regen_scb

Hash_Table.h

@@ -234,6 +234,10 @@ uint64_t lchain_qdp_fix(k_mer_hit* a, int64_t a_n, Chain_Data* dp, int64_t max_s
                 int64_t max_iter, int64_t max_dis, double chn_pen_gap, double chn_pen_skip, 
                 double bw_rate, int64_t xl, int64_t yl, int64_t quick_check, 
                 int64_t left_fix, int64_t right_fix);
+uint64_t lchain_qdp_fix_adv(k_mer_hit* a, int64_t a_n, Chain_Data* dp, int64_t max_skip, 
+                int64_t max_iter, int64_t max_dis, double chn_pen_gap, double chn_pen_skip, 
+                double bw_rate, int64_t xl, int64_t yl, int64_t quick_check, 
+                int64_t left_fix, int64_t right_fix, k_mer_hit *res);
 uint64_t lchain_simple(k_mer_hit* a, int64_t a_n, k_mer_hit* des, Chain_Data* dp, 
                                                         int64_t max_skip, int64_t max_iter);
 uint64_t lchain_simple0(k_mer_hit* a, int64_t a_n, k_mer_hit* des, Chain_Data* dp, int64_t max_skip, int64_t max_iter);
@@ -253,6 +257,12 @@ uint64_t lchain_qdp_mcopy_fast(Candidates_list *cl, int64_t a_idx, int64_t a_n,
               int64_t gen_cigar, int64_t enable_mcopy, double mcopy_rate, int64_t mcopy_khit_cutoff, 
               int64_t khit_n);
 
+uint64_t lchain_qdp_global_fast(Candidates_list *cl, int64_t a_idx, int64_t a_n, int64_t des_idx, 
+              Chain_Data* dp, overlap_region_alloc* res, int64_t max_skip, int64_t max_iter, 
+              int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate, 
+              uint32_t xid, int64_t xl, int64_t yl, int64_t quick_check, uint32_t apend_be, 
+              int64_t gen_cigar, int64_t khit_n);
+
 #define kv_pushp_ol(type, v, p) do {									\
 		if ((v).length == (v).size) {										\
 			(v).list = (type*)realloc((v).list, sizeof(type)*((v).size?((v).size<<1):(2)));	\