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parse_args.cpp
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parse_args.cpp
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#include <getopt.h>
#include "ngsDist.hpp"
void init_pars(params *pars) {
pars->in_geno = NULL;
pars->in_bin = false;
pars->in_probs = false;
pars->in_logscale = false;
pars->n_ind = 0;
pars->n_sites = 0;
pars->tot_sites = 0;
pars->in_labels = NULL;
pars->in_labels_header = false;
pars->in_pos = NULL;
pars->in_pos_header = false;
pars->call_geno = false;
pars->N_thresh = 0;
pars->call_thresh = 0;
pars->pairwise_del = false;
// Distance score matrix based on:
// Gronau I et al. 2011 (eq 12)
// Freedman AH et al. 2014 (eq 8.1)
pars->score[0][0] = pars->score[1][1] = pars->score[2][2] = 0;
pars->score[0][1] = pars->score[1][0] = pars->score[1][2] = pars->score[2][1] = 0.5;
pars->score[0][2] = pars->score[2][0] = 1;
pars->evol_model = 1;
pars->indep_geno = false;
pars->n_boot_rep = 0;
pars->boot_block_size = 1;
pars->out = NULL;
pars->n_threads = 1;
pars->verbose = 1;
pars->seed = time(NULL);
pars->rnd_gen = NULL;
}
// Supported evolutionary models
const char* evol_model[] = {"Raw p-distance", // Raw p-distance
"Log transf. p-distance", // Logarithmic transformed p-distance
"JC69",
"K80", // JC69 + (transiton rates != transversions rates)
"F81", // JC69 + (base freqs != 0.25)
"HKY85/F84", // K80 + F81
"TN93", // HKY85/F84 + (A/G != T/C)
};
// Parses command line args and stores them into struct params
void parse_cmd_args(params* pars, int argc, char** argv) {
static struct option long_options[] =
{
{"geno", required_argument, NULL, 'g'},
{"probs", no_argument, NULL, 'p'},
{"log_scale", no_argument, NULL, 'l'},
{"n_ind", required_argument, NULL, 'n'},
{"n_sites", required_argument, NULL, 's'},
{"tot_sites", required_argument, NULL, 'S'},
{"labels", required_argument, NULL, 'L'},
{"labelsH", required_argument, NULL, 'H'},
{"pos", required_argument, NULL, 'a'},
{"posH", required_argument, NULL, 'A'},
{"call_geno", no_argument, NULL, 'c'},
{"N_thresh", required_argument, NULL, 'N'},
{"call_thresh", required_argument, NULL, 'C'},
{"pairwise_del", no_argument, NULL, 'D'},
{"avg_nuc_dist", no_argument, NULL, 'd'},
{"evol_model", required_argument, NULL, 'm'},
{"indep_geno", no_argument, NULL, 'I'},
{"n_boot_rep", required_argument, NULL, 'b'},
{"boot_block_size", required_argument, NULL, 'B'},
{"out", required_argument, NULL, 'o'},
{"n_threads", required_argument, NULL, 'x'},
{"verbose", required_argument, NULL, 'V'},
{"seed", required_argument, NULL, 'r'},
{0, 0, 0, 0}
};
int c = 0;
while ( (c = getopt_long_only(argc, argv, "g:pln:s:S:a:A:L:H:cN:C:Ddm:Ib:B:o:x:V:r:", long_options, NULL)) != -1 )
switch (c) {
case 'g':
pars->in_geno = optarg;
break;
case 'p':
pars->in_probs = true;
break;
case 'l':
pars->in_logscale = true;
pars->in_probs = true;
break;
case 'n':
pars->n_ind = atol(optarg);
break;
case 's':
pars->n_sites = atol(optarg);
break;
case 'S':
pars->tot_sites = atol(optarg);
break;
case 'L':
pars->in_labels = optarg;
pars->in_labels_header = false;
break;
case 'H':
pars->in_labels = optarg;
pars->in_labels_header = true;
break;
case 'a':
pars->in_pos = optarg;
pars->in_pos_header = false;
break;
case 'A':
pars->in_pos = optarg;
pars->in_pos_header = true;
break;
case 'c':
pars->call_geno = true;
break;
case 'N':
pars->N_thresh = atof(optarg);
pars->call_geno = true;
break;
case 'C':
pars->call_thresh = atof(optarg);
pars->call_geno = true;
break;
case 'D':
pars->pairwise_del = true;
break;
case 'd':
// Freedman AH et al. 2014 (eq 8.2)
pars->score[1][1] = 0.5;
break;
case 'm':
pars->evol_model = atol(optarg);
break;
case 'I':
pars->indep_geno = true;
break;
case 'b':
pars->n_boot_rep = atol(optarg);
break;
case 'B':
pars->boot_block_size = atol(optarg);
break;
case 'o':
pars->out = optarg;
break;
case 'x':
pars->n_threads = atoi(optarg);
break;
case 'V':
pars->verbose = atoi(optarg);
break;
case 'r':
pars->seed = atoi(optarg);
break;
default:
exit(-1);
}
if(pars->verbose >= 1) {
fprintf(stderr, "==> Input Arguments:\n");
fprintf(stderr, "\tgeno: %s\n\tprobs: %s\n\tlog_scale: %s\n\tn_ind: %lu\n\tn_sites: %lu\n\ttot_sites: %lu\n\tlabels: %s (%s header)\n\tpositions: %s (%s header)\n\tcall_geno: %s\n\tN_thresh: %f\n\tcall_thresh: %f\n\tpairwise_del: %s\n\tavg_nuc_dist: %s\n\tevol_model: %s\n\tgeno_indep: %s\n\tn_boot_rep: %lu\n\tboot_block_size: %lu\n\tout: %s\n\tn_threads: %d\n\tverbose: %d\n\tseed: %d\n\tversion: %s (%s @ %s)\n\n",
pars->in_geno,
pars->in_probs ? "true":"false",
pars->in_logscale ? "true":"false",
pars->n_ind,
pars->n_sites,
pars->tot_sites,
pars->in_labels,
pars->in_labels_header ? "WITH" : "WITHOUT",
pars->in_pos,
pars->in_pos_header ? "WITH" : "WITHOUT",
pars->call_geno ? "true":"false",
pars->N_thresh,
pars->call_thresh,
pars->pairwise_del ? "true":"false",
pars->score[1][1] == 0.5 ? "true":"false",
evol_model[pars->evol_model],
pars->indep_geno ? "true":"false",
pars->n_boot_rep,
pars->boot_block_size,
pars->out,
pars->n_threads,
pars->verbose,
pars->seed,
version, __DATE__, __TIME__);
}
if(pars->verbose > 4)
fprintf(stderr, "==> Verbose values greater than 4 for debugging purpose only. Expect large amounts of info on screen\n");
/////////////////////
// Check Arguments //
/////////////////////
if(pars->in_geno == NULL)
error(__FUNCTION__, "genotype input file (--geno) missing!");
if(pars->n_ind == 0)
error(__FUNCTION__, "number of individuals (--n_ind) missing!");
if(pars->n_sites == 0)
error(__FUNCTION__, "number of sites (--n_sites) missing!");
if(pars->tot_sites > 0 && pars->pairwise_del)
error(__FUNCTION__, "cannot specify total number of sites (--tot_sites) with pairwise deletion (--pairwise_del)!");
if(pars->call_geno && !pars->in_probs)
error(__FUNCTION__, "can only call genotypes from likelihoods/probabilities!");
if(pars->evol_model < 0 || pars->evol_model > 6)
error(__FUNCTION__, "invalid correction method specified!");
if(pars->evol_model > 2 && pars->in_pos == NULL)
error(__FUNCTION__, "use of more complex evolutionary models requires position information!");
if(pars->out == NULL)
error(__FUNCTION__, "output prefix (--out) missing!");
if(pars->n_threads < 1)
error(__FUNCTION__, "number of threads cannot be less than 1!");
}