#most_(up/down)stream_position added to gene_region, gene_region_list
full_gene_region is now calculated from exons, not stored in memory. Several methods added to GenomeRegion in order to simplify code
transcript#utr_5_with_upstream refactored
transcript expansion refactored a lot, added help about peak trimming/expansion
rename a bit
remove unused methods, merge calculate_exons_on_utr into place it's invoked
#associate_peaks and #utr_region now don't expand region, it just selects peaks to be attached to a transcript. So gene_data_loader should expand peaks itself. #utr_region thus became the same as #utr_5. It should be mentioned, that before this comit only peaks intersecting exons were selected as associated, now all peaks, intersecting whole transcript are associated
Gene.genes_from_file now loads list, not a hash; reading table refactored (column indices detection extracted)
remove lots of logging, refactored gene infos loading
reorder methods
refactor peak intron-exon fraction normalizing
refactor transcript grouping and move from Gene into TranscriptGroup class methods
peak expression from exons calculation extracted into a separate method