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Bug fixing for merging of read fragments when one fragment contained an indel

This commit is contained in:
Ryan Poplin 2012-01-17 14:39:27 -05:00
parent 8e23c98dd9
commit ae259f81cc
2 changed files with 2 additions and 3 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
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@ -27,7 +27,6 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.util.List; import java.util.List;
@ -126,7 +125,7 @@ public class VariantRecalibratorEngine {
iteration++; iteration++;
model.maximizationStep( data ); model.maximizationStep( data );
currentChangeInMixtureCoefficients = model.normalizePMixtureLog10(); 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 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)); logger.info("Finished iteration " + iteration + ". \tCurrent change in mixture coefficients = " + String.format("%.5f", currentChangeInMixtureCoefficients));
} }

2
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -608,7 +608,7 @@ public class ReadUtils {
* Example: Locus => {read1, read2, ..., readN} * Example: Locus => {read1, read2, ..., readN}
* *
* - Second: readToLocusMap -- a HashMap that describes for each read what loci it contributes to the coverage. * - 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} * Example: Read => {true, true, false, ... false}
* *
* @param readList the list of reads to generate the association mappings * @param readList the list of reads to generate the association mappings