# input: in.bam, in.fastq, chunk_size
i <- 0
for fastq_read in in.fastq:
    bam_read <- extract fastq_read.read_name from in.bam
    n <- i modulo chunk_size
    write fastq_read to out.n.fastq
    write bam_read to out.n.bam
    i <- i + 1