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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

This commit is contained in:
Ryan Poplin 2012-02-02 10:17:04 -05:00
parent 2109122cdd
commit 4ed06801a7
1 changed files with 2 additions and 3 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
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@ -377,7 +377,6 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
RecalDataManager.computeCovariates( gatkRead, requestedCovariates )); RecalDataManager.computeCovariates( gatkRead, requestedCovariates ));
} }
// Skip this position if base quality is zero // Skip this position if base quality is zero
if( gatkRead.getBaseQualities()[offset] > 0 ) { if( gatkRead.getBaseQualities()[offset] > 0 ) {