finish the math for RMS

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1362 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 16:18:09 +00:00 · 2009-08-03 16:18:09 +00:00 · ba07f057ac
parent 8bc925a216
commit ba07f057ac
1 changed files with 2 additions and 0 deletions
--- a/java/src/org/broadinstitute/sting/utils/genotype/calls/SSGGenotypeCall.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/calls/SSGGenotypeCall.java
@ -107,6 +107,8 @@ public class SSGGenotypeCall implements GenotypeCall, GenotypeOutput {
        for (SAMRecord r : pileup.getReads()) {
            rms += r.getMappingQuality() * r.getMappingQuality();
        }
+        rms /= pileup.getReads().size();
+        rms = Math.sqrt(rms);
        return rms;
    }