CGATOxford/cgat — pull request #26 by IanSudbery (2014-09-11 10:30:14+00:00)
Title: Gtf introns

GTF.py's toIntronIntervals function simply inverts a collection of GTF entries. However, ensembl formatted GTF files contain "transcript" entries. These entries cover the whole range of the transcript and thus the intron model is always empty. To get around this I have made GTF only consider "exon" features when computing intron models.