diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java index 110078246..60436fb15 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java @@ -31,6 +31,7 @@ import org.broad.tribble.*; import org.broad.tribble.index.Index; import org.broad.tribble.index.IndexFactory; import org.broad.tribble.index.linear.LinearIndex; +import org.broad.tribble.index.linear.LinearIndexCreator; import org.broad.tribble.source.BasicFeatureSource; import org.broad.tribble.vcf.NameAwareCodec; import org.broadinstitute.sting.gatk.refdata.tracks.TribbleTrack; @@ -279,6 +280,7 @@ public class TribbleRMDTrackBuilder extends PluginManager implemen private static Index createIndexInMemory(File inputFile, FeatureCodec codec) throws IOException { // this can take a while, let them know what we're doing logger.info("Creating Tribble index in memory for file " + inputFile); - return new LinearIndex(16000,inputFile.getAbsolutePath()); + LinearIndexCreator creator = new LinearIndexCreator(inputFile,codec,null); + return creator.createIndex(); } } diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java index 01a25663b..262c32b87 100644 --- a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java @@ -97,7 +97,7 @@ public class TribbleRMDTrackBuilderUnitTest extends BaseTest { @Test public void testBuilderIndexDirectoryUnwritable() { - File vcfFile = new File(validationDataLocation + "/ROD_validation/read_only/no_index.vcf.vcf"); + File vcfFile = new File(validationDataLocation + "/ROD_validation/read_only/no_index.vcf"); File vcfFileIndex = new File(validationDataLocation + "/ROD_validation/read_only/no_index.vcf.idx"); Index ind = null; diff --git a/settings/repository/org.broad/tribble-121M.jar b/settings/repository/org.broad/tribble-122M.jar similarity index 89% rename from settings/repository/org.broad/tribble-121M.jar rename to settings/repository/org.broad/tribble-122M.jar index 56bf4a1cf..a39750e2f 100644 Binary files a/settings/repository/org.broad/tribble-121M.jar and b/settings/repository/org.broad/tribble-122M.jar differ diff --git a/settings/repository/org.broad/tribble-121M.xml b/settings/repository/org.broad/tribble-122M.xml similarity index 64% rename from settings/repository/org.broad/tribble-121M.xml rename to settings/repository/org.broad/tribble-122M.xml index a9f018f41..3d74b4640 100644 --- a/settings/repository/org.broad/tribble-121M.xml +++ b/settings/repository/org.broad/tribble-122M.xml @@ -1,3 +1,3 @@ - +