uint64_t read_chunk(double **chunk_data, params *pars, uint64_t chunk) {
uint64_t total_elems_read = 0;
if(chunk >= pars->n_chunks)
error("invalid chunk number!");
// Define chunk start and end positions
uint64_t start_pos = chunk * pars->max_chunk_size;
uint64_t end_pos = start_pos + pars->max_chunk_size - 1;
if(end_pos >= pars->n_sites) end_pos = pars->n_sites - 1;
uint64_t chunk_size = end_pos - start_pos + 1;
if( pars->verbose >= 6 ) printf("\tReading chunk %lu from position %lu to %lu (%lu)\n", chunk+1, start_pos, end_pos, chunk_size);
// Search start position
#ifdef _USE_BGZF
if( bgzf_seek(pars->in_glf_fh, pars->chunks_voffset[chunk], SEEK_SET) < 0 )
error("cannot seek GLF file (BGZF)!");
#endif
// Read data from file
for(uint64_t c = 0; c < chunk_size; c++) {
#ifdef _USE_BGZF
int bytes_read = bgzf_read(pars->in_glf_fh, chunk_data[c], (int) pars->n_ind * 3 * sizeof(double));
if(pars->call_geno)
call_geno(chunk_data[c], pars->n_ind, 3);
uint64_t elems_read = (uint64_t) bytes_read / sizeof(double);
#else
chunk_data[c] = pars->data[start_pos+c];
uint64_t elems_read = pars->n_ind * 3;
#endif
if( elems_read != pars->n_ind * 3 )
error("cannot read GLF file!");
total_elems_read += elems_read;
}
#ifdef _USE_BGZF
// Update index for next chunk
if( chunk+1 != pars->n_chunks && pars->chunks_voffset[chunk+1] == 0 )
pars->chunks_voffset[chunk+1] = bgzf_tell(pars->in_glf_fh);
#endif
return( total_elems_read/(pars->n_ind * 3) );
}
int main (int argc, char **argv) {
/////////////////////
// Parse Arguments //
/////////////////////
params *pars = new params;
init_pars(pars);
parse_cmd_args(argc, argv, pars);
if( pars->version ) {
printf("ngsF v%s\nCompiled on %s @ %s", version, __DATE__, __TIME__);
#ifdef _USE_BGZF
printf(" (BGZF library)\n");
#else
printf(" (STD library)\n");
#endif
exit(0);
}
if( pars->verbose >= 1 ) {
printf("==> Input Arguments:\n");
printf("\tglf file: %s\n\tinit_values: %s\n\tfreq_fixed: %s\n\tout file: %s\n\tn_ind: %d\n\tn_sites: %lu\n\tchunk_size: %lu\n\tfast_lkl: %s\n\tapprox_EM: %s\n\tcall_geno: %s\n\tmax_iters: %d\n\tmin_epsilon: %.10f\n\tn_threads: %d\n\tseed: %lu\n\tquick: %s\n\tversion: %s\n\tverbose: %d\n\n",
pars->in_glf, pars->init_values, pars->freq_fixed ? "true":"false", pars->out_file, pars->n_ind, pars->n_sites, pars->max_chunk_size, pars->fast_lkl ? "true":"false", pars->approx_EM ? "true":"false", pars->call_geno ? "true":"false", pars->max_iters, pars->min_epsilon, pars->n_threads, pars->seed, pars->quick ? "true":"false", version, pars->verbose);
}
if( pars->verbose > 4 ) printf("==> Verbose values greater than 4 for debugging purpose only. Expect large amounts of info on screen\n");
/////////////////////
// Check Arguments //
/////////////////////
if(pars->in_glf == NULL)
error(__FUNCTION__,"GL input file (-glf) missing!");
else if( strcmp(pars->in_glf, "-") == 0 ) {
pars->in_glf_type = new char[6];
pars->in_glf_type = strcat(pars->in_glf_type, "STDIN");
} else {
pars->in_glf_type = strrchr(pars->in_glf, '.');
if(pars->in_glf_type == NULL)
error(__FUNCTION__,"invalid file type!");
}
if(pars->out_file == NULL)
error(__FUNCTION__,"output file (-out) 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!");
///////////////////////
// Check input files //
///////////////////////
// Get file total size
struct stat st;
stat(pars->in_glf, &st);
if( strcmp(pars->in_glf_type, "STDIN") != 0 ) {
if( pars->n_sites == st.st_size/sizeof(double)/pars->n_ind/3 && strcmp(pars->in_glf_type, ".glf") == 0 ) {
if(pars->verbose >= 1)
printf("==> UNCOMP input file (\"%s\"): number of sites (%lu) match expected file size\n", pars->in_glf_type, pars->n_sites);
} else if( strcmp(pars->in_glf_type, ".glf") != 0 ) {
if( pars->verbose >= 1)
printf("==> COMPRESSED input file (\"%s\"): number of sites (%lu) do NOT match expected file size\n", pars->in_glf_type, pars->n_sites);
} else
error(__FUNCTION__,"wrong number of sites or invalid/corrupt file!");
}
// Adjust max_chunk_size in case of fewer sites
if(pars->max_chunk_size > pars->n_sites) {
if( pars->verbose >= 1 ) printf("==> Fewer sites (%lu) than chunk_size (%lu). Reducing chunk size to match number of sites\n", pars->n_sites, pars->max_chunk_size);
pars->max_chunk_size = pars->n_sites;
}
// Calculate total number of chunks
pars->n_chunks = ceil( (double) pars->n_sites/ (double) pars->max_chunk_size );
if( pars->verbose >= 1 ) printf("==> Analysis will be run in %ld chunk(s)\n", pars->n_chunks);
// Alocate memory for the chunk index
pars->chunks_voffset = new int64_t[pars->n_chunks];
memset(pars->chunks_voffset, 0, pars->n_chunks*sizeof(int64_t));
// Adjust thread number to chunks
if(pars->n_chunks < pars->n_threads) {
if( pars->verbose >= 1 ) printf("==> Fewer chunks (%ld) than threads (%d). Reducing the number of threads to match number of chunks\n", pars->n_chunks, pars->n_threads);
pars->n_threads = pars->n_chunks;
}
// Open input file
#ifdef _USE_BGZF
if( pars->verbose >= 1 ) printf("==> Using BGZF I/O library\n");
// Open BGZIP file
if( strcmp(pars->in_glf_type, ".bgz") == 0 ) {
if( (pars->in_glf_fh = bgzf_open(pars->in_glf, "rb")) < 0 )
error(__FUNCTION__,"Cannot open BGZIP file!");
} else
error(__FUNCTION__,"BGZF library only supports BGZIP files!");
bgzf_set_cache_size(pars->in_glf_fh, CACHE_SIZE * 1024uL * 1024uL * 1024uL);
#else
if( pars->verbose >= 1 ) printf("==> Using native I/O library\n");
// Open GLF file
if( strcmp(pars->in_glf_type, "STDIN") == 0 )
pars->in_glf_fh = stdin;
else if( strcmp(pars->in_glf_type, ".glf") == 0 ) {
if( (pars->in_glf_fh = fopen(pars->in_glf, "rb")) == NULL )
error(__FUNCTION__,"Cannot open GLF file!");
} else
error(__FUNCTION__,"Standard library only supports UNCOMPRESSED GLF files!");
// Allocate memory and read from the file
pars->data = new double* [pars->n_sites];
for(uint64_t s = 0; s < pars->n_sites; s++) {
pars->data[s] = new double[pars->n_ind * 3];
if( fread (pars->data[s], sizeof(double), pars->n_ind * 3, pars->in_glf_fh) != pars->n_ind * 3)
error(__FUNCTION__,"cannot read GLF file!");
if(pars->call_geno)
call_geno(pars->data[s], pars->n_ind, 3);
}
#endif
if( pars->in_glf_fh == NULL )
error(__FUNCTION__,"cannot open GLF file!");
///////////////////////////////////
// Declare variables for results //
///////////////////////////////////
out_data *output = new out_data;
output->site_freq = new double[pars->n_sites];
output->site_freq_num = new double[pars->n_sites];
output->site_freq_den = new double[pars->n_sites];
output->site_prob_var = new double[pars->n_sites];
output->site_tmpprob_var = new double[pars->n_sites];
output->indF = new double[pars->n_ind];
output->indF_num = new double[pars->n_ind];
output->indF_den = new double[pars->n_ind];
output->ind_lkl = new double[pars->n_ind];
// Initialize output
init_output(pars, output);
//////////////////
// Analyze Data //
//////////////////
if( pars->verbose >= 1 && !pars->fast_lkl && strcmp("e", pars->init_values) != 0 ) {
printf("==> Initial LogLkl: %.15f\n", full_HWE_like(pars, output->site_freq, output->indF, 0, pars->n_ind));
fflush(stdout);
}
do_EM(pars, output);
if( pars->verbose >= 1 ) printf("\nFinal logLkl: %f\n", output->global_lkl);
//////////////////
// Print Output //
//////////////////
FILE *out_file;
if( pars->verbose >= 1 ) printf("Printing Output...\n");
out_file = fopen(pars->out_file, "w");
if(out_file == NULL)
error(__FUNCTION__,"Cannot open OUTPUT file!");
for(uint16_t i = 0; i < pars->n_ind; i++)
fprintf(out_file,"%f\n", output->indF[i]);
fclose(out_file);
//////////////////////
// Close Input File //
//////////////////////
if( pars->verbose >= 1 ) printf("Exiting...\n");
#ifdef _USE_BGZF
bgzf_close(pars->in_glf_fh);
#else
for(uint64_t s = 0; s < pars->n_sites; s++)
delete [] pars->data[s];
delete [] pars->data;
fclose(pars->in_glf_fh);
#endif
/////////////////
// Free Memory //
/////////////////
delete [] output->site_freq;
delete [] output->site_freq_num;
delete [] output->site_freq_den;
delete [] output->site_prob_var;
delete [] output->indF;
delete [] output->indF_num;
delete [] output->indF_den;
delete [] output->ind_lkl;
delete output;
//if( strcmp("e", pars->init_values) == 0 )
//delete [] pars->init_values;
delete [] pars->chunks_voffset;
delete pars;
return 0;
}
