From 11001ab9a2fe7815ad514634ad298184bd735340 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Thu, 19 Apr 2012 11:32:10 -0400 Subject: [PATCH] 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. --- .../sting/gatk/walkers/annotator/RMSMappingQuality.java | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java index 97c15e747..ea7d6ae33 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java @@ -80,9 +80,8 @@ public class RMSMappingQuality extends InfoFieldAnnotation implements StandardAn } } - double rms = MathUtils.rms(qualities); - Map map = new HashMap(); - map.put(getKeyNames().get(0), String.format("%.2f", rms)); + final Map map = new HashMap(); + map.put(getKeyNames().get(0), String.format("%.2f", MathUtils.rms(qualities))); return map; }