python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Oikopleura_dioica-SL-CAGE.SL-trimmed-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Oikopleura_dioica-SL-CAGE.SL-trimmed -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Tunicata/Oikopleura_dioica-ASM20953v1/GCA_000209535.1_ASM20953v1_genomic.chrom.sizes  samtools -paired