fixed gtf2juncs --tophat to more closely emulate tophat junctions.bed output, removed extra newline, chromStart is last nt in exon, chromEnd is last nt in intron (this was fine), now also includes exon ids for the junction (conditional on presence of exon_id in gtf, otherwise uses transcript_id), added '.' for score, so now the first 6 columns line up with the BED standard
Merge pull request #2 from jkgoya/master

minor edit to gtf2juncs, thanks to jkgoya