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added MQ of low MQ/BQ to consensus RMS 

Bases that were excluded for MQ and BQ filters are now contributing to the MQ RMS (but not to consensus base counts and variant/not variant region triggers).
This commit is contained in:
Mauricio Carneiro 2011-11-01 17:46:12 -04:00
parent 18f4c63d44
commit 36600fd8e9
1 changed files with 2 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/utils/MathUtils.java
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@ -408,12 +408,12 @@ public class MathUtils {
return Math.sqrt(rms); return Math.sqrt(rms);
} }
public static double rms(Collection<Double> l) { public static double rms(Collection<Integer> l) {
if (l.size() == 0) if (l.size() == 0)
return 0.0; return 0.0;
double rms = 0.0; double rms = 0.0;
for (Double i : l) for (int i : l)
rms += i*i; rms += i*i;
rms /= l.size(); rms /= l.size();
return Math.sqrt(rms); return Math.sqrt(rms);