C:\\path\\to\\bin\\julia.exe polyOrigin_main.jl -g geno.csv -p ped.csv

C:\\path\\to\\bin\\julia.exe polyOrigin_main.jl --help

usage: polyOrigin_main.jl -g GENOFILE -p PEDFILE
                        [--delimchar DELIMCHAR]
                        [--missingstring MISSINGSTRING]
                        [--commentstring COMMENTSTRING]
                        [--isphysmap ISPHYSMAP]
                        [--recomrate RECOMRATE] [--epsilon EPSILON]
                        [--seqerr SEQERR]
                        [--chrpairing_phase CHRPAIRING_PHASE]
                        [--chrpairing CHRPAIRING]
                        [--chrsubset CHRSUBSET] [--snpthin SNPTHIN]
                        [--nworker NWORKER]
                        [--delsiglevel DELSIGLEVEL]
                        [--maxstuck MAXSTUCK] [--maxiter MAXITER]
                        [--minrun MINRUN] [--maxrun MAXRUN]
                        [--byparent BYPARENT]
                        [--refhapfile REFHAPFILE]
                        [--correctthreshold CORRECTTHRESHOLD]
                        [--refinemap REFINEMAP]
                        [--refineorder REFINEORDER]
                        [--maxwinsize MAXWINSIZE]
                        [--inittemperature INITTEMPERATURE]
                        [--coolingrate COOLINGRATE]
                        [--stripdis STRIPDIS]
                        [--maxepsilon MAXEPSILON]
                        [--skeletonsize SKELETONSIZE] [-o OUTSTEM]
                        [--isplot ISPLOT]
                        [-w WORKDIR] [-v VERBOSE] [-h]

Haplotype reconstruction in polypoid multiparental populations

optional arguments:
  -g, --genofile GENOFILE
                        filename for genotypic data file
  -p, --pedfile PEDFILE
                        filename for pedigree info
  --delimchar DELIMCHAR
                        text delimiter (type: AbstractChar, default:
                        ',')
  --missingstring MISSINGSTRING
                        string code for missing value (default: "NA")
  --commentstring COMMENTSTRING
                        rows that begins with commentstring will be
                        ignored (default: "#")
  --isphysmap ISPHYSMAP
                        if true, input markermap is physical map
                        (location in bp) (type: Bool, default: false)
  --recomrate RECOMRATE
                        recombination rate in unit of cM/Mbp (type:
                        Float64, default: 1.0)
  --epsilon EPSILON     genotypic error probability in offspring
                        (type: Float64, default: 0.01)
  --seqerr SEQERR       sequencing read error probability for GBS data
                        (type: Float64, default: 0.001)
  --chrpairing_phase CHRPAIRING_PHASE
                        chromosome pairing in parental phasing, with
                        22 being only        bivalent formations and
                        44 being bi- and quadri-valent formations
                        (type: Int64, default: 22)
  --chrpairing CHRPAIRING
                        chromosome pairing in offspring decoding, with
                        22 being only        bivalent formations and
                        44 being bivalent and quadrivalent formations
                        (type: Int64, default: 44)
  --chrsubset CHRSUBSET
                        subset of chromosomes, with nothing denoting
                        all chromosomes,        e.g, "[2,10]" denotes
                        the second and tenth chromosomes (default:
                        "nothing")
  --snpthin SNPTHIN     subset of markers by taking every snpthin-th
                        markers (type: Int64, default: 1)
  --nworker NWORKER     number of parallel workers for computing among
                        chromosomes (type: Int64, default: 1)
  --delsiglevel DELSIGLEVEL
                        if true, delete markers during parental
                        phasing (type: Float64, default: 0.05)
  --maxstuck MAXSTUCK   the max number of consecutive iterations that
                        are rejected        in a phasing run (type:
                        Int64, default: 5)
  --maxiter MAXITER     the max number of iterations in a phasing run
                        (type: Int64, default: 30)
  --minrun MINRUN       if the min number of phasing runs that are at
                        the same local maximimum or        have the
                        same parental phases reaches minrun, phasing
                        algorithm will stop before reaching the
                        maxrun. (type: Int64, default: 3)
  --maxrun MAXRUN       the max number of phasing runs (type: Int64,
                        default: 10)
  --byparent BYPARENT   if true, update parental phases         parent
                        by parent; if false, update parental phases
                        one subpopulation by subpopulation. (type:
                        Bool, default: true)
  --refhapfile REFHAPFILE
                        reference haplotype file        for setting
                        absolute parental phases. It has the same
                        format as the input genofile,        except
                        that parental genotypes are phased and
                        offspring genotypes are ignored if they exist.
                        (default: "nothing")
  --correctthreshold CORRECTTHRESHOLD
                        a candidate marker is selected for
                        parental error correction if the fraction of
                        offspring genotypic error >= correctthreshold.
                        (type: Float64, default: 0.15)
  --refinemap REFINEMAP
                        if true, refine marker map (type: Bool,
                        default: false)
  --refineorder REFINEORDER
                        if true, refine marker mordering, valid only
                        if refinemap=true (type: Bool, default: false)
  --maxwinsize MAXWINSIZE
                        max size of sliding windown in map refinning
                        (type: Int64, default: 50)
  --inittemperature INITTEMPERATURE
                        initial temperature of simulated annealing in
                        map refinning (type: Float64, default: 4.0)
  --coolingrate COOLINGRATE
                        cooling rate of annealing temperature in map
                        refinning (type: Float64, default: 0.5)
  --stripdis STRIPDIS   a chromosome end in map refinement is removed
                        if it has a distance gap > stripdis
                        (centiMorgan) and it contains less than 5%
                        markers. (type: Float64, default: 20.0)
  --maxepsilon MAXEPSILON
                        markers in map refinement are removed it they
                        have error        rates > maxepsilon. (type:
                        Float64, default: 0.5)
  --skeletonsize SKELETONSIZE
                        the number of markers in the skeleton map that
                        is used        to reduce map length inflation
                        by subsampling markers (type: Int64, default:
                        50)
  --isplot ISPLOT
                        if true, plot haploprob (type: Bool, default: false)                        
  -o, --outstem OUTSTEM
                        stem of output filenames (default: "outstem")
  -w, --workdir WORKDIR
                        directory for reading and writing files
                        (default: pwd())
  -v, --verbose VERBOSE
                        if true, print messages on console (type:
                        Bool, default: true)
  -h, --help            show this help message and exit