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Oops, I broke the build. NOW we shouldn't have any more public->protected dependancies.

This commit is contained in:
Eric Banks 2013-01-09 11:12:28 -05:00
parent a921b06e02
commit 3a0dd4b175
1 changed files with 2 additions and 1 deletions
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3
protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCountConstants;
import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts; import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts;
import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel; import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection; import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
@ -423,7 +424,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
headerLines.add(new VCFInfoHeaderLine("AF_Orig", 1, VCFHeaderLineType.Float, "Original AF")); headerLines.add(new VCFInfoHeaderLine("AF_Orig", 1, VCFHeaderLineType.Float, "Original AF"));
headerLines.add(new VCFInfoHeaderLine("AN_Orig", 1, VCFHeaderLineType.Integer, "Original AN")); headerLines.add(new VCFInfoHeaderLine("AN_Orig", 1, VCFHeaderLineType.Integer, "Original AN"));
} }
headerLines.addAll(Arrays.asList(ChromosomeCounts.descriptions)); headerLines.addAll(Arrays.asList(ChromosomeCountConstants.descriptions));
headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.DEPTH_KEY)); headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.DEPTH_KEY));
for (int i = 0; i < SELECT_EXPRESSIONS.size(); i++) { for (int i = 0; i < SELECT_EXPRESSIONS.size(); i++) {