From ae259f81cc46dbb4966b52c1affe73951ea8494d Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Tue, 17 Jan 2012 14:39:27 -0500 Subject: [PATCH] Bug fixing for merging of read fragments when one fragment contained an indel --- .../variantrecalibration/VariantRecalibratorEngine.java | 3 +-- .../java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java index 6d2ac643b..378765051 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java @@ -27,7 +27,6 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.exceptions.UserException; import java.util.List; @@ -126,7 +125,7 @@ public class VariantRecalibratorEngine { iteration++; model.maximizationStep( data ); currentChangeInMixtureCoefficients = model.normalizePMixtureLog10(); - model.expectationStep(data); + model.expectationStep( data ); if( iteration % 5 == 0 ) { // cut down on the number of output lines so that users can read the warning messages logger.info("Finished iteration " + iteration + ". \tCurrent change in mixture coefficients = " + String.format("%.5f", currentChangeInMixtureCoefficients)); } diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java index cc0b1ae67..d1e3ce26b 100755 --- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java @@ -608,7 +608,7 @@ public class ReadUtils { * Example: Locus => {read1, read2, ..., readN} * * - Second: readToLocusMap -- a HashMap that describes for each read what loci it contributes to the coverage. - * Note: Locus is a boolean array, indexed from 0 (= startLocation) to N (= stopLocation), with true meaning it contributes to the coverage. + * Note: Locus is a boolean array, indexed from 0 (= startLocation) to N (= stopLocation), with value==true meaning it contributes to the coverage. * Example: Read => {true, true, false, ... false} * * @param readList the list of reads to generate the association mappings