def _check_contigs_to_use(self, ref_dict):
        '''Checks that the set of contigs to use are all in the reference
        fasta lengths dict made by self._get_ref_lengths()'''
        if self.contigs_to_use is None:
            return True

        for contig in self.contigs_to_use:
            if contig not in ref_dict:
                raise Error('Requested to use contig "' + contig + '", but not found in input BAM file "' + self.bam + '"')

        return True
Checks that the set of contigs to use are all in the reference
        fasta lengths dict made by self._get_ref_lengths()