new ul

Assembly.h

@@ -2,6 +2,9 @@
 #define __ASSEMBLY__
 #include "CommandLines.h"
 #include "Overlaps.h"
+#include "Process_Read.h"
+#include "Hash_Table.h"
+#include "Correct.h"
 
 #define FORWARD 0
 #define REVERSE_COMPLEMENT (0x8000000000000000)
@@ -14,7 +17,34 @@
 #define RESEED_LEN 2000
 #define RESEED_HP_RATE 0.9
 
+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_alloc olist_hp;
+	ha_abuf_t *ab;
+    ha_abufl_t *abl;
+	// error correction related buffers
+	int64_t num_read_base, num_correct_base, num_recorrect_base;
+	Cigar_record cigar1;
+	Graph POA_Graph;
+	Graph DAGCon;
+	Correct_dumy correct;
+	haplotype_evdience_alloc hap;
+	Round2_alignment round2;
+    kvec_t_u32_warp b_buf;
+    kvec_t_u64_warp r_buf;
+    kvec_t_u8_warp k_flag;
+    overlap_region tmp_region;
+    ma_utg_v *ua;
+    st_mt_t sp;
+} ha_ovec_buf_t;
+
 int ha_assemble(void);
 void ug_idx_build(ma_ug_t *ug, int hap_n);
+ha_ovec_buf_t *ha_ovec_init(int is_final, int save_ov, int is_ug);
+void ha_ovec_destroy(ha_ovec_buf_t *b);
 
 #endif