From da9c8ab38601c2fd893307869c46221cd37d68ba Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 6 Sep 2011 20:39:42 -0400 Subject: [PATCH] Revving the Tribble jar where the DbsnpCodec class was renamed to OldDbsnpCodec. Updating GATK code accordingly. --- .../gatk/refdata/VariantContextAdaptors.java | 24 +++++++++--------- .../variantutils/ValidateVariants.java | 11 ++------ .../VariantsToVCFIntegrationTest.java | 2 +- .../{tribble-23.jar => tribble-24.jar} | Bin 299168 -> 299210 bytes .../{tribble-23.xml => tribble-24.xml} | 2 +- 5 files changed, 16 insertions(+), 23 deletions(-) rename settings/repository/org.broad/{tribble-23.jar => tribble-24.jar} (93%) rename settings/repository/org.broad/{tribble-23.xml => tribble-24.xml} (51%) 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 40e2d4c5ec85a3fd0c7f14b55a1d0ba3c283c217..b1c39e60a14ce895e515cadb07c356d6d428bbc4 100644 GIT binary patch delta 5617 zcmZu#30T!t7XL37cH(lDftgvI7Rfh zVEmV5zKAQSns6DJJ+{t#<+$DNeC3c+Jr|ziJWjHwW+L~+#n$YU1z{&dCCcuQm`ny6 z@Alot#kadZ;o|RmZssc?`ZCTO_l@98m!HfTi-1%sj4V536uRFV@}>r%c0^{=tP>JLjML`2*dmjjT49gOA-wTt81T?I|@R% zBNR>*-OK`EwNFIY87rDi8{^*HDiIfE`_9&CZo4O#x?)e`!EFOEeTE-*jlfcste&~8 zqpu)z7`=8+*N72@=zaYRvHLVc&qAo#S1PK53O%5~G#R6hmh-f?Hr?jTk>-yum7p6h z`5Fo?+4Sl}x(#Ff#bvyxZdVo}V_4f3in%}3c7YqM=(uN%CCu-936ak`^Q1m32VeZR zxMTBBL0~k*kTkciq4BY^G4zCr6P?cdX2pRTIM5tKo*Z*CZ3>|qCJ-Dd(bC$=o~EMvQUYEZ zrdz*Bmt|Bw{z$rMfhu3LUFvEN5QO#sXw^w>wLej{9mO>6w~t5~)17BhM*!1+%P+_; zqN-hhe2c5z`LJnTn71H=d2?_2VX_w-Uq^MP`Vft2T(BJBjXp|_U8yOzpvT(++k?uv zz=7$qqv=eXyp8WGHC}G!i3m-UU3s`M3uP+@^f@y}o`pxyba1u&9q*B<5_v10bW>op zynwg&Z|`^-D`>$hAWBaLz<~(S8dCZbN7IEZa;1o|9BW-GCJYjUgh5ajPWr>QTV*?# zw}Dui{t9y1Al80heN4WJe%p`9Ej+%1P4ab1Tzl_~{41|O)m1s1bFH`K(>(gEo$}H? 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