#region_list, #most_up(down)stream added to region in order to represent the same interface as region_list
TODO
extract fasta now can make transcript poly-N-ed on top expressed positions
make expansion of exons upstream correctly behaved. Renormalize peak to count only those cages that are under exons. Refactor output to allow preprocessing inside of block
region and region list replaced with GenomeRegion
transcript fixed in order to simplify and make correct obtaining of utr region (expanded with peaks) and exons on then
whitespaces removed
score(N) now works not via exception handling, #percent_of_starts_matching_motif now uses just length as argument instead of whole sequence
peaks having 0 cages in intersection with exons are rejected
fasta format changed
kozak fixed to play with new algorithm of exon expansion
enumerator each_region for genome_region (temporary fix before refactoring)
Refactoring for expression calculations. Fix: new algorithm for exon-structure expansion on utr needs cages - so they are here
some changes to statistics by pattern|motif
statistics by motif now live in separate file with all methods it need