python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py IMR90-NOMe-seq-GSM1001125.Bismark_v0.19.0.bowtie2.sorted.bam SAMstats-IMR90-NOMe-seq-GSM1001125.Bismark_v0.19.0.bowtie2.sorted.bam -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM