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Merge pull request #342 from broadinstitute/eb_fix_mq_in_rbp 

Fixing ReadBackedPileup to represent mapping qualities as ints, not (signed) bytes.
This commit is contained in:
Ryan Poplin 2013-07-24 09:42:13 -07:00
parent 71222bff45 6df43f730a
commit e5aab22680
4 changed files with 26 additions and 7 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
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@ -156,7 +156,7 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
baseQual += qual; baseQual += qual;
} }
double mapQual = 0.0; double mapQual = 0.0;
for (byte qual : pileup.getMappingQuals()) { for (int qual : pileup.getMappingQuals()) {
mapQual += qual; mapQual += qual;
} }

2
public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java
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@ -270,7 +270,7 @@ public interface ReadBackedPileup extends Iterable<PileupElement>, HasGenomeLoca
* Get an array of the mapping qualities * Get an array of the mapping qualities
* @return * @return
*/ */
public byte[] getMappingQuals(); public int[] getMappingQuals();
/** /**
* Returns a new ReadBackedPileup that is sorted by start coordinate of the reads. * Returns a new ReadBackedPileup that is sorted by start coordinate of the reads.

8
public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java
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@ -969,11 +969,11 @@ public class ReadBackedPileupImpl implements ReadBackedPileup {
* @return * @return
*/ */
@Override @Override
public byte[] getMappingQuals() { public int[] getMappingQuals() {
byte[] v = new byte[getNumberOfElements()]; final int[] v = new int[getNumberOfElements()];
int pos = 0; int pos = 0;
for (PileupElement pile : pileupElementTracker) { for ( final PileupElement pile : pileupElementTracker ) {
v[pos++] = (byte) pile.getRead().getMappingQuality(); v[pos++] = pile.getRead().getMappingQuality();
} }
return v; return v;
} }

21
public/java/test/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java
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@ -296,7 +296,6 @@ public class ReadBackedPileupUnitTest {
testRBPCounts(pileup, new RBPCountTest(params.nReads + 2, params.nMapq0 + 1, params.nDeletions + 1)); testRBPCounts(pileup, new RBPCountTest(params.nReads + 2, params.nMapq0 + 1, params.nDeletions + 1));
} }
private void testRBPCounts(final ReadBackedPileup rbp, RBPCountTest expected) { private void testRBPCounts(final ReadBackedPileup rbp, RBPCountTest expected) {
for ( int cycles = 0; cycles < 3; cycles++ ) { for ( int cycles = 0; cycles < 3; cycles++ ) {
// multiple cycles to make sure caching is working // multiple cycles to make sure caching is working
@ -306,4 +305,24 @@ public class ReadBackedPileupUnitTest {
Assert.assertEquals(rbp.getNumberOfMappingQualityZeroReads(), expected.nMapq0); Assert.assertEquals(rbp.getNumberOfMappingQualityZeroReads(), expected.nMapq0);
} }
} }
@Test
public void testRBPMappingQuals() {
// create a read with high MQ
final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read", 0, 1, 10);
read.setReadBases(Utils.dupBytes((byte) 'A', 10));
read.setBaseQualities(Utils.dupBytes((byte) 30, 10));
read.setCigarString("10M");
read.setMappingQuality(200); // set a MQ higher than max signed byte
// now create the RBP
final List<PileupElement> elts = new LinkedList<>();
elts.add(new PileupElement(read, 0, read.getCigar().getCigarElement(0), 0, 0));
final Map<String, ReadBackedPileupImpl> pileupsBySample = new HashMap<>();
pileupsBySample.put("foo", new ReadBackedPileupImpl(loc, elts));
final ReadBackedPileup pileup = new ReadBackedPileupImpl(loc, pileupsBySample);
Assert.assertEquals(pileup.getMappingQuals()[0], 200);
}
} }