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

Fixing on-the-fly recalibration (caught by Ryan) 

low quality bases in the tails were being turned to N's in the final read.
This commit is contained in:
Mauricio Carneiro 2012-05-02 14:05:08 -04:00
parent 623b36fbc4
commit 940029fa5d
1 changed files with 5 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariate.java
View File

@ -64,20 +64,20 @@ public class ContextCovariate implements StandardCovariate {
}
@Override
public CovariateValues getValues(GATKSAMRecord read) {
public CovariateValues getValues(final GATKSAMRecord read) {
int l = read.getReadLength();
BitSet[] mismatches = new BitSet[l];
BitSet[] insertions = new BitSet[l];
BitSet[] deletions = new BitSet[l];
read = ReadClipper.clipLowQualEnds(read, LOW_QUAL_TAIL, ClippingRepresentation.WRITE_NS); // Write N's over the low quality tail of the reads to avoid adding them into the context
GATKSAMRecord clippedRead = ReadClipper.clipLowQualEnds(read, LOW_QUAL_TAIL, ClippingRepresentation.WRITE_NS); // Write N's over the low quality tail of the reads to avoid adding them into the context
final boolean negativeStrand = read.getReadNegativeStrandFlag();
byte[] bases = read.getReadBases();
final boolean negativeStrand = clippedRead.getReadNegativeStrandFlag();
byte[] bases = clippedRead.getReadBases();
if (negativeStrand)
bases = BaseUtils.simpleReverseComplement(bases);
for (int i = 0; i < read.getReadLength(); i++) {
for (int i = 0; i < clippedRead.getReadLength(); i++) {
mismatches[i] = contextWith(bases, i, mismatchesContextSize);
insertions[i] = contextWith(bases, i, insertionsContextSize);
deletions[i] = contextWith(bases, i, deletionsContextSize);