def _check_reads_hit(self, alignment_io, min_aligned_fraction):
to_return = []<EOL>alignment_length = None<EOL>for s in SeqIO.parse(alignment_io, "<STR_LIT>"):<EOL><INDENT>if not alignment_length:<EOL><INDENT>alignment_length = len(s.seq)<EOL>min_length = int(min_aligned_fraction * alignment_length)<EOL>logging.debug("<STR_LIT>" % min_length)<EOL><DEDENT>elif len(s.seq) != alignment_length:<EOL><INDENT>raise Exception("<STR_LIT>")<EOL><DEDENT>num_unaligned = s.seq.count('<STR_LIT:->')<EOL>num_aligned = alignment_length-num_unaligned<EOL>logging.debug("<STR_LIT>" % (s.name, alignment_length-num_unaligned))<EOL>if num_aligned <= min_length:<EOL><INDENT>to_return.append(s.name)<EOL><DEDENT><DEDENT>return to_return<EOL>
Given an alignment return a list of sequence names that are less
        than the min_aligned_fraction