diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java index bf490e28c..7bf518fd5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.refdata; import net.sf.samtools.util.SequenceUtil; import org.broad.tribble.Feature; import org.broad.tribble.annotation.Strand; -import org.broad.tribble.dbsnp.DbSNPFeature; +import org.broad.tribble.dbsnp.OldDbSNPFeature; import org.broad.tribble.gelitext.GeliTextFeature; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.classloader.PluginManager; @@ -93,27 +93,27 @@ public class VariantContextAdaptors { // -------------------------------------------------------------------------------------------------------------- private static class DBSnpAdaptor implements VCAdaptor { - private static boolean isSNP(DbSNPFeature feature) { + private static boolean isSNP(OldDbSNPFeature feature) { return feature.getVariantType().contains("single") && feature.getLocationType().contains("exact"); } - private static boolean isMNP(DbSNPFeature feature) { + private static boolean isMNP(OldDbSNPFeature feature) { return feature.getVariantType().contains("mnp") && feature.getLocationType().contains("range"); } - private static boolean isInsertion(DbSNPFeature feature) { + private static boolean isInsertion(OldDbSNPFeature feature) { return feature.getVariantType().contains("insertion"); } - private static boolean isDeletion(DbSNPFeature feature) { + private static boolean isDeletion(OldDbSNPFeature feature) { return feature.getVariantType().contains("deletion"); } - private static boolean isIndel(DbSNPFeature feature) { + private static boolean isIndel(OldDbSNPFeature feature) { return isInsertion(feature) || isDeletion(feature) || isComplexIndel(feature); } - public static boolean isComplexIndel(DbSNPFeature feature) { + public static boolean isComplexIndel(OldDbSNPFeature feature) { return feature.getVariantType().contains("in-del"); } @@ -125,7 +125,7 @@ public class VariantContextAdaptors { * * @return an alternate allele list */ - public static List getAlternateAlleleList(DbSNPFeature feature) { + public static List getAlternateAlleleList(OldDbSNPFeature feature) { List ret = new ArrayList(); for (String allele : getAlleleList(feature)) if (!allele.equals(String.valueOf(feature.getNCBIRefBase()))) ret.add(allele); @@ -139,7 +139,7 @@ public class VariantContextAdaptors { * * @return an alternate allele list */ - public static List getAlleleList(DbSNPFeature feature) { + public static List getAlleleList(OldDbSNPFeature feature) { List alleleList = new ArrayList(); // add ref first if ( feature.getStrand() == Strand.POSITIVE ) @@ -156,14 +156,14 @@ public class VariantContextAdaptors { /** * Converts non-VCF formatted dbSNP records to VariantContext. - * @return DbSNPFeature. + * @return OldDbSNPFeature. */ @Override - public Class getAdaptableFeatureType() { return DbSNPFeature.class; } + public Class getAdaptableFeatureType() { return OldDbSNPFeature.class; } @Override public VariantContext convert(String name, Object input, ReferenceContext ref) { - DbSNPFeature dbsnp = (DbSNPFeature)input; + OldDbSNPFeature dbsnp = (OldDbSNPFeature)input; if ( ! Allele.acceptableAlleleBases(dbsnp.getNCBIRefBase()) ) return null; Allele refAllele = Allele.create(dbsnp.getNCBIRefBase(), true); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java index c0f695966..2c7902914 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java @@ -26,7 +26,6 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broad.tribble.TribbleException; -import org.broad.tribble.dbsnp.DbSNPFeature; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; @@ -41,7 +40,6 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.io.File; import java.util.Collection; import java.util.HashSet; -import java.util.List; import java.util.Set; @@ -168,14 +166,9 @@ public class ValidateVariants extends RodWalker { // get the RS IDs Set rsIDs = null; if ( tracker.hasValues(dbsnp.dbsnp) ) { - List dbsnpList = tracker.getValues(dbsnp.dbsnp, ref.getLocus()); rsIDs = new HashSet(); - for ( Object d : dbsnpList ) { - if (d instanceof DbSNPFeature ) - rsIDs.add(((DbSNPFeature)d).getRsID()); - else if (d instanceof VariantContext ) - rsIDs.add(((VariantContext)d).getID()); - } + for ( VariantContext rsID : tracker.getValues(dbsnp.dbsnp, ref.getLocus()) ) + rsIDs.add(rsID.getID()); } try { diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java index e740acf05..95fafac8d 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java @@ -23,7 +23,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b36KGReference + - " --variant:dbsnp " + GATKDataLocation + "Comparisons/Validated/dbSNP/dbsnp_129_b36.rod" + + " --variant:OldDbsnp " + GATKDataLocation + "Comparisons/Validated/dbSNP/dbsnp_129_b36.rod" + " -T VariantsToVCF" + " -L 1:1-30,000,000" + " -o %s" + diff --git a/settings/repository/org.broad/tribble-23.jar b/settings/repository/org.broad/tribble-24.jar similarity index 93% rename from settings/repository/org.broad/tribble-23.jar rename to settings/repository/org.broad/tribble-24.jar index 40e2d4c5e..b1c39e60a 100644 Binary files a/settings/repository/org.broad/tribble-23.jar and b/settings/repository/org.broad/tribble-24.jar differ diff --git a/settings/repository/org.broad/tribble-23.xml b/settings/repository/org.broad/tribble-24.xml similarity index 51% rename from settings/repository/org.broad/tribble-23.xml rename to settings/repository/org.broad/tribble-24.xml index 2f6a16a03..9b2b967f8 100644 --- a/settings/repository/org.broad/tribble-23.xml +++ b/settings/repository/org.broad/tribble-24.xml @@ -1,3 +1,3 @@ - +