From 14e492fa80541b6fe14aa8c17c37b8a3c34c648c Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 11 Aug 2010 17:01:38 +0000
Subject: [PATCH] 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
---
 .../sting/gatk/contexts/variantcontext/VariantContextUtils.java | 2 +-
 .../sting/gatk/walkers/annotator/HardyWeinberg.java             | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
index a094707a1..03b7e6214 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
@@ -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 {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
index 46058a826..22bbc874b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
@@ -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;