- geneModelFlag = "NM"
- for (start, stop, gid, featureSense, featureType) in featuresByChromDict[chromNum]:
- if start < alignedread.pos and stop > alignedread.pos:
- geneModelFlag = gid
- continue
+ #new direct query
+ geneFeatures = genome.getFeaturesIntersecting(chromNum, alignedread.pos, readLength)
+ try:
+ (name, version, chromosome, start, stop, orientation, atype) = geneFeatures[0]
+ geneModelFlag = name
+ except IndexError:
+ geneModelFlag = "NM"