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fix merge from Khalid's Queue fix

This commit is contained in:
Mark DePristo 2011-08-07 10:33:20 -04:00
parent 4d88e72958
commit b0e91f85cf
2 changed files with 1 additions and 7 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -108,12 +108,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
@Argument(fullName="keepOriginalAC", shortName="keepOriginalAC", doc="Don't include filtered loci.", required=false)
private boolean KEEP_ORIGINAL_CHR_COUNTS = false;
@Argument(fullName="discordance", shortName = "disc", doc="Output variants that were not called on a ROD comparison track", required=false)
private RodBinding<VariantContext> discordanceTrack = RodBinding.makeUnbound(VariantContext.class);
@Argument(fullName="concordance", shortName = "conc", doc="Output variants that were also called on a ROD comparison track", required=false)
private RodBinding<VariantContext> concordanceTrack = RodBinding.makeUnbound(VariantContext.class);
@Hidden
@Argument(fullName="keepAFSpectrum", shortName="keepAF", doc="Don't include loci found to be non-variant after the subsetting procedure.", required=false)
private boolean KEEP_AF_SPECTRUM = false;

2
public/java/test/org/broadinstitute/sting/BaseTest.java
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@ -64,7 +64,7 @@ public abstract class BaseTest {
public static final String b37Refseq = refseqAnnotationLocation + "refGene-big-table-b37.txt";
public static final String dbsnpDataLocation = GATKDataLocation;
public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf";
public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_129_b36.vcf";
public static final String b37dbSNP132 = dbsnpDataLocation + "dbsnp_132_b37.vcf";
public static final String hapmapDataLocation = comparisonDataLocation + "Validated/HapMap/3.3/";