int main(int argc, char *argv[])
{
int c, ec_k = -1, unitig_k = -1;
char *seq, *qual;
FILE *fp;
int64_t l;
while ((c = getopt(argc, argv, "k:l:")) >= 0) {
switch (c) {
case 'k': ec_k = atoi(optarg); break;
case 'l': unitig_k = atoi(optarg); break;
}
}
if (optind + 1 >= argc) {
fprintf(stderr, "Local assembler for small peak regions. Output cleaned unitigs.\nUsage: SAPPER_fermi [-k ecKmer] [-l utgKmer] <in.fq> <out.fq>\n");
return 1;
}
fp = fopen( argv[optind+1], "wb");
l = fm6_api_readseq(argv[optind], &seq, &qual);
fm6_api_correct(ec_k, l, seq, qual);
mag_t *g;
free(qual);
g = fm6_api_unitig(unitig_k, l, seq);
magopt_t *opt = mag_init_opt();
//opt->flag |= MOG_F_AGGRESSIVE | MOG_F_CLEAN;
opt->flag |= MOG_F_CLEAN;
opt->min_merge_len = 30;
mag_g_clean(g, opt);
free(opt);
mag_g_fprint(g, fp);
mag_g_destroy(g);
free(seq);
return 0;
}
void fml_opt_init(fml_opt_t *opt)
{
opt->n_threads = 1;
opt->ec_k = 0;
opt->min_cnt = 4;
opt->max_cnt = 8;
opt->min_asm_ovlp = 33;
opt->min_merge_len = 0;
mag_init_opt(&opt->mag_opt);
opt->mag_opt.flag = MAG_F_NO_SIMPL | MAG_F_POPOPEN;
}
