

set -ex



atlas | grep "successfully"
atlas simulate
atlas HKY85 --bam ATLAS_simulations.bam --fasta ATLAS_simulations.fasta
atlas GLF --bam ATLAS_simulations.bam
atlas saf --glf ATLAS_simulations.glf.gz --fasta ATLAS_simulations.fasta
atlas majorMinor --glf ATLAS_simulations.glf.gz
rm ATLAS_* *.parameters saf.saf.* || exit 1
exit 0
