def rna_bases(rna_cov, scaffold, bases, line):
start = int(line[<NUM_LIT:3>])<EOL>stop = start + bases - <NUM_LIT:1><EOL>if scaffold not in rna_cov:<EOL><INDENT>return rna_cov<EOL><DEDENT>for pos in rna_cov[scaffold][<NUM_LIT:2>]:<EOL><INDENT>ol = get_overlap([start, stop], pos)<EOL>rna_cov[scaffold][<NUM_LIT:0>] += ol<EOL><DEDENT>return rna_cov<EOL>
determine if read overlaps with rna, if so count bases