static int promia_put(CHAR *fc, CHAR *fs, FILE *fo) {
uint nc, *mc;
if(mc = fmap(fc, &nc)) promia_put_local(mc, nc, fo);
if(fo = FOPENW(fs)) { fwrite(mc, 1, nc, fo); fclose(fo); }
mem_free(mc);
return 0;
}
int
main(int argc, char *argv[])
{
unsigned int i, n;
SIMULATION sim;
MCMC mcmc;
GraphvizCluster cluster; /* for the GRAPHVIZ output */
FILE *freqsout = NULL, *out = NULL, *pout = NULL;
time_t now;
/* make the cursor visible again when user killed FRANz */
(void)signal(SIGABRT, &sighandler);
(void)signal(SIGTERM, &sighandler);
(void)signal(SIGINT, &sighandler);
#ifndef NDEBUG
WARN("Reconfigure without --enable-assertions for optimal performance!");
#endif
(void)time(&Data.StartTime);
/* Load default and specified options and data */
OPTIONSinit();
CMDLINEparse(argc, argv);
DATAIOinfile(Options.Infilename);
/* load coordinates of sampling locations if available */
if (strlen(Options.Coordfilename) > 0)
DATAIOgeofile(Options.Coordfilename, false);
/* and/or use user provided distances of sampling locations */
if (strlen(Options.Geofilename) > 0)
DATAIOgeofile(Options.Geofilename, true);
/* use frequency file, otherwise calculate allele frequencies */
if (strlen(Options.FreqInfilename) > 0)
DATAIOfreqfile(Options.FreqInfilename, 0);
else {
FREQcalcAlleleFrequencies();
/* and then dump the frequencies in our own format */
FOPENW(freqsout, Options.FreqOutfilename);
FREQdump(freqsout);
FCLOSE(freqsout);
}
/* load prior pedigree (known mothers, sub-pedigrees) */
if (strlen(Options.PedigreeInfilename) > 0)
DATAIOinitInpedigree();
/* load known fullsibs if available */
if (strlen(Options.FullsibInfilename) > 0)
DATAIOfullsibFile(Options.FullsibInfilename);
/* create n random number streams, one for each thread */
#ifdef HAVE_OPENMP
n = omp_get_max_threads();
#else
n = 1;
#endif
VTPROGRESSBARinit(PROGRESSBARSIZE);
SRAND(Options.Seed, i, n);
/* calculate the loci summary statistics */
FREQcalcSummaryStatistics();
/* simulate the sampling (mismatch distributions, IBD deltas) */
sim = SIMstart();
FOPENW(out, Options.SimulationOutfilename);
SIMdumpDetailed(out, sim);
FCLOSE(out);
/* Calculate probabilities of all parents-offspring triples *
* and dyads with the allowed number of mismatches */
PROBcalcTriplesAndDyads();
/* This now generates an efficient data structure with the *
* likelihoods of all possible arcs in the pedigree. It also *
* filters very unlikely parentages. */
PROBcalcPosteriors();
/* Now we know all candidate parents, so we can create the
* CERVUS output */
if (strlen(Options.GenotypeOutfilenameCERVUS) > 0)
DATAIOdumpGenotypesCERVUS();
if (strlen(Options.OffspringOutfilenameCERVUS) > 0)
DATAIOdumpOffspringCERVUS();
if (strlen(Options.GenotypeOutfilenameGenepop) > 0)
DATAIOdumpGenotypesGenepop();
if (strlen(Options.GenotypeOutfilenameRMES) > 0)
DATAIOdumpGenotypesRMES();
if (strlen(Options.GenotypeOutfilenamePARENTE) > 0)
DATAIOdumpGenotypesParente();
/* Create the summary.txt file */
FOPENW(out, Options.Outfilename);
DATAIOdumpDatasetDetails(out);
FREQdumpSummaryStatistics(out);
OPTIONSdump(out);
DATAIOcheckData(out);
if (Data.num_populations > 1)
DATAIOdumpSamplingLocations(out);
SIMdump(out, sim);
/* Cleanup memory */
SIMdestroy(sim);
PROBdestroyPreMCMC();
DATAIOdestroyPreMCMC();
FREQdestroyPreMCMC();
mcmc = MCMCinit();
if (!Options.NoReconstruction) {
/* now start MCMC chains */
MCMCstart(&mcmc);
if (Options.PedigreeOutformat[1]) {
/* output DAG, cluster sampling locations in graphviz output */
cluster = DATAIOgraphvizCluster();
/* display meta data in graphviz output */
DATAIOaddGVNodeStyle(mcmc.best.D);
DAGgraphviz(mcmc.best.D, Options.PedigreeOutfilename[1], cluster, true);
DATAIOgraphvizClusterDestroy(cluster);
}
/* --pedigreeincheck compares our results with the true pedigree */
MCMCcheckML(&mcmc);
MCMCdumpResults(out, &mcmc);
}
/* write parentage files */
for (i = 0; i < 2; i++)
if (Options.POutformat[i]) {
FOPENW(pout, Options.POutfilename[i]);
PROBdumpPosteriors(pout, Probs.posteriors, mcmc.best.D,
mcmc.D_true, i);
FCLOSE(pout);
}
/* output pedigree in our input format */
if (Options.PedigreeOutformat[0])
DATAIOpedigreeout(Options.PedigreeOutfilename[0], mcmc.best.D);
if (Options.PedigreeOutformat[2])
DATAIOpedigreeoutText(Options.PedigreeOutfilename[2], mcmc.best.D);
(void)time(&now);
fprintf(out, "\nRunning Time : %d sec.\n", (unsigned int)( now - Data.StartTime));
FCLOSE(out);
DATAIOdumpMismatches();
MCMCdestroy(mcmc);
PROBdestroyPostMCMC();
DATAIOdestroyPostMCMC();
FREQdestroyPostMCMC();
RANDDESTROY(i, n);
VTPROGRESSBARcursorVisible();
exit(EXIT_SUCCESS);
}
