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Added hardClipByReferenceCoordinates (left and right tails) UnitTest for the ReadClipper

This commit is contained in:
Mauricio Carneiro 2011-12-16 17:05:46 -05:00
parent 5bba44d693
commit 075be52adc
1 changed files with 24 additions and 1 deletions
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25
public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java
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@ -110,13 +110,36 @@ public class ReadClipperUnitTest extends BaseTest {
@Test(enabled = true) @Test(enabled = true)
public void testHardClipByReferenceCoordinatesLeftTail() { public void testHardClipByReferenceCoordinatesLeftTail() {
for (Cigar cigar : cigarList) {
GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
int alnStart = read.getAlignmentStart();
int alnEnd = read.getAlignmentEnd();
if (ReadUtils.getRefCoordSoftUnclippedStart(read) == alnStart) { // we can't test left clipping if the read has hanging soft clips on the left side
for (int i=alnStart; i<=alnEnd; i++) {
GATKSAMRecord clipLeft = (new ReadClipper(read)).hardClipByReferenceCoordinates(alnStart, i);
if (!clipLeft.isEmpty())
Assert.assertTrue(clipLeft.getAlignmentStart() >= i + 1, String.format("Clipped alignment start (%d) is less the expected (%d): %s -> %s", clipLeft.getAlignmentStart(), i + 1, read.getCigarString(), clipLeft.getCigarString()));
}
}
}
logger.warn("PASSED"); logger.warn("PASSED");
} }
@Test(enabled = true) @Test(enabled = true)
public void testHardClipByReferenceCoordinatesRightTail() { public void testHardClipByReferenceCoordinatesRightTail() {
for (Cigar cigar : cigarList) {
GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
int alnStart = read.getAlignmentStart();
int alnEnd = read.getAlignmentEnd();
if (ReadUtils.getRefCoordSoftUnclippedEnd(read) == alnEnd) { // we can't test right clipping if the read has hanging soft clips on the right side
for (int i=alnStart; i<=alnEnd; i++) {
GATKSAMRecord clipRight = (new ReadClipper(read)).hardClipByReferenceCoordinates(i, alnEnd);
if (!clipRight.isEmpty() && clipRight.getAlignmentStart() <= clipRight.getAlignmentEnd()) // alnStart > alnEnd if the entire read is a soft clip now. We can't test those.
Assert.assertTrue(clipRight.getAlignmentEnd() <= i - 1, String.format("Clipped alignment end (%d) is greater than expected (%d): %s -> %s", clipRight.getAlignmentEnd(), i - 1, read.getCigarString(), clipRight.getCigarString()));
}
}
}
logger.warn("PASSED"); logger.warn("PASSED");
} }
@Test(enabled = true) @Test(enabled = true)