Format of image title: (bam file)__(contig id)__(starting bp to plot)-(ending bp to plot)__(average depth of k-mer)
# get depth file from bam file
$ samtools depth 9D27.bam > 9D27.depth
# plot depth for a specified region of a reference sequence
$ python ~/PycharmProjects/FlowCellBiofilm/plot_sam_depth.py -r 2.10wt_illumina.fasta -d 9D27.depth -i 2.10_plasmid1 -s 2000 -e 10000 -k 100
# plot depth for the full length of a specified reference sequence
$ python ~/PycharmProjects/FlowCellBiofilm/plot_sam_depth.py -r 2.10wt_illumina.fasta -d 9D27.depth -i plasmid1 -k 1000
# plot depth for the full length of all reference sequences in bam file
$ python ~/PycharmProjects/FlowCellBiofilm/plot_sam_depth.py -r 2.10wt_illumina.fasta -d 9D27.depth -k 1000
