int main(int argc, char **argv) {
byte_vector B;
vector C;
comp_matrix O;
comp_vector S, Scomp, R, Rcomp;
if (argc!=3) {
printf("Syntax:\n\t%s input_dir nucleotides\n", argv[0]);
return 1;
}
timevars();
initReplaceTable(argv[2]);
tic("Loading data structures from input directory");
readUIntVector(&C, argv[1], "C");
readCompMatrix(&O, argv[1], "O");
readCharVector(&B, argv[1], "B");
readUIntCompVector(&S, argv[1], "S");
readUIntCompVector(&Scomp, argv[1], "Scomp");
readUIntCompVector(&R, argv[1], "R");
readUIntCompVector(&Rcomp, argv[1], "Rcomp");
toc();
for (unsigned int i=0; i<S.n; i++) {
if (getScompValue(i, &Scomp, &C, &O) != S.vector[i]) {
printf("S diferent!\n");
}
if (getRcompValue(i, &Rcomp, &C, &O) != R.vector[i]) {
printf("R diferent!\n");
}
}
printf("Memory frees\n");
free(B.vector);
free(S.vector);
free(Scomp.vector);
free(R.vector);
free(Rcomp.vector);
return 0;
}
int main(int argc, char *argv[]) {
if (argc != 4) {
printf("Error.\n");
printf("Usage: %s index-dirname seq num-errors\n", argv[0]);
exit(-1);
}
char *index_dirname = argv[1];
char *seq = argv[2];
int num_errors = atoi(argv[3]);
// initializations
initReplaceTable();
bwt_optarg_t *bwt_optarg = bwt_optarg_new(num_errors, 1, 10000, 1, 0, 0);
bwt_index_t *bwt_index = bwt_index_new(index_dirname);
// seq
{
array_list_t *mapping_list = array_list_new(100000, 1.25f,
COLLECTION_MODE_SYNCHRONIZED);
size_t num_mappings;
num_mappings = bwt_map_seq(seq, bwt_optarg,
bwt_index, mapping_list);
printf("seq: %s\n", seq);
printf("num_mappings = %lu\n", num_mappings);
for (size_t i = 0; i < num_mappings; i++) {
printf("%lu\t---------------------\n", i);
alignment_print(array_list_get(i, mapping_list));
}
}
// seed
{
array_list_t *mapping_list = array_list_new(100000, 1.25f,
COLLECTION_MODE_SYNCHRONIZED);
size_t num_mappings;
size_t len = strlen(seq);
char *code_seq = (char *) calloc(len + 10, sizeof(char));
replaceBases(seq, code_seq, len);
num_mappings = bwt_map_exact_seeds_seq(code_seq, 18, 16,
bwt_optarg, bwt_index, mapping_list);
region_t *region;
for (size_t i = 0; i < num_mappings; i++) {
region = array_list_get(i, mapping_list);
printf("Region: chr = %lu, strand = %d, start = %lu, end = %lu\n",
region->chromosome_id, region->strand, region->start, region->end);
}
}
printf("Done.\n");
}
int main(int argc, char **argv) {
char *h_Worig, *h_We, *d_We;
unsigned int *h_nWe;
vector h_C, d_C, h_C1, d_C1;
comp_matrix h_O, d_O, h_Oi, d_Oi;
comp_vector h_S, h_Si, h_R, h_Ri;
blocked_results_lists rl_prev_cpu, rl_next_cpu, rl_prev_i_cpu, rl_next_i_cpu, rl_final_cpu;
blocked_results_lists rl_prev_gpu, rl_next_gpu, rl_prev_i_gpu, rl_next_i_gpu, rl_final_gpu;
results_list rl_prev, rl_next, rl_prev_i, rl_next_i, rl_final;
unsigned int read_index=0;
FILE *queries_file, *output_file;
int RESULTS, FRAGSIZE;
cudaError_t error;
if (argc!=7) {
printf("Syntax:\n\t%s search_file input_dir output_file results_buffer frag_size nucleotides\n", argv[0]);
return 1;
}
cudaSetDevice(0);
timevars();
initReplaceTable(argv[6]);
queries_file = fopen(argv[1], "r");
checkFileOpen(queries_file, argv[1]);
output_file = fopen(argv[3], "w");
checkFileOpen(output_file, argv[3]);
RESULTS = atoi(argv[4]);
FRAGSIZE = atoi(argv[5]);
if (FRAGSIZE <= 0) {
fprintf(stderr, "Fragsize must be greater than 0\n");
exit(1);
}
tic("Loading FM-Index");
readUIntVector(&h_C, argv[2], "C");
readUIntVector(&h_C1, argv[2], "C1");
readCompMatrixGPU(&h_O, argv[2], "O");
readCompMatrixGPU(&h_Oi, argv[2], "Oi");
readUIntCompVector(&h_S, argv[2], "Scomp");
readUIntCompVector(&h_Si, argv[2], "Scompi");
readUIntCompVector(&h_R, argv[2], "Rcomp");
readUIntCompVector(&h_Ri, argv[2], "Rcompi");
copyVectorGPU(&d_C, &h_C, sizeof(unsigned int));
copyVectorGPU(&d_C1, &h_C1, sizeof(unsigned int));
copyCompMatrixGPU(&d_O, &h_O);
copyCompMatrixGPU(&d_Oi, &h_Oi);
toc();
tic("Preparing search space");
load_exome_file(&ex, argv[2]);
declare_blocked_results_list_cpu(&rl_prev_cpu, RESULTS, MAX_BUS_GPU);
declare_blocked_results_list_cpu(&rl_prev_i_cpu, RESULTS, MAX_BUS_GPU);
declare_blocked_results_list_cpu(&rl_next_cpu, RESULTS, MAX_BUS_GPU);
declare_blocked_results_list_cpu(&rl_next_i_cpu, RESULTS, MAX_BUS_GPU);
declare_blocked_results_list_cpu(&rl_final_cpu, RESULTS, MAX_BUS_GPU);
declare_blocked_results_list_gpu(&rl_prev_gpu, RESULTS, MAX_BUS_GPU);
declare_blocked_results_list_gpu(&rl_prev_i_gpu, RESULTS, MAX_BUS_GPU);
declare_blocked_results_list_gpu(&rl_next_gpu, RESULTS, MAX_BUS_GPU);
declare_blocked_results_list_gpu(&rl_next_i_gpu, RESULTS, MAX_BUS_GPU);
declare_blocked_results_list_gpu(&rl_final_gpu, RESULTS, MAX_BUS_GPU);
toc();
h_Worig = (char*)malloc(MAX_BUS_GPU * MAXLINE * sizeof(char));
cudaMallocHost((void**) &h_We, MAX_BUS_GPU * MAXLINE * sizeof(char));
cudaMallocHost((void**) &h_nWe, MAX_BUS_GPU * sizeof(unsigned int));
cudaMalloc((void**) &d_We, MAX_READ_GPU * MAXLINE * sizeof(char));
manageCudaError();
int TAM_BUS_GPU=0, NUM_BLOQUES_GPU=0;
tic("Read mappings from disk");
while(nextFASTAToken(queries_file, h_Worig + TAM_BUS_GPU * MAXLINE, h_We + TAM_BUS_GPU * MAXLINE, h_nWe + TAM_BUS_GPU)) {
TAM_BUS_GPU++;
if (TAM_BUS_GPU == MAX_BUS_GPU) break;
}
toc();
NUM_BLOQUES_GPU = (TAM_BUS_GPU / TAM_BLOQUE_GPU);
if (TAM_BUS_GPU % TAM_BLOQUE_GPU) NUM_BLOQUES_GPU++;
cudaThreadSynchronize();
tic("CPU -> GPU");
cudaMemcpy(d_We, h_We, TAM_BUS_GPU * MAXLINE * sizeof(char), cudaMemcpyHostToDevice);
manageCudaError();
cudaThreadSynchronize();
toc();
cudaThreadSynchronize();
tic("GPU Kernel");
//cudaPrintfInit();
printf("%d %d\n", NUM_BLOQUES_GPU, TAM_BLOQUE_GPU);
BWSearchGPU(NUM_BLOQUES_GPU, TAM_BLOQUE_GPU, d_We, h_We, h_nWe[0], &d_C, &h_C, &d_C1, &h_C1, &d_O, &h_O, &d_Oi, &h_Oi, &h_S, &h_R, &h_Si, &h_Ri, &rl_prev_cpu, &rl_next_cpu, &rl_prev_i_cpu, &rl_next_i_cpu, &rl_final_cpu, &rl_prev_gpu, &rl_next_gpu, &rl_prev_i_gpu, &rl_next_i_gpu, &rl_final_gpu, FRAGSIZE, RESULTS);
/* cudaPrintfDisplay(stdout, true); */
/* cudaPrintfEnd(); */
cudaThreadSynchronize();
toc();
cudaThreadSynchronize();
tic("GPU -> CPU");
copy_blocked_results_list_cpu(&rl_final_cpu, &rl_final_gpu, RESULTS, TAM_BUS_GPU);
cudaThreadSynchronize();
toc();
//printf("%d\n", rl_final_cpu.num_results[0]);
write_blocked_results(&rl_final_cpu, &ex, &h_S, &h_Si, &h_C, &h_O, &h_Oi, h_Worig, h_nWe[0], 1, output_file, RESULTS, TAM_BUS_GPU, 0);
new_results_list(&rl_prev, RESULTS); new_results_list(&rl_prev_i, RESULTS);
new_results_list(&rl_next, RESULTS); new_results_list(&rl_next_i, RESULTS);
new_results_list(&rl_final, RESULTS);
tic("CPU kernel");
for(int i=0; i<MAX_BUS_GPU; i++) {
rl_prev.num_results = 0; rl_prev_i.num_results = 0;
rl_next.num_results = 0; rl_next_i.num_results = 0;
rl_final.num_results = 0;
rl_prev.read_index = read_index; rl_prev_i.read_index = read_index;
rl_next.read_index = read_index; rl_next_i.read_index = read_index;
rl_final.read_index = read_index;
BWSearchCPU(h_We + i*MAXLINE, h_nWe[0], &h_C, &h_C1, &h_O, &h_Oi, &h_S, &h_R, &h_Si, &h_Ri, &rl_prev, &rl_next, &rl_prev_i, &rl_next_i, &rl_final, FRAGSIZE, 1);
read_index++;
}
toc();
/*
for (int i=0; i<TAM_BUS_GPU; i++) {
for (int j=0; j<h_nWe[i]; j++) {
if (h_k[i*MAXLINE + j] != h_k2[i*MAXLINE + j]) {
printf("Diferente %d %d\n", i, j);
goto salir;
}
}
}
salir:
*/
/*
for (int i=0; i<h_nWe[0]; i++) {
printf("%u ", h_k[i]);
}
printf("\n");
printf("\n");
for (int i=0; i<h_nWe[0]; i++) {
printf("%u ", h_k2[i]);
}
printf("\n");
*/
cudaFreeHost(h_We);
cudaFreeHost(h_nWe);
cudaFree(d_We);
free(h_C.vector);
cudaFree(d_C.vector);
free(h_C1.vector);
cudaFree(d_C1.vector);
freeCompMatrixGPUHost(&h_O);
freeCompMatrixGPUDevice(&d_O);
freeCompMatrixGPUHost(&h_Oi);
freeCompMatrixGPUDevice(&d_Oi);
fclose(queries_file);
fclose(output_file);
return 0;
}
