void FragmentList::addFragMatchRC(uint32_t refStart, uint32_t refEnd, uint32_t queryStart, uint32_t queryEnd) { slmatch_t frag; bl_slmatchInit(&frag, 0); frag.p = refStart; frag.q = refEnd; frag.i = queryStart; frag.j = queryEnd; frag.scr = static_cast<double>(queryEnd) - queryStart; bl_containerAdd(fragmentsRC, &frag); }
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); }