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Fixing unit test 

with the new clipping behavior for weird cigars, we no longer can assert the final number of bases in the unit test, so I'm taking this bit off the unit test.
This commit is contained in:
Mauricio Carneiro 2012-07-06 12:07:57 -04:00
parent f603d4c48c
commit e93b025b39
1 changed files with 1 additions and 9 deletions
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10
public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java
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@ -119,7 +119,6 @@ public class ReadClipperUnitTest extends BaseTest {
GATKSAMRecord clipLeft = ReadClipper.hardClipByReferenceCoordinatesLeftTail(read, i);
if (!clipLeft.isEmpty()) {
// System.out.println(String.format("Left Tail [%d]: %s (%d,%d,%d : %d,%d,%d) -> %s (%d,%d,%d : %d,%d,%d)", i, cigar.toString(), read.getUnclippedStart(), read.getSoftStart(), read.getAlignmentStart(), read.getAlignmentEnd(), read.getSoftEnd(), read.getUnclippedEnd(), clipLeft.getCigarString(), clipLeft.getUnclippedStart(), clipLeft.getSoftStart(), clipLeft.getAlignmentStart(), clipLeft.getAlignmentEnd(), clipLeft.getSoftEnd(), clipLeft.getUnclippedEnd()));
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()));
assertUnclippedLimits(read, clipLeft);
}
@ -137,7 +136,7 @@ public class ReadClipperUnitTest extends BaseTest {
if (read.getSoftEnd() == 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 = ReadClipper.hardClipByReferenceCoordinatesRightTail(read, i);
if (!clipRight.isEmpty() && clipRight.getAlignmentStart() <= clipRight.getAlignmentEnd()) { // alnStart > alnEnd if the entire read is a soft clip now. We can't test those.
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()));
assertUnclippedLimits(read, clipRight);
}
@ -278,7 +277,6 @@ public class ReadClipperUnitTest extends BaseTest {
private void checkClippedReadsForLowQualEnds(GATKSAMRecord read, GATKSAMRecord clippedRead, byte lowQual, int nLowQualBases) {
assertUnclippedLimits(read, clippedRead); // Make sure limits haven't changed
assertNoLowQualBases(clippedRead, lowQual); // Make sure the low qualities are gone
assertNumberOfBases(read, clippedRead, nLowQualBases); // Make sure only low quality bases were clipped
}
/**
@ -294,12 +292,6 @@ public class ReadClipperUnitTest extends BaseTest {
}
}
private void assertNumberOfBases(GATKSAMRecord read, GATKSAMRecord clipLeft, int nLowQualBases) {
if (read.getCigarString().contains("M"))
Assert.assertEquals(clipLeft.getReadLength(), read.getReadLength() - nLowQualBases, String.format("Clipped read size (%d) is different than the number high qual bases (%d) -- Cigars: %s -> %s", clipLeft.getReadLength(), read.getReadLength() - nLowQualBases, read.getCigarString(), clipLeft.getCigarString()));
}
private boolean startsWithInsertion(Cigar cigar) {
return leadingCigarElementLength(cigar, CigarOperator.INSERTION) > 0;
}