update 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)
 {

README.md

@@ -43,8 +43,8 @@ assembly in a few hours. Hifiasm has been tested on the following datasets:
 
 |<sub>Dataset<sub>|<sub>GSize<sub>|<sub>Cov<sub>|<sub>Asm options<sub>|<sub>CPU time<sub>|<sub>Wall time<sub>|<sub>RAM<sub>|<sub>[unitig][unitig]/[contig][unitig] N50<sup>[1]</sup><sub>|
 |:---------------|-----:|-----:|:---------------------|-------:|--------:|----:|----------------:|
-|<sub>[Human NA12878]<sub>|<sub>3Gb<sub>|<sub>x28<sub>|<sub>-k 40 -t 42 -r 2<sub>|<sub>200h<sub>|    <sub>5h32m<sub>|<sub>114G<sub>|<sub>93.5Kb/18.6Mb<sub>|
-|<sub>[Human HG002]<sub>|<sub>3Gb<sub>|<sub>x43<sub>|<sub>-k 40 -t 42 -r 2<sub>|<sub>405h10m<sub>|<sub>12h7m<sub>|<sub>146G<sub>|<sub>320kb/29.3Mb<sub>|
+|<sub>[Human NA12878]<sub>|<sub>3Gb<sub>|<sub>x28<sub>|<sub>-k 40 -t 42 -r 2<sub>|<sub>200h<sub>|    <sub>5h32m<sub>|<sub>114G<sub>|<sub>93.5Kb/21.5Mb<sub>|
+|<sub>[Human HG002]<sub>|<sub>3Gb<sub>|<sub>x43<sub>|<sub>-k 40 -t 42 -r 2<sub>|<sub>405h10m<sub>|<sub>12h7m<sub>|<sub>146G<sub>|<sub>320kb/31.9Mb<sub>|
 |<sub>[Human CHM13]<sub>|<sub>3Gb<sub>|<sub>x27<sub>|<sub>-k 40 -t 42 -r 2<sub>|<sub>157h28m<sub>|<sub>5h10m<sub>|<sub>85.8G<sub>|<sub>NA<sup>[2]</sup>/39.8Mb<sub>|
 |<sub>[Butterfly]<sub>|<sub>358Mb<sub>|<sub>x35<sub>|<sub>-k 40 -t 42 -r 2 -z 20<sub>|<sub>17h6m<sub>|<sub>36m<sub>|<sub>16G<sub>|<sub>7.5Mb/NA<sup>[3]</sup><sub>|