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Adding option to HaplotypeCaller to genotype the events on the chosen haplotypes as independent events. The filtered reads are now kept around so they can be passed to the variant annotations. Unfortunately the filtered reads aren't assigned a likelihood yet so they are all thrown in the Allele.NO_CALL bin.

This commit is contained in:
Ryan Poplin 2012-04-19 11:32:10 -04:00
parent 4999ae87ad
commit 11001ab9a2
1 changed files with 2 additions and 3 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
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@ -80,9 +80,8 @@ public class RMSMappingQuality extends InfoFieldAnnotation implements StandardAn
}
}
double rms = MathUtils.rms(qualities);
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%.2f", rms));
final Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%.2f", MathUtils.rms(qualities)));
return map;
}