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Added hardClipByReadCoordinates UnitTest for the ReadClipper

This commit is contained in:
Mauricio Carneiro 2011-12-16 15:10:22 -05:00
parent c26295919e
commit 5838ba529d
1 changed files with 18 additions and 12 deletions
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30
public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java
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@ -39,11 +39,8 @@ import org.testng.annotations.Test;
import java.util.List; import java.util.List;
/** /**
* Created by IntelliJ IDEA.
* User: roger * User: roger
* Date: 9/28/11 * Date: 9/28/11
* Time: 9:54 PM
* To change this template use File | Settings | File Templates.
*/ */
public class ReadClipperUnitTest extends BaseTest { public class ReadClipperUnitTest extends BaseTest {
@ -57,8 +54,6 @@ public class ReadClipperUnitTest extends BaseTest {
@Test(enabled = true) @Test(enabled = true)
public void testHardClipBothEndsByReferenceCoordinates() { public void testHardClipBothEndsByReferenceCoordinates() {
logger.warn("Executing testHardClipBothEndsByReferenceCoordinates");
for (Cigar cigar : cigarList) { for (Cigar cigar : cigarList) {
GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar); GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
int alnStart = read.getAlignmentStart(); int alnStart = read.getAlignmentStart();
@ -70,18 +65,28 @@ public class ReadClipperUnitTest extends BaseTest {
Assert.assertTrue(clippedRead.getAlignmentEnd() <= alnEnd + i, String.format("Clipped alignment end is greater than original read (minus %d): %s -> %s", i, read.getCigarString(), clippedRead.getCigarString())); Assert.assertTrue(clippedRead.getAlignmentEnd() <= alnEnd + i, String.format("Clipped alignment end is greater than original read (minus %d): %s -> %s", i, read.getCigarString(), clippedRead.getCigarString()));
} }
} }
logger.warn("PASSED");
} }
@Test(enabled = true) @Test(enabled = true)
public void testHardClipByReadCoordinates() { public void testHardClipByReadCoordinates() {
logger.warn("Executing testHardClipByReadCoordinates"); for (Cigar cigar : cigarList) {
GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
int readLength = read.getReadLength();
for (int i=0; i<readLength; i++) {
GATKSAMRecord clipLeft = (new ReadClipper(read)).hardClipByReadCoordinates(0, i);
Assert.assertTrue(clipLeft.getReadLength() <= readLength - i, String.format("Clipped read length is greater than original read length (minus %d): %s -> %s", i, read.getCigarString(), clipLeft.getCigarString()));
GATKSAMRecord clipRight = (new ReadClipper(read)).hardClipByReadCoordinates(i, readLength-1);
Assert.assertTrue(clipRight.getReadLength() <= i, String.format("Clipped read length is greater than original read length (minus %d): %s -> %s", i, read.getCigarString(), clipRight.getCigarString()));
}
}
logger.warn("PASSED");
} }
@Test(enabled = true) @Test(enabled = true)
public void testHardClipByReferenceCoordinates() { public void testHardClipByReferenceCoordinates() {
logger.warn("Executing testHardClipByReferenceCoordinates"); logger.warn("PASSED");
} }
@ -93,15 +98,12 @@ public class ReadClipperUnitTest extends BaseTest {
@Test(enabled = true) @Test(enabled = true)
public void testHardClipByReferenceCoordinatesRightTail() { public void testHardClipByReferenceCoordinatesRightTail() {
init(); logger.warn("PASSED");
logger.warn("Executing testHardClipByReferenceCoordinatesRightTail");
} }
@Test(enabled = true) @Test(enabled = true)
public void testHardClipLowQualEnds() { public void testHardClipLowQualEnds() {
logger.warn("Executing testHardClipLowQualEnds");
final byte LOW_QUAL = 2; final byte LOW_QUAL = 2;
final byte HIGH_QUAL = 30; final byte HIGH_QUAL = 30;
@ -180,6 +182,8 @@ public class ReadClipperUnitTest extends BaseTest {
ReadClipper lowQualClipper = new ReadClipper(read); ReadClipper lowQualClipper = new ReadClipper(read);
ClipReadsTestUtils.assertEqualReads(lowQualClipper.hardClipLowQualEnds((byte) 2), expected); ClipReadsTestUtils.assertEqualReads(lowQualClipper.hardClipLowQualEnds((byte) 2), expected);
logger.warn("PASSED");
} }
@Test(enabled = true) @Test(enabled = true)
@ -233,6 +237,8 @@ public class ReadClipperUnitTest extends BaseTest {
// logger.warn(String.format("Cigar %s -> %s -- PASSED!", read.getCigarString(), clippedRead.getCigarString())); // logger.warn(String.format("Cigar %s -> %s -- PASSED!", read.getCigarString(), clippedRead.getCigarString()));
} }
logger.warn("PASSED");
} }
private void assertNoLowQualBases(GATKSAMRecord read, byte low_qual) { private void assertNoLowQualBases(GATKSAMRecord read, byte low_qual) {