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fix for a problem in readNextRecord() of BFS, where we'd go looking for the next record far into in the next contig because (f.getEnd() >= start) was never true once we cycled to a new conitg. Added a check for contig identity. Also, removed duplicate HW calculation classes in the GATK and Tribble. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4011 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-08-11 17:01:38 +00:00
parent e0abb73fd7
commit 14e492fa80
2 changed files with 2 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
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@ -26,9 +26,9 @@ package org.broadinstitute.sting.gatk.contexts.variantcontext;
import java.io.Serializable;
import java.util.*;
import org.apache.commons.jexl2.*;
import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
import org.broad.tribble.util.variantcontext.*;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.genotype.HardyWeinbergCalculation;
import org.broad.tribble.vcf.VCFConstants;
public class VariantContextUtils {

2
java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
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@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.VCFHeaderLineType;
@ -8,7 +9,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
import org.broadinstitute.sting.utils.genotype.HardyWeinbergCalculation;
import org.broadinstitute.sting.utils.QualityUtils;
import java.util.Map;