Program options

Can be specified via the command line or a .ini file passed to the -c option.

Command line options:
  -h [ --help ]                         Print a help message
  -b [ --bam ] arg                      Path to BAM file
  -x [ --bam-index ] arg                Path to BAM index, (defalult is 
                                        <bam_path>.bai
  -r [ --reference ] arg                Path to reference genome
  -a [ --ancestor ] arg                 Ancestor RG sample ID
  -s [ --sample-name ] arg              Sample tags to include
  -q [ --qual ] arg (=13)               Base quality cuttoff
  -m [ --mapping-qual ] arg (=13)       Mapping quality cuttoff
  -p [ --prob ] arg (=0.10000000000000001)
                                        Mutaton probability cut-off
  -o [ --out ] arg                      Out file name (default is std out)
  -i [ --intervals ] arg                Path to bed file
  -c [ --config ] arg                   Path to config file
  --theta arg                           theta
  --nfreqs arg                          Nucleotide frequencies
  --mu arg                              Experiment-long mutation rate
  --seq-error arg                       Probability of sequencing error
  --ploidy-ancestor arg (=2)            Polidy of ancestor (1 or 2)
  --ploidy-descendant arg (=2)          Ploidy of descendant (1 or 2)
  --phi-haploid arg                     Over-dispersion for haploid sequencing
  --phi-diploid arg                     Over-dispersion for diploid sequencing