void FragmentList::freeFragList(Container* frags) {
for (uint32_t i = 0; i < bl_containerSize(frags); i++){
slmatch_t *sl = (slmatch_t *) bl_containerGet(frags, i);
if (sl->chain != nullptr){
std::cerr << "still at least one chain not freed before end: " << i << "\n";
exit(-1);
bl_slchainDestruct(sl->chain);
free(sl->chain);
}
}
bl_containerDestruct(frags, bl_slmatchDestruct);
free(frags);
}
void suffix_mng_create_cals(fastq_read_t *read, int min_area, int strand,
sa_index3_t *sa_index, array_list_t *cal_list,
suffix_mng_t *p) {
if (!p) return;
if (!p->suffix_lists) return;
if (p->num_seeds <= 0) return;
int read_area, chrom;
seed_t *seed;
seed_cal_t *cal;
linked_list_t *seed_list;
claspinfo_t info;
bl_claspinfoInit(&info);
// initialization
info.fragments = (Container *) malloc(sizeof(Container));
bl_containerInit(info.fragments, p->num_seeds, sizeof(slmatch_t));
info.subject = p->subject;
slmatch_t frag;
linked_list_t *suffix_list;
for (unsigned int i = 0; i < p->num_chroms; i++) {
suffix_list = p->suffix_lists[i];
if (suffix_list) {
for (linked_list_item_t *item = suffix_list->first;
item != NULL;
item = item->next) {
seed = item->item;
bl_slmatchInit(&frag, 0);
frag.i = seed->read_start;
frag.j = seed->read_end - seed->read_start + 1;
frag.p = seed->genome_start;
frag.q = seed->genome_end - seed->genome_start + 1;
frag.scr = seed->genome_end - seed->genome_start + 1;
frag.subject = seed->chromosome_id;
bl_containerAdd(info.fragments, &frag);
}
}
}
// sort fragments
qsort(info.fragments->contspace, bl_containerSize(info.fragments),
sizeof(slmatch_t), cmp_slmatch_qsort);
int begin = 0;
for (int i = 1; i <= bl_containerSize(info.fragments); i++){
// end of fragments list or different database sequence
// --> process fragment[begin]...fragment[i-1], write output
// and free chains (less memory consumption with large input files)
if (i == bl_containerSize(info.fragments) ||
((slmatch_t *) bl_containerGet(info.fragments, begin))->subject !=
((slmatch_t *) bl_containerGet(info.fragments, i))->subject){
if (info.chainmode == SOP){
// only use chaining without clustering if no ids are specified
bl_slClusterSop((slmatch_t *) info.fragments->contspace + begin, i - begin,
info.epsilon, info.lambda, info.maxgap);
}
else {
bl_slClusterLin((slmatch_t *) info.fragments->contspace + begin, i - begin,
info.epsilon, info.lambda, info.maxgap);
}
for (int j = begin; j < i; j++) {
slmatch_t *match = (slmatch_t *) bl_containerGet(info.fragments, j);
if (match->chain) {
slchain_t *chain = (slchain_t *) match->chain;
if (chain->scr >= info.minscore &&
bl_containerSize(chain->matches) >= info.minfrag) {
chrom = atoi(*(char **) bl_containerGet(info.subject, chain->subject));
read_area = 0;
seed_list = linked_list_new(COLLECTION_MODE_ASYNCHRONIZED);
for (int k = 0; k < bl_containerSize(chain->matches); k++){
slmatch_t *frag = *(slmatch_t **) bl_containerGet(chain->matches, k);
seed = seed_new(frag->i, frag->i + frag->j - 1, frag->p, frag->p + frag->q - 1);
seed->chromosome_id = chrom;
seed->strand = strand;
read_area += frag->j;
cigar_append_op(frag->j, '=', &seed->cigar);
linked_list_insert_last(seed, seed_list);
}
// extend seeds
cal = seed_cal_new(chrom, strand, chain->p, chain->p + chain->q - 1, seed_list);
cal->read = read;
extend_seeds(cal, sa_index);
seed_cal_update_info(cal);
if (cal->read_area >= min_area) {
array_list_insert(cal, cal_list);
} else {
seed_cal_free(cal);
}
}
bl_slchainDestruct(chain);
free(chain);
match->chain = NULL;
}
} // END OF for (j = begin; j < i; j++)
begin = i;
} // END OF if (i == bl_containerSize(info.fragments) ||
} // END OF for (i = 1; i <= bl_containerSize(info.fragments); i++)
// destruct everything
info.subject = NULL;
bl_claspinfoDestruct(&info);
// finally, clear suffix manager
suffix_mng_clear(p);
}
bool FragmentList::computeBestChain_(Container* frags, double& maxScore, uint32_t& bestPos) {
double epsilon = 0.0;
double lambda = 1.0;
unsigned char chainMode = LIN;
// Did we find a chain with a score higher than the original
// maxScore parameter?
bool updatedMaxScore = false;
/* sort fragments */
qsort(frags->contspace, bl_containerSize(frags),
sizeof(slmatch_t), cmp_slmatch_qsort);
uint32_t begin = 0;
for (uint32_t i = 1; i <= bl_containerSize(frags); i++){
/*
* end of fragments list or different database sequence
* --> process fragment[begin]...fragment[i-1], write output
* and free chains (less memory consumption with large input files)
*/
if (i == bl_containerSize(frags) ||
((slmatch_t *) bl_containerGet(frags, begin))->subject !=
((slmatch_t *) bl_containerGet(frags, i))->subject){
//fprintf(info.dev, "%d\t%d\n", begin, i-begin);
if (chainMode == SOP){
/* only use chaining without clustering if no ids are specified */
bl_slChainSop((slmatch_t *) frags->contspace + begin, i - begin,
epsilon, lambda, 10);
/*
bl_slClusterSop((slmatch_t *) info.fragments->contspace + begin, i - begin,
info.epsilon, info.lambda, info.maxgap);
*/
}
else {
bl_slChainLin((slmatch_t *) frags->contspace + begin, i - begin,
epsilon, lambda, 10);
/*
bl_slClusterLin((slmatch_t *) info.fragments->contspace + begin, i - begin,
info.epsilon, info.lambda, info.maxgap);
*/
}
for (uint32_t j = begin; j < i; j++){
slmatch_t *match = (slmatch_t *) bl_containerGet(frags, j);
if (match->chain) {
slchain_t* chain = (slchain_t*) match->chain;
if (chain->scr >= maxScore) {
maxScore = chain->scr;
bestPos = chain->p;
updatedMaxScore = true;
}
/*
// output matches (if desired)
if (info.outputm){
fprintf(info.dev, "M\t");
if (!info.outputorig){
if (info.idcol != NULL){
fprintf(info.dev, "%s\t",
*(char **) bl_containerGet(info.subject, match->subject));
}
fprintf(info.dev, "%d\t%d\t%d\t%d\t%.3f\n", match->i,
match->i + match->j - 1, match->p,
match->p + match->q - 1, match->scr);
}
// output in original format as input
else {
fprintf(info.dev, "%s\n", *(char **) bl_containerGet(info.lines, j));
}
}
if (match->chain){
slchain_t *chain = (slchain_t *) match->chain;
if (info.outputc && chain->scr >= info.minscore &&
bl_containerSize(chain->matches) >= info.minfrag){
fprintf(info.dev, "C\t");
if (info.idcol != NULL){
fprintf(info.dev, "%s\t", *(char **) bl_containerGet(info.subject, chain->subject));
}
fprintf(info.dev, "%d\t%d\t%d\t%d\t%.3f\n", chain->i,
chain->i + chain->j - 1, chain->p,
chain->p + chain->q - 1, chain->scr);
}
// output chains and fragments (if requested)
if (info.outputf && chain->scr >= info.minscore &&
bl_containerSize(chain->matches) >= info.minfrag){
for (k = 0; k < bl_containerSize(chain->matches); k++){
slmatch_t *frag = *(slmatch_t **)
bl_containerGet(chain->matches, k);
fprintf(info.dev, "F\t");
if (!info.outputorig){
if (info.idcol != NULL){
fprintf(info.dev, "%s\t",
*(char **) bl_containerGet(info.subject, frag->subject));
}
fprintf(info.dev, "%d\t%d\t%d\t%d\t%.3f\n", frag->i,
frag->i + frag->j - 1, frag->p, frag->p + frag->q - 1,
frag->scr);
}
// output in original format as input
else {
fprintf(info.dev, "%s\n",
*(char **) bl_containerGet(info.lines, frag->idx));
}
}
}
*/
bl_slchainDestruct(chain);
free(chain);
match->chain = nullptr;
} /* END OF if (frag->chain) */
} /* END OF for (j = begin; j < i; j++) */
begin = i;
} /* END OF if (i == bl_containerSize(info.fragments) ||
((slmatch_t *) bl_containerGet(info.fragments, begin))->subject !=
((slmatch_t *) bl_containerGet(info.fragments, i))->subject) */
} /* END OF for (i = 1; i <= bl_containerSize(info.fragments); i++) */
return updatedMaxScore;
}
