python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ChCUC1_halo_REP1.SE.a.bam SAMstats-ChCUC1_halo_REP1.SE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/Cardamine_hirsuta-ddCarHirs1.hap2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ChCUC1_halo_REP2.SE.a.bam SAMstats-ChCUC1_halo_REP2.SE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/Cardamine_hirsuta-ddCarHirs1.hap2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ChCUC1_halo_REP3.SE.a.bam SAMstats-ChCUC1_halo_REP3.SE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/Cardamine_hirsuta-ddCarHirs1.hap2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py halo_REP1.SE.a.bam SAMstats-halo_REP1.SE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/Cardamine_hirsuta-ddCarHirs1.hap2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py halo_REP2.SE.a.bam SAMstats-halo_REP2.SE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/Cardamine_hirsuta-ddCarHirs1.hap2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py halo_REP3.SE.a.bam SAMstats-halo_REP3.SE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/Cardamine_hirsuta-ddCarHirs1.hap2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired