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updates to tribble with fixes for some bugs I've found in some new indexing code. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3842 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-07-20 22:08:04 +00:00
parent ff6748d1cd
commit 1cba81c16f
4 changed files with 5 additions and 3 deletions
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4
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
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@ -31,6 +31,7 @@ import org.broad.tribble.*;
import org.broad.tribble.index.Index; import org.broad.tribble.index.Index;
import org.broad.tribble.index.IndexFactory; import org.broad.tribble.index.IndexFactory;
import org.broad.tribble.index.linear.LinearIndex; import org.broad.tribble.index.linear.LinearIndex;
import org.broad.tribble.index.linear.LinearIndexCreator;
import org.broad.tribble.source.BasicFeatureSource; import org.broad.tribble.source.BasicFeatureSource;
import org.broad.tribble.vcf.NameAwareCodec; import org.broad.tribble.vcf.NameAwareCodec;
import org.broadinstitute.sting.gatk.refdata.tracks.TribbleTrack; import org.broadinstitute.sting.gatk.refdata.tracks.TribbleTrack;
@ -279,6 +280,7 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
private static Index createIndexInMemory(File inputFile, FeatureCodec codec) throws IOException { private static Index createIndexInMemory(File inputFile, FeatureCodec codec) throws IOException {
// this can take a while, let them know what we're doing // this can take a while, let them know what we're doing
logger.info("Creating Tribble index in memory for file " + inputFile); 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();
} }
} }

2
java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java
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@ -97,7 +97,7 @@ public class TribbleRMDTrackBuilderUnitTest extends BaseTest {
@Test @Test
public void testBuilderIndexDirectoryUnwritable() { 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"); File vcfFileIndex = new File(validationDataLocation + "/ROD_validation/read_only/no_index.vcf.idx");
Index ind = null; Index ind = null;

BIN
settings/repository/org.broad/tribble-121M.jar → settings/repository/org.broad/tribble-122M.jar
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2
settings/repository/org.broad/tribble-121M.xml → settings/repository/org.broad/tribble-122M.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0"> <ivy-module version="1.0">
<info organisation="org.broad" module="tribble" revision="121M" status="integration" publication="201007191154200" /> <info organisation="org.broad" module="tribble" revision="122M" status="integration" publication="201007191854200" />
</ivy-module> </ivy-module>