0.20.0-r631

ecovlp.h

@@ -5,60 +5,59 @@
 #include <stdint.h>
 #include "Hash_Table.h"
 #include "Process_Read.h"
+#include "kdq.h"
+
+KDQ_INIT(uint32_t)
 
 typedef struct {
 	uint32_t v:31, f:1;
 	uint32_t sc;
 } cns_arc;
-typedef struct {size_t n, m; cns_arc *a;} cns_arc_v;
+typedef struct {size_t n, m, nou; cns_arc *a; } cns_arc_v;
 
 typedef struct {
 	// uint16_t c:2, t:2, f:1, sc:3;
 	uint32_t c:2, f:1, sc:29;
-	cns_arc_v in, ou;
+	cns_arc_v arc;
 }cns_t;
 
 typedef struct {
 	size_t n, m; 
 	cns_t *a;
-	uint32_t si, ei;
+	uint32_t si, ei, off, bn, bb0, bb1, cns_g_wl;
+	kdq_t(uint32_t) *q;
 }cns_gfa;
 
 typedef struct {
-	int is_final, save_ov;
 	// chaining and overlapping related buffers
 	UC_Read self_read, ovlp_read;
 	Candidates_list clist;
 	overlap_region_alloc olist;
-    overlap_region tmp;
 	ha_abuf_t *ab;
-	// error correction related buffers
-	int64_t num_read_base, num_correct_base, num_recorrect_base;
-	Cigar_record cigar;
-	Correct_dumy correct;
+	// int64_t num_read_base, num_correct_base, num_recorrect_base;
+	uint64_t cnt[6], rr;
 	haplotype_evdience_alloc hap;
 	bit_extz_t exz;
-	// asg32_v v32;
 	kv_ul_ov_t pidx;
 	asg64_v v64;
 	asg32_v v32;
 	asg16_v v16;
 
-    kvec_t_u64_warp r_buf;
     kvec_t_u8_warp k_flag;
 	st_mt_t sp;
-	cns_gfa cns;
-	
+	cns_gfa cns;	
 } ec_ovec_buf_t0;
 
 typedef struct {
 	ec_ovec_buf_t0 *a;
-	uint32_t n;
+	uint32_t n, rev;
 } ec_ovec_buf_t;
 
-ec_ovec_buf_t* gen_ec_ovec_buf_t(uint32_t n, uint32_t is_final, uint32_t save_ov);
+ec_ovec_buf_t* gen_ec_ovec_buf_t(uint32_t n);
 void destroy_ec_ovec_buf_t(ec_ovec_buf_t *p);
-void cal_ec_multiple(ec_ovec_buf_t *b, uint64_t n_thre, uint64_t n_a);
 void prt_chain(overlap_region_alloc *o);
+void cal_ec_r(uint64_t n_thre, uint64_t round, uint64_t n_round, uint64_t n_a, uint64_t is_sv, uint64_t *tot_b, uint64_t *tot_e);
+void sl_ec_r(uint64_t n_thre, uint64_t n_a);
+void cal_ov_r(uint64_t n_thre, uint64_t n_a, uint64_t new_idx);
 
 #endif