From 5d0a7335ead24af1b63a92c1846cd8f3f6a7c344 Mon Sep 17 00:00:00 2001 From: Ami Levy Moonshine Date: Fri, 13 Jul 2012 15:19:45 -0400 Subject: [PATCH] remove unnecessary use in the PRIORITY list remove unneeded imports --- .../sting/gatk/walkers/variantutils/CombineVariants.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java index 94fa29173..c7bc790a9 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java @@ -35,7 +35,6 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.variantcontext.VariantContext; @@ -185,7 +184,8 @@ public class CombineVariants extends RodWalker { logger.warn("VCF output file not an instance of VCFWriterStub; cannot enable sites only output option"); if ( PRIORITY_STRING == null ) { - PRIORITY_STRING = Utils.join(",", vcfRods.keySet()); + genotypeMergeOption = VariantContextUtils.GenotypeMergeType.UNSORTED; + //PRIORITY_STRING = Utils.join(",", vcfRods.keySet()); Deleted by Ami (7/10/12) logger.info("Priority string not provided, using arbitrary genotyping order: " + PRIORITY_STRING); }