diff --git a/CommandLines.h b/CommandLines.h index 92b17b8..cf66a14 100644 --- a/CommandLines.h +++ b/CommandLines.h @@ -4,7 +4,7 @@ #include #include -#define HA_VERSION "0.18.3-r493" +#define HA_VERSION "0.18.3-r495" #define VERBOSE 0 diff --git a/Correct.cpp b/Correct.cpp index 235bcf4..9e07c44 100644 --- a/Correct.cpp +++ b/Correct.cpp @@ -3485,6 +3485,24 @@ inline void recalcate_window_advance(overlap_region_alloc* overlap_list, All_rea ///note!!! need notification end_site = Reserve_Banded_BPM_PATH(y_string, Window_Len, x_string, x_len, threshold, &error, &real_y_start, &(dumy->path_length), dumy->matrix_bit, dumy->path, p->error, p->y_end - y_start); + // if(!(error != (unsigned int)-1)) { + // fprintf(stderr, "[M::%s::]\tqid::%u\tqlen::%lu\tq::[%d,\t%d)\ttid::%u\ttlen::%lu\tt::[%d,\t%d)\te_beg::%d\te_end::%d\terr::%d\n", __func__, + // overlap_list->list[j].x_id, Get_READ_LENGTH((*rref), overlap_list->list[j].x_id), + // p->x_start, p->x_end+1, + // overlap_list->list[j].y_id, Get_READ_LENGTH((*rref), overlap_list->list[j].y_id), + // p->y_start, p->y_end+1, + // p->extra_begin, p->extra_end, p->error); + // fprintf(stderr, "[M::%s::]\tqcal_len::%lld\ttcal_len::%lld\tthres::%d\n", __func__, + // x_len, Window_Len, threshold); + // fprintf(stderr, "qid::%u\nqname::%.*s\n\t%.*s\n", overlap_list->list[j].x_id, + // (int32_t)Get_NAME_LENGTH((*rref), overlap_list->list[j].x_id), + // Get_NAME((*rref), overlap_list->list[j].x_id), (int32_t)x_len, x_string); + + // fprintf(stderr, "tid::%u\ntname::%.*s\n\t%.*s\n", overlap_list->list[j].y_id, + // (int32_t)Get_NAME_LENGTH((*rref), overlap_list->list[j].y_id), + // Get_NAME((*rref), overlap_list->list[j].y_id), (int32_t)Window_Len, y_string); + + // } assert(error != (unsigned int)-1); { diff --git a/hic.cpp b/hic.cpp index 202b62b..d60847c 100644 --- a/hic.cpp +++ b/hic.cpp @@ -16746,7 +16746,7 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o ////dedup_hits(&(sl.hits), sl.idx); ///write_hc_hits_v14(&sl.hits, asm_opt.output_file_name); - if(asm_opt.misjoin_len > 0) + if(asm_opt.misjoin_len > 0/** && (!(asm_opt.ar))**/)//disable it for the UL assembly { update_switch_unitig(idx->ug, idx->read_g, &(sl.hits), &(idx->t_ch->k_trans), 10, 20, asm_opt.misjoin_len, 0.15); renew_idx_para(idx, idx->ug);