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Four-base probs are now decoded with the relevant method in QualityUtils 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@351 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-04-09 20:52:17 +00:00
parent 9bc763a835
commit c5220c0822
1 changed files with 3 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
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@ -167,9 +167,9 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
//System.out.printf("SQ field (hex): %s\n", bytesToHexString(hex_quals));
//System.out.printf("SAM record: %s\n", read.format());
int hex_qual = hex_quals[offset];
int called2num = hex_qual & 0x3;
double qual2 = (double)(hex_qual >> 2) / 100.0;
byte hex_qual = hex_quals[offset];
int called2num = QualityUtils.compressedQualityToBaseIndex(hex_qual);
double qual2 = QualityUtils.compressedQualityToProb(hex_qual);
//System.out.printf("2ND %x %d %f\n", hex_qual, called2num, qual2);
quals[i][called2num] = qual2;