update unitig distance

rcut.h

@@ -0,0 +1,42 @@
+#ifndef __RCUT__
+#define __RCUT__
+#include <stdio.h>
+#include <stdint.h>
+#include "kvec.h"
+#include "Overlaps.h"
+#include "Purge_Dups.h"
+
+typedef struct {
+    uint32_t bS, bE;
+    uint32_t nS, nE;
+    uint32_t uID;
+    uint8_t hs;
+}mc_interval_t;
+
+#define mc_node_t int8_t
+// #define w_t int32_t
+// #define t_w_t int64_t
+#define w_t double
+#define t_w_t double
+
+typedef struct {
+	uint64_t x; ///(uint64_t)nid1 << 32 | nid2;
+	w_t w;  ///might be negative or positive
+} mc_edge_t;
+
+typedef struct {
+    kvec_t(uint64_t) idx;
+    kvec_t(mc_edge_t) ma;
+    uint64_t* cc;
+    uint32_t n_seq;
+} mc_match_t;
+
+typedef struct {
+    kvec_t(mc_node_t) s;
+    ma_ug_t *ug;
+    asg_t *rg;
+    mc_match_t* e;
+}mc_g_t;
+
+void mc_solve(hap_overlaps_list* ovlp, trans_chain* t_ch, kv_u_trans_t *ta, ma_ug_t *ug, asg_t *read_g, double f_rate, uint8_t* trio_flag);
+#endif