def _all_reads_from_contig(self, contig, fout):
        '''Gets all reads from contig called "contig" and writes to fout'''
        sam_reader = pysam.Samfile(self.bam, "rb")
        for read in sam_reader.fetch(contig):
            print(mapping.aligned_read_to_read(read, ignore_quality=not self.fastq_out), file=fout)
Gets all reads from contig called "contig" and writes to fout