code clean

inter.h

@@ -3,6 +3,98 @@
 #include "Overlaps.h"
 #include "Process_Read.h"
 
+#define G_CHAIN_BW 16//128
+#define FLANK_M (0x7fffU)
+#define P_CHAIN_COV 0.985
+#define P_FRAGEMENT_CHAIN_COV 0.20
+#define P_FRAGEMENT_PRIMARY_CHAIN_COV 0.70
+#define P_FRAGEMENT_PRIMARY_SECOND_COV 0.25
+#define P_CHAIN_SCORE 0.6
+#define G_CHAIN_GAP 0.1
+#define UG_SKIP 5
+#define RG_SKIP 25
+#define G_CHAIN_TRANS_RATE 0.25
+#define G_CHAIN_TRANS_WEIGHT -1
+#define G_CHAIN_INDEL 128
+#define W_CHN_PEN_GAP 0.1
+#define N_GCHAIN_RATE 0.04
+#define PRIMARY_UL_CHAIN_MIN 75000
+
+typedef struct {
+	int w, k, bw, max_gap, is_HPC, hap_n, occ_weight, max_gap_pre, max_gc_seq_ext, seed;
+	int max_lc_skip, max_lc_iter, min_lc_cnt, min_lc_score, max_gc_skip, ref_bonus;
+	int min_gc_cnt, min_gc_score, sub_diff, best_n;
+    float chn_pen_gap, mask_level, pri_ratio;
+	///base-alignment
+	double bw_thres, diff_ec_ul, diff_ec_ul_low; int max_n_chain, ec_ul_round;
+} mg_idxopt_t;
+
+struct mg_tbuf_s {
+	void *km;
+	int frag_gap;
+};
+typedef struct mg_tbuf_s mg_tbuf_t;
+
+
+mg_tbuf_t *mg_tbuf_init(void);
+
+void mg_tbuf_destroy(mg_tbuf_t *b);
+
+void *mg_tbuf_get_km(mg_tbuf_t *b);
+
+typedef struct {
+	FILE *fp;
+	ul_vec_t u;
+	uint64_t flag;
+} ucr_file_t;
+
+typedef struct {
+	int32_t off, cnt;
+	uint32_t v;
+	int32_t score;
+} mg_llchain_t;
+
+typedef struct {
+	int32_t id, parent;
+	int32_t off, cnt;
+	int32_t n_anchor, score;
+	int32_t qs, qe;
+	int32_t plen, ps, pe;
+	int32_t blen, mlen;
+	float div;
+	uint32_t hash;
+	int32_t subsc, n_sub;
+	uint32_t mapq:8, flt:1, dummy:23;
+} mg_gchain_t;
+
+typedef struct {
+	size_t n,m;
+    uint64_t *a, tl;
+	kvec_t(char) cc;
+} mg_dbn_t;
+
+typedef struct {
+	int32_t cnt;
+	uint32_t v;
+	int32_t score;
+	uint32_t qs, qe, ts, te;
+} mg_lres_t;
+
+typedef struct {
+    int32_t n_gc, n_lc;
+    mg_gchain_t *gc;///g_chain; idx in l_chains
+    mg_lres_t *lc;///l_chain
+    uint64_t qid, qlen;
+} mg_gres_t;
+
+typedef struct {
+	size_t n,m;
+    mg_gres_t *a;
+	uint64_t total_base;
+    uint64_t total_pair;
+} mg_gres_a;
+
+void push_uc_block_t(const ug_opt_t *uopt, kv_ul_ov_t *z, char **seq, uint64_t *len, uint64_t b_id);
 void ul_resolve(ma_ug_t *ug, const asg_t *rg, const ug_opt_t *uopt, int hap_n);
 void ul_load(const ug_opt_t *uopt);
 uint64_t* get_hifi2ul_list(all_ul_t *x, uint64_t hid, uint64_t* a_n);