static void *worker_pipeline(void *shared, int step, void *_data)
{
int i;
ta_opt_t *opt = (ta_opt_t*)shared;
if (step == 0) {
data_for_t *ret;
ret = calloc(1, sizeof(data_for_t));
ret->seqs = bseq_read(opt->ks, opt->chunk_size, &ret->n_seqs);
ret->opt = opt;
if (ret->seqs) return ret;
else free(ret);
} else if (step == 1) {
data_for_t *data = (data_for_t*)_data;
kt_for(opt->n_threads, worker_for, data, data->n_seqs);
return data;
} else if (step == 2) {
data_for_t *data = (data_for_t*)_data;
for (i = 0; i < data->n_seqs; ++i) {
bseq1_t *s = &data->seqs[i];
putchar(s->qual? '@' : '>'); puts(s->name);
puts(s->seq);
if (s->qual) {
puts("+"); puts(s->qual);
}
free(s->seq); free(s->qual); free(s->name);
}
free(data->seqs); free(data);
}
return 0;
}
int main(int argc, char *argv[])
{
fml_opt_t opt;
int c, n_seqs, n_utg, gfa_out = 0;
bseq1_t *seqs;
fml_utg_t *utg;
fml_opt_init(&opt);
while ((c = getopt(argc, argv, "gOAe:l:r:t:c:d:v:")) >= 0) {
if (c == 'e') opt.ec_k = atoi(optarg);
else if (c == 'l') opt.min_asm_ovlp = atoi(optarg);
else if (c == 'r') opt.mag_opt.min_dratio1 = atof(optarg);
else if (c == 'A') opt.mag_opt.flag |= MAG_F_AGGRESSIVE;
else if (c == 'O') opt.mag_opt.flag &= ~MAG_F_POPOPEN;
else if (c == 'd') opt.mag_opt.max_bdiff = atoi(optarg);
else if (c == 't') opt.n_threads = atoi(optarg);
else if (c == 'g') gfa_out = 1;
else if (c == 'v') fm_verbose = atoi(optarg);
else if (c == 'c') {
char *p;
opt.min_cnt = strtol(optarg, &p, 10);
if (*p == ',') opt.max_cnt = strtol(p + 1, &p, 10);
}
}
if (argc == optind) {
fprintf(stderr, "Usage: fml-asm [options] <in.fq>\n");
fprintf(stderr, "Options:\n");
fprintf(stderr, " -e INT k-mer length for error correction (0 for auto; -1 to disable) [%d]\n", opt.ec_k);
fprintf(stderr, " -c INT1[,INT2] range of k-mer & read count thresholds for ec and graph cleaning [%d,%d]\n", opt.min_cnt, opt.max_cnt);
fprintf(stderr, " -l INT min overlap length during initial assembly [%d]\n", opt.min_asm_ovlp);
fprintf(stderr, " -r FLOAT drop an overlap if its length is below maxOvlpLen*FLOAT [%g]\n", opt.mag_opt.min_dratio1);
fprintf(stderr, " -t INT number of threads (don't use multi-threading for small data sets) [%d]\n", opt.n_threads);
fprintf(stderr, " -d INT retain a bubble if one side is longer than the other side by >INT-bp [%d]\n", opt.mag_opt.max_bdiff);
fprintf(stderr, " -A discard heterozygotes (apply this to assemble bacterial genomes; override -O)\n");
fprintf(stderr, " -O don't apply aggressive tip trimming\n");
fprintf(stderr, " -g output the assembly graph in the GFA format\n");
return 1;
}
seqs = bseq_read(argv[optind], &n_seqs);
utg = fml_assemble(&opt, n_seqs, seqs, &n_utg);
if (!gfa_out) fml_utg_print(n_utg, utg);
else fml_utg_print_gfa(n_utg, utg);
fml_utg_destroy(n_utg, utg);
return 0;
}
int main(int argc, char *argv[])
{
fml_opt_t opt;
int c, n_seqs, n_utg;
bseq1_t *seqs;
fml_utg_t *utg;
fml_opt_init(&opt);
while ((c = getopt(argc, argv, "Ae:l:r:t:c:")) >= 0) {
if (c == 'e') opt.ec_k = atoi(optarg);
else if (c == 'l') opt.min_asm_ovlp = atoi(optarg);
else if (c == 'r') opt.mag_opt.min_dratio1 = atof(optarg);
else if (c == 'A') opt.mag_opt.flag |= MAG_F_AGGRESSIVE;
else if (c == 't') opt.n_threads = atoi(optarg);
else if (c == 'c') {
char *p;
opt.min_cnt = strtol(optarg, &p, 10);
if (*p == ',') opt.max_cnt = strtol(p + 1, &p, 10);
}
}
if (argc == optind) {
fprintf(stderr, "Usage: fml-asm [options] <in.fq>\n");
fprintf(stderr, "Options:\n");
fprintf(stderr, " -e INT k-mer length for error correction (0 for auto; -1 to disable) [%d]\n", opt.ec_k);
fprintf(stderr, " -c INT1[,INT2] range of k-mer & read count thresholds for ec and graph cleaning [%d,%d]\n", opt.min_cnt, opt.max_cnt);
fprintf(stderr, " -l INT min overlap length during initial assembly [%d]\n", opt.min_asm_ovlp);
fprintf(stderr, " -r FLOAT drop an overlap if its length is below maxOvlpLen*FLOAT [%g]\n", opt.mag_opt.min_dratio1);
fprintf(stderr, " -t INT number of threads (don't use multi-threading for small data sets) [%d]\n", opt.n_threads);
fprintf(stderr, " -A discard heterozygotes (apply this to assemble bacterial genomes)\n");
return 1;
}
seqs = bseq_read(argv[optind], &n_seqs);
utg = fml_assemble(&opt, n_seqs, seqs, &n_utg);
fml_utg_print(n_utg, utg);
fml_utg_destroy(n_utg, utg);
return 0;
}
