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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Guillermo del Angel 2012-05-10 16:00:58 -04:00
parent da6f16986e c9dd0f3173
commit 9acef4b206
3 changed files with 8 additions and 6 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
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@ -451,12 +451,12 @@ public class LocusIteratorByState extends LocusIterator {
nextAlignmentContext = new AlignmentContext(loc, new ReadBackedExtendedEventPileupImpl(loc, fullExtendedEventPileup), hasBeenSampled); nextAlignmentContext = new AlignmentContext(loc, new ReadBackedExtendedEventPileupImpl(loc, fullExtendedEventPileup), hasBeenSampled);
} }
else { // this is a regular event pileup (not extended) else { // this is a regular event pileup (not extended)
GenomeLoc location = getLocation(); final GenomeLoc location = getLocation();
Map<String, ReadBackedPileupImpl> fullPileup = new HashMap<String, ReadBackedPileupImpl>(); final Map<String, ReadBackedPileupImpl> fullPileup = new HashMap<String, ReadBackedPileupImpl>();
boolean hasBeenSampled = false; boolean hasBeenSampled = false;
for (final String sample : samples) { for (final String sample : samples) {
Iterator<SAMRecordState> iterator = readStates.iterator(sample); final Iterator<SAMRecordState> iterator = readStates.iterator(sample);
List<PileupElement> pile = new ArrayList<PileupElement>(readStates.size(sample)); final List<PileupElement> pile = new ArrayList<PileupElement>(readStates.size(sample));
hasBeenSampled |= location.getStart() <= readStates.getDownsamplingExtent(sample); hasBeenSampled |= location.getStart() <= readStates.getDownsamplingExtent(sample);
size = 0; // number of elements in this sample's pileup size = 0; // number of elements in this sample's pileup

3
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
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@ -86,8 +86,7 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati
continue; continue;
for ( final Map.Entry<Allele, List<GATKSAMRecord>> alleleBin : alleleBins.entrySet() ) { for ( final Map.Entry<Allele, List<GATKSAMRecord>> alleleBin : alleleBins.entrySet() ) {
if ( !alleleBin.getKey().equals(Allele.NO_CALL) ) depth += alleleBin.getValue().size();
depth += alleleBin.getValue().size();
} }
} }

3
public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java
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@ -166,6 +166,9 @@ public class FragmentUtils {
if( firstReadQuals[iii] > MIN_QUAL_BAD_OVERLAP && secondReadQuals[iii-firstReadStop] > MIN_QUAL_BAD_OVERLAP && firstReadBases[iii] != secondReadBases[iii-firstReadStop] ) { if( firstReadQuals[iii] > MIN_QUAL_BAD_OVERLAP && secondReadQuals[iii-firstReadStop] > MIN_QUAL_BAD_OVERLAP && firstReadBases[iii] != secondReadBases[iii-firstReadStop] ) {
return overlappingPair;// high qual bases don't match exactly, probably indel in only one of the fragments, so don't merge them return overlappingPair;// high qual bases don't match exactly, probably indel in only one of the fragments, so don't merge them
} }
if( firstReadQuals[iii] < MIN_QUAL_BAD_OVERLAP && secondReadQuals[iii-firstReadStop] < MIN_QUAL_BAD_OVERLAP ) {
return overlappingPair; // both reads have low qual bases in the overlap region so don't merge them because don't know what is going on
}
bases[iii] = ( firstReadQuals[iii] > secondReadQuals[iii-firstReadStop] ? firstReadBases[iii] : secondReadBases[iii-firstReadStop] ); bases[iii] = ( firstReadQuals[iii] > secondReadQuals[iii-firstReadStop] ? firstReadBases[iii] : secondReadBases[iii-firstReadStop] );
quals[iii] = ( firstReadQuals[iii] > secondReadQuals[iii-firstReadStop] ? firstReadQuals[iii] : secondReadQuals[iii-firstReadStop] ); quals[iii] = ( firstReadQuals[iii] > secondReadQuals[iii-firstReadStop] ? firstReadQuals[iii] : secondReadQuals[iii-firstReadStop] );
} }