python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Physcomitrella_patens_plate_culture_5GRO-seq_r1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Physcomitrella_patens_plate_culture_5GRO-seq_r1 -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Physcomitrella_patens-Phypa_V3/GCA_000002425.2_Phypa_V3_genomic.chrom.sizes  samtools -paired