java -jar ../../diCal2.jar --paramFile mutRec.param --vcfFile contig.0.vcf --vcfFilterPassString PASS --vcfReferenceFile output.ref --lociPerHmmStep 1000 --configFile piecewise_constant.config --demoFile piecewise_constant.demo --intervalType loguniform --intervalParams '8,0.01,4' --compositeLikelihood pcl --startPoint '1,2,0.5,1' --bounds '0.01,20;0.01,20;0.01,20;0.01,20'  --numberIterationsEM 10 --numberIterationsMstep 5 --seed 4711 --verbose
