add_new_exons	add_new_exons
adjust_for_collision	adjust_for_collision
debug_msg	debug_msg
extend_granges	extend_granges
extend_using_overlap	extend_using_overlap
extract_last_exons	extract_last_exons
filter_new_exons	filter_new_exons
five_prime_pos	five_prime_pos
overlap_different_genes	overlap_different_genes
progression_msg	progression_msg
three_prime_pos	three_prime_pos
