fml_utg_t *fml_assemble(const fml_opt_t *opt0, int n_seqs, bseq1_t *seqs, int *n_utg)
{
rld_t *e;
mag_t *g;
fml_utg_t *utg;
fml_opt_t opt = *opt0;
float kcov;
*n_utg = 0;
fml_opt_adjust(&opt, n_seqs, seqs);
if (opt.ec_k >= 0) fml_correct(&opt, n_seqs, seqs);
kcov = fml_fltuniq(&opt, n_seqs, seqs);
e = fml_seq2fmi(&opt, n_seqs, seqs);
if (e == 0) return 0; // this may happen when all sequences are filtered out
g = fml_fmi2mag(&opt, e);
opt.mag_opt.min_ensr = opt.mag_opt.min_ensr > kcov * MAG_MIN_NSR_COEF? opt.mag_opt.min_ensr : (int)(kcov * MAG_MIN_NSR_COEF + .499);
opt.mag_opt.min_ensr = opt.mag_opt.min_ensr < opt0->max_cnt? opt.mag_opt.min_ensr : opt0->max_cnt;
opt.mag_opt.min_ensr = opt.mag_opt.min_ensr > opt0->min_cnt? opt.mag_opt.min_ensr : opt0->min_cnt;
opt.mag_opt.min_insr = opt.mag_opt.min_ensr - 1;
fml_mag_clean(&opt, g);
utg = fml_mag2utg(g, n_utg);
return utg;
}
int main(int argc, char **argv)
{
fml_opt_t options;
bseq1_t *seqs = NULL;
PONE_READ reads = NULL;
size_t readCount = 0;
ERR_VALUE ret = ERR_INTERNAL_ERROR;
fml_opt_init(&options);
options.n_threads = omp_get_num_procs();
options.ec_k = 31;
utils_allocator_init(options.n_threads);
fprintf(stderr, "Loading reads from %s...\n", argv[1]);
ret = input_get_reads(argv[1], "sam", &reads, &readCount);
if (ret == ERR_SUCCESS) {
fprintf(stderr, "Converting to fermi-lite format...\n");
ret = utils_calloc(readCount, sizeof(bseq1_t), &seqs);
if (ret == ERR_SUCCESS) {
for (size_t i = 0; i < readCount; ++i) {
memset(seqs + i, 0, sizeof(seqs[i]));
seqs[i].l_seq = reads[i].ReadSequenceLen;
read_quality_encode(reads + i);
seqs[i].seq = _copy_string(reads[i].ReadSequence, reads[i].ReadSequenceLen);
if (reads[i].Quality != NULL)
seqs[i].qual = _copy_string(reads[i].Quality, reads[i].QualityLen);
read_quality_decode(reads + i);
}
fml_opt_adjust(&options, readCount, seqs);
fprintf(stderr, "Correcting...\n");
fml_correct(&options, readCount, seqs);
fprintf(stderr, "Fitting unique k-mers...\n");
fml_fltuniq(&options, readCount, seqs);
fprintf(stderr, "Converting back to our format...\n");
for (size_t i = 0; i < readCount; ++i) {
if (reads[i].ReadSequenceLen != seqs[i].l_seq) {
utils_copy_string("*", &reads[i].CIGAR);
reads[i].CIGARLen = 1;
}
reads[i].ReadSequenceLen = seqs[i].l_seq;
reads[i].QualityLen = seqs[i].l_seq;
ret = utils_copy_string(seqs[i].seq, &reads[i].ReadSequence);
if (ret == ERR_SUCCESS)
ret = utils_copy_string(seqs[i].qual, &reads[i].Quality);
for (size_t j = 0; j < reads[i].ReadSequenceLen; ++j)
reads[i].ReadSequence[j] = toupper(reads[i].ReadSequence[j]);
if (reads[i].ReadSequenceLen > 0 && reads[i].QualityLen > 0)
read_write_sam(stdout, reads + i);
read_quality_decode(reads + i);
}
fprintf(stderr, "Freeing fermi-lite resources...\n");
utils_free(seqs);
}
fprintf(stderr, "Freeing our reads...\n");
read_set_destroy(reads, readCount);
}
return 0;
}
