fixed missing read names

Overlapping not working yet (now confirmed)

Assembly.cpp

@@ -10,8 +10,6 @@
 #include "Output.h"
 #include "htab.h"
 
-void *ha_flt_tab;
-ha_pt_t *ha_idx;
 void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, Candidates_list *cl, double band_width_threshold, int keep_whole_chain);
 
 All_reads R_INF;

anchor.cpp

@@ -65,7 +65,7 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
 		REALLOC(ab->a, ab->m_a);
 	}
 	for (i = 0, k = 0; i < ab->mz.n; ++i) {
-		uint32_t j;
+		int j;
 		ha_mz1_t *z = &ab->mz.a[i];
 		seed1_t *s = &ab->seed[i];
 		for (j = 0; j < s->n; ++j) {
@@ -96,7 +96,7 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
 	}
 
 	// copy over to _cl_
-	if (ab->m_a >= cl->size) {
+	if (ab->m_a >= (uint64_t)cl->size) {
 		cl->size = ab->m_a;
 		REALLOC(cl->list, cl->size);
 	}

htab.cpp

@@ -33,6 +33,9 @@ const unsigned char seq_nt4_table[256] = { // translate ACGT to 0123
 	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4
 };
 
+void *ha_flt_tab;
+ha_pt_t *ha_idx;
+
 /***************************
  * Yak specific parameters *
  ***************************/
@@ -571,6 +574,7 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
 							if (seq_nt4_table[(uint8_t)p->ks->seq.s[i]] >= 4)
 								++n_N;
 						ha_compress_base(Get_READ(*p->rs_out, p->n_seq), p->ks->seq.s, l, &p->rs_out->N_site[p->n_seq], n_N);
+						memcpy(&p->rs_out->name[p->rs_out->name_index[p->n_seq]], p->ks->name.s, p->ks->name.l);
 					}
 				}
 				if (s->n_seq == s->m_seq) {

htab.h

@@ -23,6 +23,8 @@ struct ha_abuf_s;
 typedef struct ha_abuf_s ha_abuf_t;
 
 extern const unsigned char seq_nt4_table[256];
+extern void *ha_flt_tab;
+extern ha_pt_t *ha_idx;
 
 void *ha_ft_gen(const hifiasm_opt_t *asm_opt, All_reads *rs);
 int ha_ft_isflt(const void *hh, uint64_t y);

main.cpp

@@ -9,21 +9,12 @@
 int main(int argc, char *argv[])
 {
 	int i;
-	void *flt_tab;
-	ha_pt_t *idx;
-
     init_opt(&asm_opt);
-
     if (!CommandLine_process(argc, argv, &asm_opt)) return 1;
-
 	yak_reset_realtime();
-	flt_tab = ha_ft_gen(&asm_opt, &R_INF);
-	idx = ha_pt_gen(&asm_opt, flt_tab, 0, &R_INF);
-	ha_pt_destroy(idx);
-	ha_ft_destroy(flt_tab);
-	if (0) {
-	    Correct_Reads(asm_opt.number_of_round);
-	}
+	ha_flt_tab = ha_ft_gen(&asm_opt, &R_INF);
+    Correct_Reads(asm_opt.number_of_round);
+	ha_ft_destroy(ha_flt_tab);
 	destory_All_reads(&R_INF);
     destory_opt(&asm_opt);
 	fprintf(stderr, "[M::%s] Version: %s\n", __func__, "dummy");