improved N50

CommandLines.cpp

@@ -46,6 +46,7 @@ void Print_H(hifiasm_opt_t* asm_opt)
 
 void init_opt(hifiasm_opt_t* asm_opt)
 {
+    asm_opt->coverage = -1;
     asm_opt->num_reads = 0;
     asm_opt->read_file_names = NULL;
     asm_opt->output_file_name = (char*)(DEFAULT_OUTPUT);

CommandLines.h

@@ -36,6 +36,7 @@ typedef struct {
     long long num_bases;
     long long num_corrected_bases;
     long long num_recorrected_bases;
+    long long coverage;
 } hifiasm_opt_t;
 
 extern hifiasm_opt_t asm_opt;

Overlaps.h

@@ -102,6 +102,8 @@ typedef struct {
 	uint32_t m_arc, n_arc:31, is_srt:1;
 	asg_arc_t *arc;
 	uint32_t m_seq, n_seq:31, is_symm:1;
+	uint32_t r_seq;
+
 	asg_seq_t *seq;
 	uint64_t *idx;
 
@@ -304,6 +306,13 @@ typedef struct {
 	kvec_t(uint32_t) e; // visited edges/arcs
 } buf_t;
 
+
+typedef struct {
+	kvec_t(uint64_t) Nodes; 
+	kvec_t(uint64_t) Edges; 
+	uint32_t pre_n_seq, seqID; 
+} C_graph;
+
 // count the number of outgoing arcs, including reduced arcs
 static inline int count_out_with_del(const asg_t *g, uint32_t v)
 {