAlignmentStart());
Assert.assertEquals(read.getAlignmentEnd(), read.getOriginalAlignmentEnd());
// Both alignments shifted
read.setAttribute(GATKSAMRecord.REDUCED_READ_ORIGINAL_ALIGNMENT_END_SHIFT, alignmentShift);
Assert.assertEquals(read.getAlignmentStart() + alignmentShift, read.getOriginalAlignmentStart());
Assert.assertEquals(read.getAlignmentEnd() - alignmentShift, read.getOriginalAlignmentEnd());
// Alignment end shifted
read.setAttribute(GATKSAMRecord.REDUCED_READ_ORIGINAL_ALIGNMENT_START_SHIFT, null);
Assert.assertEquals(read.getAlignmentStart(), read.getOriginalAlignmentStart());
Assert.assertEquals(read.getAlignmentEnd() - alignmentShift, read.getOriginalAlignmentEnd());
}
}

46
public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java
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@ -1,57 +1,11 @@
package org.broadinstitute.sting.utils.sam;
import net.sf.samtools.SAMFileHeader;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.testng.Assert;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
public class ReadUtilsUnitTest extends BaseTest {
GATKSAMRecord read, reducedRead;
final static String BASES = "ACTG";
final static String QUALS = "!+5?";
final private static byte[] REDUCED_READ_COUNTS = new byte[]{10, 20, 30, 40, 1};
final private static byte[] REDUCED_READ_COUNTS_TAG = new byte[]{10, 10, 20, 30, -9}; // just the offsets
@BeforeTest
public void init() {
SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
read = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 1, BASES.length());
read.setReadUnmappedFlag(true);
read.setReadBases(new String(BASES).getBytes());
read.setBaseQualityString(new String(QUALS));
reducedRead = ArtificialSAMUtils.createArtificialRead(header, "reducedRead", 0, 1, BASES.length());
reducedRead.setReadBases(BASES.getBytes());
reducedRead.setBaseQualityString(QUALS);
reducedRead.setAttribute(GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, REDUCED_READ_COUNTS_TAG);
}
@Test
public void testReducedReads() {
Assert.assertFalse(read.isReducedRead(), "isReducedRead is false for normal read");
Assert.assertEquals(read.getReducedReadCounts(), null, "No reduced read tag in normal read");
Assert.assertTrue(reducedRead.isReducedRead(), "isReducedRead is true for reduced read");
for (int i = 0; i < reducedRead.getReadLength(); i++) {
Assert.assertEquals(reducedRead.getReducedCount(i), REDUCED_READ_COUNTS[i], "Reduced read count not set to the expected value at " + i);
}
}
@Test
public void testReducedReadPileupElement() {
PileupElement readp = new PileupElement(read, 0, false, false, false);
PileupElement reducedreadp = new PileupElement(reducedRead, 0, false, false, false);
Assert.assertFalse(readp.getRead().isReducedRead());
Assert.assertTrue(reducedreadp.getRead().isReducedRead());
Assert.assertEquals(reducedreadp.getRepresentativeCount(), REDUCED_READ_COUNTS[0]);
Assert.assertEquals(reducedreadp.getQual(), readp.getQual());
}
@Test
public void testGetAdaptorBoundary() {
final byte[] bases = {'A', 'C', 'G', 'T', 'A', 'C', 'G', 'T'};