From 69d92fab4fd6a428b1c30bee2f00524640db8be7 Mon Sep 17 00:00:00 2001 From: aaron Date: Mon, 30 Aug 2010 21:49:23 +0000 Subject: [PATCH] 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 --- .../gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 d1f31c92e..eeec135aa 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 @@ -140,7 +140,7 @@ public class TribbleRMDTrackBuilder extends PluginManager 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(new BasicFeatureSource(inputFile.getAbsolutePath(), createCodec(targetClass, name)),null); + return new Pair(BasicFeatureSource.getFeatureSource(inputFile.getAbsolutePath(), createCodec(targetClass, name)),null); } catch (IOException e) { throw new StingException("Unable to create feature reader from file " + inputFile); }