python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A632-root-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-A632-root -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py A632-shoot-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-A632-shoot -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.chrom.sizes  samtools -paired