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finish the math for RMS 

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