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adding the ability to get iterators from Tribble without having an index, and updating the Tabix code to the latest Samtools SVN version (this still doesn't fix the outstanding tabix bugs, waiting for Heng on that). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4167 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-08-30 21:49:23 +00:00
parent 50f7f18cbd
commit 69d92fab4f
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
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@ -140,7 +140,7 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
// we might not know the index type, try loading with the default reader constructor
logger.info("Attempting to blindly load " + inputFile + " as a tabix indexed file");
try {
return new Pair<BasicFeatureSource, SAMSequenceDictionary>(new BasicFeatureSource(inputFile.getAbsolutePath(), createCodec(targetClass, name)),null);
return new Pair<BasicFeatureSource, SAMSequenceDictionary>(BasicFeatureSource.getFeatureSource(inputFile.getAbsolutePath(), createCodec(targetClass, name)),null);
} catch (IOException e) {
throw new StingException("Unable to create feature reader from file " + inputFile);
}