int compare_regions(void *region_1, void *region_2, char **chromosome_ordering, int num_chromosomes) {
if (region_1 == NULL || region_2 == NULL) {
return INT_MIN;
}
region_t *reg_1 = (region_t *) region_1;
region_t *reg_2 = (region_t *) region_2;
// TODO This could be avoided while inserting, because regions are classified by chromosome
int result = compare_chromosomes(reg_1->chromosome, reg_2->chromosome, chromosome_ordering, num_chromosomes);
if (result != 0) {
return result;
} else {
// return compare_position_ranges(reg_1, reg_2);
return compare_positions(reg_1->start_position, reg_2->start_position);
}
}
int merge_interval(kh_pos_t* positions_read, char *max_chromosome_merged, unsigned long max_position_merged,
char **chromosome_order, int num_chromosomes, vcf_file_t **files,
shared_options_data_t *shared_options_data, merge_options_data_t *options_data, list_t *output_list) {
int num_entries = 0;
#pragma omp parallel for num_threads(shared_options_data->num_threads) reduction(+:num_entries)
for (int k = kh_begin(positions_read); k < kh_end(positions_read); k++) {
if (kh_exist(positions_read, k)) {
array_list_t *records_in_position = kh_value(positions_read, k);
assert(records_in_position);
vcf_record_t *record = ((vcf_record_file_link*) array_list_get(0, records_in_position))->record;
vcf_record_file_link **links = NULL;
int num_links = 0;
// Remove positions prior to the last chromosome:position to merge
int cmp_chrom = compare_chromosomes(record->chromosome, max_chromosome_merged, chromosome_order, num_chromosomes);
if (cmp_chrom < 0 || (cmp_chrom == 0 && compare_positions(record->position, max_position_merged) <= 0)) {
links = records_in_position->items;
num_links = records_in_position->size;
}
// Launch merge
if (num_links > 0) {
// printf("links[0] = %s:%ld in file %s\n", links[0]->record->chromosome, links[0]->record->position, links[0]->file->filename);
int err_code = 0;
vcf_record_t *merged = merge_position(links, num_links, files, options_data->num_files, options_data, &err_code);
if (!err_code) {
list_item_t *item = list_item_new(k, MERGED_RECORD, merged);
list_insert_item(item, output_list);
num_entries += 1;
}
// Free empty nodes (lists of records in the same position)
array_list_free(records_in_position, vcf_record_file_link_free);
kh_del(pos, positions_read, k);
}
} // End kh_exist
}
return num_entries;
}
void calculate_merge_interval(vcf_record_t* current_record, char** max_chromosome_merged, long unsigned int* max_position_merged,
char **chromosome_order, int num_chromosomes) {
if (*max_chromosome_merged == NULL) {
// Max merged chrom:position not set, assign without any other consideration
*max_chromosome_merged = strndup(current_record->chromosome, current_record->chromosome_len);
*max_position_merged = current_record->position;
} else {
char *current_chromosome = strndup(current_record->chromosome, current_record->chromosome_len);
long unsigned int current_position = current_record->position;
// printf("current = %s:%ld\tmax = %s:%ld\n", current_chromosome, current_position, *max_chromosome_merged, *max_position_merged);
int chrom_comparison = compare_chromosomes(current_chromosome, *max_chromosome_merged, chromosome_order, num_chromosomes);
int position_comparison = compare_positions(current_position, *max_position_merged);
// Max merged chrom:position is posterior to the last one in this batch
if (chrom_comparison < 0 || (chrom_comparison == 0 && position_comparison < 0)) {
*max_chromosome_merged = current_chromosome;
*max_position_merged = current_position;
} else {
assert(current_chromosome);
free(current_chromosome);
}
}
}
int main(int argc, char ** argv){
MPI_Init(&argc,&argv);
particle thing1,thing2;
int nEach = 5;
particle things1[nEach];
particle things2[nEach];
int i;
MPI_Status status_ignore;
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &size);
if(size != 1){
printf("%d/%d: too many processes\n", rank, size);
MPI_Finalize();
return 1;
}
//MPI_Datatype MPI_particle;
create_MPI_struct(&MPI_particle);
MPI_Type_commit(&MPI_particle);
double epsilon = DBL_EPSILON;
double min = DBL_MIN;
printf("epsilon = %g\n", epsilon);
printf("dbl min = %g\n", min);
for(i=0;i<nEach;i++){
basicParticle(things1+i);
basicParticle(things2+i);
}
printf("things1 \n");
fprintParticles(stdout, things1,nEach);
printf("things2 \n");
fprintParticles(stdout, things2,nEach);
double diff, diffx, diffv, diffa;
diff = compareMultipleParticles(things1, things2, nEach);
printf("total diff of %d = %g\t expected 0\n", nEach, diff);
diffx = compare_positions(things1, things2);
printf("pos diff of %d = %g\t expected 0\n", 1, diffx);
diffv = compare_positions(things1, things2);
printf("vel diff of %d = %g\t expected 0\n", 1, diffv);
diffa = compare_positions(things1, things2);
printf("acc diff of %d = %g\t expected 0\n", 1, diffa);
printf("\nchanging the values of stuff\n");
printf("0 and 1\t expected ~1/eps = %g\n",1/epsilon);
things1[0].x = 0;
things2[0].x = 1;
diff = compareMultipleParticles(things1, things2, nEach);
printf("total diff of %d = %g\n", nEach, diff);
diffx = compare_positions(things1, things2);
printf("pos diff of %d = %g\n", 1, diffx);
printf("\n0 and dbl_min\t expected 0\n");
things1[0].x = 0;
things2[0].x = min;
diff = compareMultipleParticles(things1, things2, nEach);
printf("total diff of %d = %g\n", nEach, diff);
diffx = compare_positions(things1, things2);
printf("pos diff of %d = %g\n", 1, diffx);
printf("\n0 and eps\t expected 1/eps = %g\n", 1/epsilon);
things2[0].x = epsilon;
diff = compareMultipleParticles(things1, things2, nEach);
printf("total diff of %d = %g\n", nEach, diff);
diffx = compare_positions(things1, things2);
printf("pos diff of %d = %g\n", 1, diffx);
printf("\n1 and 1+eps\t expected 0\n");
things1[0].x = 1;
things2[0].x = 1+ epsilon;
diff = compareMultipleParticles(things1, things2, nEach);
printf("total diff of %d = %g\n", nEach, diff);
diffx = compare_positions(things1, things2);
printf("pos diff of %d = %g\n", 1, diffx);
printf("\n1^20 and 10^20+eps*10^20\t expected 0\n");
things1[0].x = 1E20;
things2[0].x = 1E20 + 1E20 * epsilon;
diff = compareMultipleParticles(things1, things2, nEach);
printf("total diff of %d = %g\n", nEach, diff);
diffx = compare_positions(things1, things2);
printf("pos diff of %d = %g\n", 1, diffx);
double y;
printf("\ncomparing 1 and 1+y, expect eps*10\n");
things2[0].x = 1;
for(y = 10;y>0;y*=0.5){
things1[0]. x = 1+y;
diffx = compare_positions(things1, things2);
if(diffx == 0){
printf("at y = %g, 1+y compares equal to 1\n", y);
break;
}
}
printf("\ncomparing 0 and y, expect min*10\n");
things2[0].x = 0;
for(y = 10;y>0;y*=0.5){
things1[0]. x = y;
diffx = compare_positions(things1, things2);
if(diffx == 0){
printf("at y = %g, y compares equal to 0\n", y);
break;
}
}
printf("x position compared\n");
MPI_Type_free(&MPI_particle);
MPI_Finalize();
return 0;
}
