zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Fixed ReadClipperUnitTest 

The behavior of the clipping on weird cigar strings such as 1I1S1H and 9S56H has changed, and the test has to change accordingly.
This commit is contained in:
Mauricio Carneiro 2012-07-03 16:37:21 -04:00
parent f09141bd2f
commit 17efbbf8b1
2 changed files with 31 additions and 33 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperTestUtils.java
View File

@ -102,17 +102,14 @@ public class ReadClipperTestUtils {
cigarElementStack.push(cigarElement); cigarElementStack.push(cigarElement);
} }
readHasStarted = false; // search the inverted list of elements (stack) for the stopping operator
while (!cigarElementStack.empty()) { while (!cigarElementStack.empty()) {
CigarElement cigarElement = cigarElementStack.pop(); CigarElement cigarElement = cigarElementStack.pop();
if (cigarElement.getOperator() != CigarOperator.SOFT_CLIP && cigarElement.getOperator() != CigarOperator.HARD_CLIP) { if (cigarElement.getOperator() != CigarOperator.SOFT_CLIP && cigarElement.getOperator() != CigarOperator.HARD_CLIP) {
readHasStarted = true;
endingOp = cigarElement.getOperator(); endingOp = cigarElement.getOperator();
break; break;
} }
} }
// if (startingOp != CigarOperator.DELETION && endingOp != CigarOperator.DELETION && startingOp != CigarOperator.INSERTION && endingOp != CigarOperator.INSERTION)
if (startingOp != CigarOperator.DELETION && endingOp != CigarOperator.DELETION) if (startingOp != CigarOperator.DELETION && endingOp != CigarOperator.DELETION)
return true; // we don't accept reads starting or ending in deletions (add any other constraint here) return true; // we don't accept reads starting or ending in deletions (add any other constraint here)
} }

49
public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java
View File

@ -151,51 +151,40 @@ public class ReadClipperUnitTest extends BaseTest {
final byte LOW_QUAL = 2; final byte LOW_QUAL = 2;
final byte HIGH_QUAL = 30; final byte HIGH_QUAL = 30;
// create a read for every cigar permutation /** create a read for every cigar permutation */
for (Cigar cigar : cigarList) { for (Cigar cigar : cigarList) {
GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar); GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
int readLength = read.getReadLength(); int readLength = read.getReadLength();
byte[] quals = new byte[readLength]; byte[] quals = new byte[readLength];
for (int nLowQualBases = 0; nLowQualBases < readLength; nLowQualBases++) { for (int nLowQualBases = 0; nLowQualBases < readLength; nLowQualBases++) {
Utils.fillArrayWithByte(quals, HIGH_QUAL); // create a read with nLowQualBases in the left tail
/** create a read with nLowQualBases in the left tail */
Utils.fillArrayWithByte(quals, HIGH_QUAL);
for (int addLeft = 0; addLeft < nLowQualBases; addLeft++) for (int addLeft = 0; addLeft < nLowQualBases; addLeft++)
quals[addLeft] = LOW_QUAL; quals[addLeft] = LOW_QUAL;
read.setBaseQualities(quals); read.setBaseQualities(quals);
GATKSAMRecord clipLeft = ReadClipper.hardClipLowQualEnds(read, LOW_QUAL); GATKSAMRecord clipLeft = ReadClipper.hardClipLowQualEnds(read, LOW_QUAL);
checkClippedReadsForLowQualEnds(read, clipLeft, LOW_QUAL, nLowQualBases);
assertUnclippedLimits(read, clipLeft); // Make sure limits haven't changed /** create a read with nLowQualBases in the right tail */
assertNoLowQualBases(clipLeft, LOW_QUAL); // Make sure the low qualities are gone Utils.fillArrayWithByte(quals, HIGH_QUAL);
Assert.assertEquals(clipLeft.getReadLength(), readLength - nLowQualBases, // Make sure only low quality bases were clipped
String.format("Clipped read size (%d) is different than the number high qual bases (%d) -- Cigars: %s -> %s", clipLeft.getReadLength(), readLength - nLowQualBases, read.getCigarString(), clipLeft.getCigarString()));
Utils.fillArrayWithByte(quals, HIGH_QUAL); // create a read with nLowQualBases in the right tail
for (int addRight = 0; addRight < nLowQualBases; addRight++) for (int addRight = 0; addRight < nLowQualBases; addRight++)
quals[readLength - addRight - 1] = LOW_QUAL; quals[readLength - addRight - 1] = LOW_QUAL;
read.setBaseQualities(quals); read.setBaseQualities(quals);
GATKSAMRecord clipRight = ReadClipper.hardClipLowQualEnds(read, LOW_QUAL); GATKSAMRecord clipRight = ReadClipper.hardClipLowQualEnds(read, LOW_QUAL);
checkClippedReadsForLowQualEnds(read, clipRight, LOW_QUAL, nLowQualBases);
// System.out.println(String.format("Debug [%d]: %s -> %s / %s", nLowQualBases, cigar.toString(), clipLeft.getCigarString(), clipRight.getCigarString())); /** create a read with nLowQualBases on both tails */
assertUnclippedLimits(read, clipRight); // Make sure limits haven't changed
assertNoLowQualBases(clipRight, LOW_QUAL); // Make sure the low qualities are gone
Assert.assertEquals(clipLeft.getReadLength(), readLength - nLowQualBases, // Make sure only low quality bases were clipped
String.format("Clipped read size (%d) is different than the number high qual bases (%d) -- Cigars: %s -> %s", clipRight.getReadLength(), readLength - nLowQualBases, read.getCigarString(), clipRight.getCigarString()));
if (nLowQualBases <= readLength / 2) { if (nLowQualBases <= readLength / 2) {
Utils.fillArrayWithByte(quals, HIGH_QUAL); // create a read with nLowQualBases on both tails Utils.fillArrayWithByte(quals, HIGH_QUAL);
for (int addBoth = 0; addBoth < nLowQualBases; addBoth++) { for (int addBoth = 0; addBoth < nLowQualBases; addBoth++) {
quals[addBoth] = LOW_QUAL; quals[addBoth] = LOW_QUAL;
quals[readLength - addBoth - 1] = LOW_QUAL; quals[readLength - addBoth - 1] = LOW_QUAL;
} }
read.setBaseQualities(quals); read.setBaseQualities(quals);
GATKSAMRecord clipBoth = ReadClipper.hardClipLowQualEnds(read, LOW_QUAL); GATKSAMRecord clipBoth = ReadClipper.hardClipLowQualEnds(read, LOW_QUAL);
checkClippedReadsForLowQualEnds(read, clipBoth, LOW_QUAL, 2*nLowQualBases);
assertUnclippedLimits(read, clipBoth); // Make sure limits haven't changed
assertNoLowQualBases(clipBoth, LOW_QUAL); // Make sure the low qualities are gone
Assert.assertEquals(clipLeft.getReadLength(), readLength - nLowQualBases, // Make sure only low quality bases were clipped
String.format("Clipped read size (%d) is different than the number high qual bases (%d) -- Cigars: %s -> %s", clipRight.getReadLength(), readLength - (2 * nLowQualBases), read.getCigarString(), clipBoth.getCigarString()));
} }
} }
} }
@ -286,11 +275,17 @@ 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
}
/** /**
* Asserts that clipping doesn't change the getUnclippedStart / getUnclippedEnd * Asserts that clipping doesn't change the getUnclippedStart / getUnclippedEnd
* *
* @param original * @param original original read
* @param clipped * @param clipped clipped read
*/ */
private void assertUnclippedLimits(GATKSAMRecord original, GATKSAMRecord clipped) { private void assertUnclippedLimits(GATKSAMRecord original, GATKSAMRecord clipped) {
if (ReadClipperTestUtils.readHasNonClippedBases(clipped)) { if (ReadClipperTestUtils.readHasNonClippedBases(clipped)) {
@ -299,6 +294,12 @@ 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) { private boolean startsWithInsertion(Cigar cigar) {
return leadingCigarElementLength(cigar, CigarOperator.INSERTION) > 0; return leadingCigarElementLength(cigar, CigarOperator.INSERTION) > 0;
} }