diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java b/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java index f74004479..ba7366039 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java @@ -67,6 +67,20 @@ public class RefMetaDataTracker { return objects; } + /** + * get all the GATK features associated with a specific track name + * @param name the name of the track we're looking for + * @param requireExactMatch do we require an exact match for the name (true) or do we require only that the name starts with + * the passed in parameter (false). + * @return a list of GATKFeatures for the target rmd + * + * Important: The list returned by this function is guaranteed not to be null, but may be empty! + */ + public List getGATKFeatureMetaData(final String name, boolean requireExactMatch) { + List feat = getTrackDataByName(name,requireExactMatch); + return (feat == null) ? new ArrayList() : feat; // to satisfy the above requirement that we don't return null + } + /** * get a singleton record, given the name and a type. This function will return the first record at the current position seen, * and emit a logger warning if there were more than one option. 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 0a7fd8ddc..b9edd742b 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 @@ -76,6 +76,7 @@ public class TribbleRMDTrackBuilder extends PluginManager implemen public Map getAvailableTrackNamesAndTypes() { Map classes = new HashMap(); for (String c : this.pluginsByName.keySet()) + if (!c.contains("BED")) // ugg the collision for Bed files is a problem right now classes.put(c,this.pluginsByName.get(c)); return classes; }