Updating HaplotypeCaller's HMM calc to use GOP as a function of the read instead of a function of the haplotype in preparation for IQSR

2012-02-02 10:17:04 -05:00 · 2012-02-02 10:17:04 -05:00 · 4ed06801a7
parent 2109122cdd
commit 4ed06801a7
1 changed files with 2 additions and 3 deletions
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
@ -377,7 +377,6 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
                            RecalDataManager.computeCovariates( gatkRead, requestedCovariates ));
                }

-
                // Skip this position if base quality is zero
                if( gatkRead.getBaseQualities()[offset] > 0 ) {