NAME

       getCounts.py - generate read counts for each input file

SYNOPSIS

       getCounts.py [options] [<inputFile.thetaMeans>]+

DESCRIPTION

              This  program  reads  supplied  .thetaMeans files and using either information from
              .prob files or Nmap option generates read counts for each input file provided.

OPTIONS

       -h, --help
              show this help message and exit

       -o OUT, --outFile=OUT
              Output file

       -v, --verbose
              Verbose output

       -p PROBDIR, --probDir=PROBDIR
              Directory with .prob files. The program will look in here for files with same  name
              except  fot extension .prob in order to find out total-aligned-read counts for each
              experiment.

       -n NMAP, --Nmap=NMAP
              Comma separated list of total aligned-read-counts for each experiment.