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remove unnecessary use in the PRIORITY list 

remove unneeded imports
This commit is contained in:
Ami Levy Moonshine 2012-07-13 15:19:45 -04:00
parent fd3bf36ed9
commit 5d0a7335ea
1 changed files with 2 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
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@ -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<Integer, Integer> {
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);
}