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;