DiploLocus likelihood -h
#usage: DiploLocus likelihood [-h] --u01 U01 [--u10 U10] --Ne NE [--gen_time GEN_TIME]
#                             (-i INFILE | --vcf VCFFILE | --read_LL_from ONGRID_LL_FILE)
#                             [--info INFOFILE] [--ID_col IDCOLNAME]
#                             [--time_col TIMECOLNAME | --time_ago_col TIMEAGOCOLNAME]
#                             [--inds IND_SUBSET] [--force_hap FORCED_HAPS] [--force_dip FORCED_DIPS]
#                             [--sample_times SAMPLETIMES | --sample_times_ago SAMPLETIMES_AGO]
#                             [--snps SNP_SUBSET] [--minMAF MAF] --init {uniform,initFreq,statBeta}
#                             [--initFreq INITFREQ] [--t0 T0] [--force_t0] [--init_u01 INIT_U01]
#                             [--init_u10 INIT_U10] [--piecewise] [--specify_piece SPECIFY_PIECE]
#                             (--fix_s2 S2 | --linear_s2_range LIN_S2_RANGE | --geom_s2_range GEOM_S2_RANGE)
#                             ([--fix_s1 S1 | --linear_s1_range LIN_S1_RANGE | --geom_s1_range
#                             GEOM_S1_RANGE |]
#                             [--fix_h H | --linear_h_range LIN_H_RANGE | --geom_h_range GEOM_H_RANGE)]
#                             -o OUTPREFIX [--long_LL_table] [--gzip_surface] [--get_on_grid_max]
#                             [--get_off_grid_max] [--get_MLR] [--get_chi2_pval]
#                             [--numStates NUMSTATES] [-v]
#
#optional arguments:
#  -h, --help            show this help message and exit
#  -v, --verbose         Option to write out selection coefficients when computing likelihoods.
#
#Population Parameters:
#  --u01 U01             Mutation rate allele 0 to allele 1 (/site/generation).
#  --u10 U10             Mutation rate allele 1 to allele 0 (/site/generation). Default to be equal to u01.
#  --Ne NE               Effective diploid population size (i.e., total #(allele)=2Ne ).
#  --gen_time GEN_TIME   Average generation time in the same unit as provided to '--sample_times' or
#                        '--sample_times_ago' argument. Default is 1.
#
#Genetic Data Input (choose one):
#  -i INFILE, --infile INFILE
#                        Path and name of the parsed input file.
#  --vcf VCFFILE         Path and name of the vcf file.
#  --read_LL_from ONGRID_LL_FILE
#                        Path and name to pre-computed log-likelihoods. File should be formatted the
#                        same as the on-grid log-likelihood output files generated by DiploLocus.
#
#For VCF input:
#  --info INFOFILE       Path and name of the annotation file. Must be tab-delimited and contain at
#                        least columns ("ID", "Gen_Ago") or ("ID", "Time_Ago") or ("ID", "Gen")
#  --ID_col IDCOLNAME    Name of the column in info table for ID names of the sample (as shown in
#                        VCF). Default is "ID".
#  --time_col TIMECOLNAME
#                        Name of the column in info table for each sample's sampling times (forward;
#                        ascending from past to present). Default name is "Time", unit is the number
#                        of generation unless specified with `--gen_time`.
#  --time_ago_col TIMEAGOCOLNAME
#                        Name of the column in info table for each sample's sampling times (backward;
#                        ascending from present to past). Default name is "Time_Ago", unit is the
#                        number of generation unless specified with `--gen_time`.
#  --inds IND_SUBSET     Comma-separated string or a plain-text file that lists a subset of sample
#                        IDs (among those included in the vcf) to consider.
#  --force_hap FORCED_HAPS
#                        Comma-separated string or a plain-text file that lists IDs (matching VCF
#                        column names) to be considered as haploids even though some may present
#                        diploid genotype calls. If "all", all samples will be considered as
#                        haploids, whose genotypes will be counted as matching haplotype (i.e. half
#                        the alleles). Force quit if any specified individual has heterozygote
#                        variant or any unmentioned diploid-formatted samples lack heterozygote
#                        variant calls. Default is "none".
#  --force_dip FORCED_DIPS
#                        Comma-separated string or a plain-text file that lists samples IDs
#                        (separated by comma) to be considered as diploids even though some may have
#                        loci with only haplotype calls. If "all", all samples will be considered as
#                        diploids, whose haploid GTs will be counted as matching homozygote diploid
#                        GTs (i.e. double-count the allele). Default is "none".
#
#For parsed allele counts (choose one):
#  --sample_times SAMPLETIMES
#                        Specify the time (ascending, from ancient to recent) of the same unit (e.g.,
#                        generations, years, weeks, etc.) when each pool of samples were taken. Must
#                        be positive numbers. Format: "<t1>,<t2>,...,<tk>". Number of time points
#                        must match the number of sample pools.
#  --sample_times_ago SAMPLETIMES_AGO
#                        Specify the time before present (descending, from ancient to recent) of the
#                        same unit (e.g., generations, years, weeks, etc.) when each pool of samples
#                        were taken. Format: "<t1>,<t2>,...,<tk>". Number of time points must match
#                        the number of sample pools.
#
#Input Options:
#  --snps SNP_SUBSET     Comma-separated string or a plain-text file that lists a subset of variant
#                        IDs (among those included in the input file) to consider.
#  --minMAF MAF          Minimum threshold (non-inclusive) for minor allele frequencies in the pooled
#                        samples. SNPs with sub-threshold frequencies will not be considered for
#                        analyses. Default is 0.
#
#Initial Condition:
#  --init {uniform,initFreq,statBeta}
#                        Specify initial condition for computing likelihoods.
#  --initFreq INITFREQ   Required when --init="initFreq". Specify the allele frequency when selection
#                        started.
#  --t0 T0               The time point (in generations) when initial distribution is assumed and selection 
#                        starts. Default is the first sampling time. IMPORTANT: This is interpreted the
#                        same way as the specified sampling times. Thus, if --sample_times or --time_col
#                        is used, this time is regular (forward), whereas with --sample_times_ago or
#                        --time_ago_col, this is time before present (backward).
#  --force_t0            Option to force implement a t0 later than the earliest samples. Data prior
#                        to t0 will be ignored.
#  --init_u01 INIT_U01   Specify mutation rate allele 0 to allele 1 for the initial distribution "statBeta".
#                        Default to be identical to u01.
#  --init_u10 INIT_U10   Specify mutation rate allele 1 to allele 0 for the initial distribution.
#                        Default to be identical to u10.
#
#Optional Mode(s):
#  --piecewise           Assume different selection coefficients in different periods. If selected, user
#                        must provide additional text file, using "--specify_piece", to specify in which
#                        period to vary [s] (and compute likelihooods on the given grid).
#  --specify_piece SPECIFY_PIECE
#                        Name of the file specifying selection periods when "--piecewise" is selected.
#                        It should be tab-delimited with 4 columns, using "x" instead of s1 and s2 to
#                        indicate the coefficients to vary in the respective time period:
#                        <from (forward gen#> <to (forward gen#> > <s1> <s2>
#Parameter Grids (specify s2 and [s1 | h]):
#  --fix_s2 S2           Provide one or more fixed values for s_AA (fitness gain in homozygotes),
#                        separated by comma (without space).
#  --linear_s2_range LIN_S2_RANGE
#                        Specify a linear grid as the parameter space for s_AA value. Format
#                        "(min,max,grid_num)".
#  --geom_s2_range GEOM_S2_RANGE
#                        Specify a geometrically-scaled grid as the parameter space for s_AA value.
#                        Format "(min,max,grid_num)". A closest number to <grid_num> will be
#                        determined such that 10^(-n)-fold values of <min> or <max> are included and
#                        that the smallest absolute value is greater than 1/2Ne. When <min> and <max>
#                        are of opposite signs, s=0 will be included, and two grids with an equal
#                        number of grid points will be formed on either side of zero.
#  --fix_s1 S1           Provide one or more fixed values for s_Aa (fitness gain in heterozygotes),
#                        separated by comma (without space).
#  --linear_s1_range LIN_S1_RANGE
#                        Specify a linear grid as the parameter space for s_Aa value. Format
#                        "(min,max,grid_num)".
#  --geom_s1_range GEOM_S1_RANGE
#                        Specify a geometrically-scaled grid as the parameter space for s_Aa value.
#                        Format "(min,max,grid_num)". A closest number to <grid_num> will be
#                        determined such that 10^(-n)-fold values of <min> or <max> are included and
#                        that the smallest absolute value is greater than 1/2Ne. When <min> and <max>
#                        are of opposite signs, s=0 will be included, and two grids with an equal
#                        number of grid points will be formed on either side of zero.
#  --fix_h H             Provide one or more fixed values for dominant coefficient h, separated by
#                        comma (without space).
#  --linear_h_range LIN_H_RANGE
#                        Specify a linear grid as the parameter space for dominant coefficient h.
#                        Format "(min,max,grid_num)".
#  --geom_h_range GEOM_H_RANGE
#                        Specify a geometrically-scaled grid as the parameter space for s_AA value.
#                        Format "(min,max,grid_num)". A closest number to <grid_num> will be
#                        determined such that 10^(-n)-fold values of <min> or <max> are included and
#                        that the smallest absolute value is greater than 1/2Ne. When <min> and <max>
#                        are of opposite signs, s=0 will be included, and two grids with an equal
#                        number of grid points will be formed on either side of zero.
#
#Output:
#  -o OUTPREFIX, --out_prefix OUTPREFIX
#                        Path and prefix of the output file.
#  --long_LL_table       Option to write out the computed loglikelihood surfaces to a plotting-
#                        friendly table with columns "locus, s1, s2, log-likelihood", instead of
#                        matrices.
#  --gzip_surface        Option to output the .gz file of computed likelihoods.
#  --get_on_grid_max     Option to output on-grid max log-likelihood and the matching (s1, s2) values
#                        among all values computed on each given locus, as `{PREFIX}_on-
#                        grid_maxLLs.txt`.
#  --get_off_grid_max    Option to interpolate the computed grid (must be at least 5x5) and infer
#                        local maximum likelihoods, written to file `{PREFIX}_off-grid_maxLLs.txt`.
#  --get_MLR             Option to write out the max-loglikelihood ratios relative to neutrality,
#                        i.e. 2(LL_opt - LL_0), for each locus, along side with the maximized log-
#                        likelihoods.
#  --get_chi2_pval       Option to write out the p-value of MLR in a standard chi-square distribution
#                        (df=1).
#
#HMM Parameters:
#  --numStates NUMSTATES
#                        Number of states across [0,1) for allele frequency. Default is 2000.

DiploLocus simulate -h
# usage: DiploLocus simulate [-h] --u01 U01 [--u10 U10] --Ne NE --s1 S1 --s2 S2
#                              [--selection_change_times SELECTIONCHANGETIMES] --sample_times
#                              SAMPLETIMES --sample_sizes SAMPLESIZES --num_rep NUMREP
#                              [--last_popfreq_nonzero] [--last_sample_nonzero] [--not_lost_ever]
#                              --init {initFreq,statBeta,uniform,custom} [--initFreq INITFREQ]
#                              [--initDistn INITDISTNFILE] [--init_u01 INIT_U01]
#                              [--init_u10 INIT_U10] [--deltaT DELTAT] [--seed SD] -o OUTPREFIX
#                              [--write_traj] [--gzip_output {s,t,st,ts}] [--plot_trajs]
#                              [--plot_samples] [--reps_to_plot REPS_TO_PLOT]
#
# optional arguments:
#  -h, --help            show this help message and exit
#
# Population Parameters:
#  --u01 U01             Mutation rate allele 0 to allele 1 (/site/generation).
#  --u10 U10             Mutation rate allele 1 to allele 0 (/site/generation). Default is u01.
#  --Ne NE               Effective diploid population size (i.e., total #(allele)=2Ne ).
#
# Selection Parameters:
#  --s1 S1               Value(s) of selection coefficient for heterozygotes. If more than one value
#                        is provided (separated by comma, no space), then user must also provide
#                        selection change time with "--selection_change_times".
#  --s2 S2               Value(s) of selection coefficient for homozygotes. If more than one value is
#                        provided (separated by comma, no space), then user must also provide
#                        selection change time with "--selection_change_times".
#  --selection_change_times SELECTIONCHANGETIMES
#                        Times (in forward generations) when either selection coefficient changes.
#                        Must be 1 fewer than the number of s values provided.
#
# Sample Parameters:
#  --sample_times SAMPLETIMES
#                        Numbers of generation times to take samples, separated by comma (no sapce).
#                        Must match the length of sample sizes.
#  --sample_sizes SAMPLESIZES
#                        Numbers of alleles to sample at each time points specified by "--
#                        sample_times". Must match the length of sample times.
#  --num_rep NUMREP      Number of replicates to generate.
#  --last_popfreq_nonzero
#                        Option to only count replicates with non-zero population frequency in the
#                        end.
#  --last_sample_nonzero
#                        Option to only count replicates where the last (i.e. most recent) sample is
#                        not zero.
#  --not_lost_ever       Option to only count replicates where the allele is not lost throughout the
#                        simulation.
#
# Initial Condition:
#  --init {initFreq,statBeta,uniform,custom}
#                        Specify initial probability distribution to generate the replicates
#  --initFreq INITFREQ   Required when --init="initFreq". Specify the allele frequency when selection
#                        started. If multiple values are provided (separated by comma), then length
#                        must match the number of replicates.
#  --initDistn INITDISTNFILE
#                        Path and name to the file specifying a particular frequency distribution as
#                        the initial condition.
#  --init_u01 INIT_U01   Specify mutation rate allele 0 to allele 1 for the initial distribution.
#                        Default is u01.
#  --init_u10 INIT_U10   Specify mutation rate allele 1 to allele 0 for the initial distribution.
#                        Default is u10.
#
# Output Options:
#  -o OUTPREFIX, --out_prefix OUTPREFIX
#                        Path and prefix of the output file.
#  --write_traj          Option to also write out the trajectories of replicates.
#  --gzip_output {none,s,t,st,ts}
#                        Option to write output in .gz format. Use "s" to indicate sample file, "t"
#                        to indicate trajectory file, and "st" (or "ts") for both. Use "none" to not
#                        zip either.
#  --plot_trajs          Option to plot the population allele frequency trajectories of up to 10
#                        replicates.
#  --plot_samples        Option to plot the sample allele frequency trajectories of up to 10
#                        replicates.
#  --reps_to_plot REPS_TO_PLOT
#                        Specify the replicates to plot. Default is the first 10 reps.
#
# Other Diffusion Parameters:
#  --deltaT DELTAT       Unit increment of time (in generations).
#  --seed SD             Specify random seed.
#