From c7fe062cb759735dbbe50f0dcf3580be33807fa2 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 1 Jun 2011 19:40:47 +0000
Subject: [PATCH] Refactored the VCF codec classes to minimize code duplication
 (which happened during the VCF3/4 split).  Now, both codecs extend the
 AbstractVCFCodec class and all shared functionality exists there.  Only
 methods that differ between the various codecs (e.g. because FILTER strings
 are encoded differently) are defined in the actual codecs.  While I was in
 there, I put in checks for invalid empty inputs in the ID, FILTER, and INFO
 fields.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5917 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/contexts/variantcontext/VariantContextUtils.java     | 4 ++--
 1 file 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 576373949..fe6464c49 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
@@ -31,9 +31,9 @@ import net.sf.samtools.util.StringUtil;
 import org.apache.commons.jexl2.*;
 import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
 import org.broad.tribble.util.variantcontext.*;
+import org.broad.tribble.vcf.AbstractVCFCodec;
 import org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker;
 import org.broadinstitute.sting.utils.*;
-import org.broad.tribble.vcf.VCFCodecUtils;
 import org.broad.tribble.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -566,7 +566,7 @@ public class VariantContextUtils {
 
         VariantContext merged = new VariantContext(name, loc.getContig(), loc.getStart(), loc.getStop(), alleles, genotypes, negLog10PError, filters, (mergeInfoWithMaxAC ? maxACAttributes : attributes) );
         // Trim the padded bases of all alleles if necessary
-        merged = VCFCodecUtils.createVariantContextWithTrimmedAlleles(merged);
+        merged = AbstractVCFCodec.createVariantContextWithTrimmedAlleles(merged);
 
         if ( printMessages && remapped ) System.out.printf("Remapped => %s%n", merged);
         return merged;