python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Macrostomum_lignano_mixed_population_grown_under_standard_conditions-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Macrostomum_lignano_mixed_population_grown_under_standard_conditions-pooled -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Plathelminthes/Macrostomum_lignano-Mlig_3_7/GCA_002269645.1_Mlig_3_7_genomic.chrom.sizes  samtools -paired