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Need to use ints for quals in HaplotypeScore instead of bytes because of overflow (they are summed when haplotypes are combined)

This commit is contained in:
Eric Banks 2013-01-16 22:33:16 -05:00
parent 79bc818022
commit dbb69a1e10
1 changed files with 20 additions and 13 deletions
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33
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
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@ -216,14 +216,14 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
final Haplotype haplotype1 = consensusHaplotypeQueue.poll(); final Haplotype haplotype1 = consensusHaplotypeQueue.poll();
List<Haplotype> hlist = new ArrayList<Haplotype>(); List<Haplotype> hlist = new ArrayList<Haplotype>();
hlist.add(new Haplotype(haplotype1.getBases(), (byte)60)); hlist.add(new Haplotype(haplotype1.getBases(), 60));
for (int k = 1; k < haplotypesToCompute; k++) { for (int k = 1; k < haplotypesToCompute; k++) {
Haplotype haplotype2 = consensusHaplotypeQueue.poll(); Haplotype haplotype2 = consensusHaplotypeQueue.poll();
if (haplotype2 == null) { if (haplotype2 == null) {
haplotype2 = haplotype1; haplotype2 = haplotype1;
} // Sometimes only the reference haplotype can be found } // Sometimes only the reference haplotype can be found
hlist.add(new Haplotype(haplotype2.getBases(), (byte)20)); hlist.add(new Haplotype(haplotype2.getBases(), 20));
} }
return hlist; return hlist;
} else } else
@ -285,10 +285,10 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
final int length = a.length; final int length = a.length;
final byte[] consensusChars = new byte[length]; final byte[] consensusChars = new byte[length];
final byte[] consensusQuals = new byte[length]; final int[] consensusQuals = new int[length];
final byte[] qualsA = haplotypeA.getQuals(); final int[] qualsA = haplotypeA.getQuals();
final byte[] qualsB = haplotypeB.getQuals(); final int[] qualsB = haplotypeB.getQuals();
for (int i = 0; i < length; i++) { for (int i = 0; i < length; i++) {
chA = a[i]; chA = a[i];
@ -308,7 +308,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
consensusQuals[i] = qualsA[i]; consensusQuals[i] = qualsA[i];
} else { } else {
consensusChars[i] = chA; consensusChars[i] = chA;
consensusQuals[i] = (byte)((int)qualsA[i] + (int)qualsB[i]); consensusQuals[i] = qualsA[i] + qualsB[i];
} }
} }
@ -442,31 +442,38 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
private static class Haplotype { private static class Haplotype {
private final byte[] bases; private final byte[] bases;
private final byte[] quals; private final int[] quals;
private int qualitySum = -1; private int qualitySum = -1;
public Haplotype( final byte[] bases, final byte[] quals ) { public Haplotype( final byte[] bases, final int[] quals ) {
this.bases = bases; this.bases = bases;
this.quals = quals; this.quals = quals;
} }
public Haplotype( final byte[] bases, final byte qual ) { public Haplotype( final byte[] bases, final int qual ) {
this.bases = bases; this.bases = bases;
quals = new byte[bases.length]; quals = new int[bases.length];
Arrays.fill(quals, qual); Arrays.fill(quals, qual);
} }
public Haplotype( final byte[] bases, final byte[] quals ) {
this.bases = bases;
this.quals = new int[quals.length];
for ( int i = 0 ; i < quals.length; i++ )
this.quals[i] = (int)quals[i];
}
public double getQualitySum() { public double getQualitySum() {
if ( qualitySum == -1 ) { if ( qualitySum == -1 ) {
qualitySum = 0; qualitySum = 0;
for ( final byte qual : quals ) { for ( final int qual : quals ) {
qualitySum += (int)qual; qualitySum += qual;
} }
} }
return qualitySum; return qualitySum;
} }
public byte[] getQuals() { public int[] getQuals() {
return quals.clone(); return quals.clone();
} }