int main_polysomy(int argc, char *argv[])
{
args_t *args = (args_t*) calloc(1,sizeof(args_t));
args->argc = argc; args->argv = argv;
args->nbins = 150;
args->fit_th = 3.3;
args->cn_penalty = 0.7;
args->peak_symmetry = 0.5;
args->min_peak_size = 0.1;
args->ra_rr_scaling = 1;
args->min_fraction = 0.1;
args->smooth = -3;
static struct option loptions[] =
{
{"ra-rr-scaling",0,0,1}, // hidden option
{"force-cn",1,0,2}, // hidden option
{"smooth",1,0,'S'}, // hidden option
{"nbins",1,0,'n'}, // hidden option
{"include-aa",0,0,'i'},
{"peak-size",1,0,'b'},
{"min-fraction",1,0,'m'},
{"verbose",0,0,'v'},
{"fit-th",1,0,'f'},
{"cn-penalty",1,0,'c'},
{"peak-symmetry",1,0,'p'},
{"output-dir",1,0,'o'},
{"sample",1,0,'s'},
{"targets",1,0,'t'},
{"targets-file",1,0,'T'},
{"regions",1,0,'r'},
{"regions-file",1,0,'R'},
{0,0,0,0}
};
char *tmp;
int c;
while ((c = getopt_long(argc, argv, "h?o:vt:T:r:R:s:f:p:c:im:b:n:S:",loptions,NULL)) >= 0)
{
switch (c)
{
case 1 : args->ra_rr_scaling = 0; break;
case 2 : args->force_cn = atoi(optarg); break;
case 'n': args->nbins = atoi(optarg); break;
case 'S': args->smooth = atoi(optarg); break;
case 'i': args->include_aa = 1; break;
case 'b':
args->min_peak_size = strtod(optarg,&tmp);
if ( *tmp ) error("Could not parse: -b %s\n", optarg);
if ( args->min_peak_size<0 || args->min_peak_size>1 ) error("Range error: -b %s\n", optarg);
break;
case 'm':
args->min_fraction = strtod(optarg,&tmp);
if ( *tmp ) error("Could not parse: -n %s\n", optarg);
if ( args->min_fraction<0 || args->min_fraction>1 ) error("Range error: -n %s\n", optarg);
break;
case 'f':
args->fit_th = strtod(optarg,&tmp);
if ( *tmp ) error("Could not parse: -f %s\n", optarg);
break;
case 'p':
args->peak_symmetry = strtod(optarg,&tmp);
if ( *tmp ) error("Could not parse: -p %s\n", optarg);
break;
case 'c':
args->cn_penalty = strtod(optarg,&tmp);
if ( *tmp ) error("Could not parse: -c %s\n", optarg);
break;
case 's': args->sample = optarg; break;
case 't': args->targets_list = optarg; break;
case 'T': args->targets_list = optarg; args->targets_is_file = 1; break;
case 'r': args->regions_list = optarg; break;
case 'R': args->regions_list = optarg; args->regions_is_file = 1; break;
case 'o': args->output_dir = optarg; break;
case 'v': args->verbose++; break;
default: usage(args); break;
}
}
if ( optind>=argc )
{
if ( !isatty(fileno((FILE *)stdin)) ) args->fname = "-";
}
else args->fname = argv[optind];
if ( !args->fname ) usage(args);
if ( !args->output_dir ) error("Missing the -o option\n");
init_data(args);
fit_curves(args);
destroy_data(args);
free(args);
return 0;
}
int main_polysomy(int argc, char *argv[])
{
args_t *args = (args_t*) calloc(1,sizeof(args_t));
args->argc = argc; args->argv = argv;
args->nbins = 150;
args->fit_th = 3.0;
args->cn_penalty = 0.7;
args->peak_symmetry = 0.7;
static struct option loptions[] =
{
{"verbose",0,0,'v'},
{"fit-th",1,0,'f'},
{"cn-penalty",1,0,'c'},
{"peak-symmetry",1,0,'p'},
{"output-dir",1,0,'o'},
{"sample",1,0,'s'},
{"targets",1,0,'t'},
{"targets-file",1,0,'T'},
{"regions",1,0,'r'},
{"regions-file",1,0,'R'},
{0,0,0,0}
};
char c, *tmp;
while ((c = getopt_long(argc, argv, "h?o:vt:T:r:R:s:f:p:c:",loptions,NULL)) >= 0)
{
switch (c)
{
case 'f':
args->fit_th = strtod(optarg,&tmp);
if ( *tmp ) error("Could not parse: -f %s\n", optarg);
break;
case 'p':
args->peak_symmetry = strtod(optarg,&tmp);
if ( *tmp ) error("Could not parse: -p %s\n", optarg);
break;
case 'c':
args->cn_penalty = strtod(optarg,&tmp);
if ( *tmp ) error("Could not parse: -c %s\n", optarg);
break;
case 's': args->sample = optarg; break;
case 't': args->targets_list = optarg; break;
case 'T': args->targets_list = optarg; args->targets_is_file = 1; break;
case 'r': args->regions_list = optarg; break;
case 'R': args->regions_list = optarg; args->regions_is_file = 1; break;
case 'o': args->output_dir = optarg; break;
case 'v': args->verbose = 1; break;
default: usage(args); break;
}
}
if ( optind>=argc )
{
if ( !isatty(fileno((FILE *)stdin)) ) args->fname = "-";
}
else args->fname = argv[optind];
if ( !args->fname ) usage(args);
if ( !args->output_dir ) error("Missing the -o option\n");
init_data(args);
fit_curves(args);
destroy_data(args);
free(args);
return 0;
}
