# Command line has been read
# Input file1 is refseq.hg38.gff
# Input file2 is gen.hg38.gff
# I have treated (sorted and put in temp file) the input files according to what the user wants
# Hashtbl of transcripts has 28031 keys/transcripts
# Hashtbl of transcripts has 27908 keys/transcripts
# I have 28031 initial transcripts in file1
# I have 27908 initial transcripts in file2
# I have divided file1 and file2 transcripts intro sublists according to strand
# I have divided file1 and file2 transcripts intro sublists according to strand and chromosome
# For each strand and chromosome I have associated each transcript of file1 to a set of strandedly overlapping transcripts from file2
# For each transcript of file1, I have decided on its class and assiated transcripts from file2
# I have printed the transcripts of file1 with their class and associated transcripts from file2, in a 3 column tsv file
# I have removed the temporary sorted files in case they have been created
# comptr did its work !