fix Print_H

CommandLines.cpp

@@ -219,9 +219,9 @@ void Print_H(hifiasm_opt_t* asm_opt)
     fprintf(stderr, "    --ont        assemble ONT simplex reads in fastq format\n");
     // fprintf(stderr, "    --sc-n       consider base qual value for assembly\n");
     fprintf(stderr, "    --chem-c     INT\n");
-    fprintf(stderr, "                 detect chemical reads with <=INT other reads support [%lu]\n", asm_opt->chemical_cov);
+    fprintf(stderr, "                 detect chimeric reads with <=INT other reads support [%lu]\n", asm_opt->chemical_cov);
     fprintf(stderr, "    --chem-f     INT\n");
-    fprintf(stderr, "                 length of flanking regions for chemical read detection [%lu]\n", asm_opt->chemical_flank);
+    fprintf(stderr, "                 length of flanking regions for chimeric read detection [%lu]\n", asm_opt->chemical_flank);
 
 
     fprintf(stderr, "Example: ./hifiasm -o NA12878.asm -t 32 NA12878.fq.gz\n");

CommandLines.h

@@ -5,7 +5,7 @@
 #include <pthread.h>
 #include <stdint.h>
 
-#define HA_VERSION "0.21.0-r686"
+#define HA_VERSION "0.22.0-r689"
 
 #define VERBOSE 0
 

Hash_Table.cpp

@@ -1749,16 +1749,6 @@ uint64_t lchain_qdp(k_mer_hit* a, int64_t a_n, k_mer_hit* des, Chain_Data* dp, o
     return cL;
 }
 
-
-#define kv_pushp_ol(type, v, p) do {									\
-		if ((v).length == (v).size) {										\
-			(v).list = (type*)realloc((v).list, sizeof(type)*((v).size?((v).size<<1):(2)));	\
-            memset((v).list+(v).size, 0, sizeof(overlap_region)*(((v).size?((v).size<<1):2)-(v).size));\
-            (v).size = (v).size?((v).size<<1):(2);							\
-		}															\
-		*(p) = &((v).list[(v).length++]); \
-	} while (0)
-
 void push_ovlp_chain_qgen(overlap_region* o, uint32_t xid, int64_t xl, int64_t yl, int64_t sc, 
 k_mer_hit *beg, k_mer_hit *end)
 {

Hash_Table.h

@@ -248,4 +248,13 @@ uint64_t lchain_qdp_mcopy_fast(Candidates_list *cl, int64_t a_idx, int64_t a_n,
               int64_t gen_cigar, int64_t enable_mcopy, double mcopy_rate, int64_t mcopy_khit_cutoff, 
               int64_t khit_n);
 
+#define kv_pushp_ol(type, v, p) do {									\
+		if ((v).length == (v).size) {										\
+			(v).list = (type*)realloc((v).list, sizeof(type)*((v).size?((v).size<<1):(2)));	\
+            memset((v).list+(v).size, 0, sizeof(overlap_region)*(((v).size?((v).size<<1):2)-(v).size));\
+            (v).size = (v).size?((v).size<<1):(2);							\
+		}															\
+		*(p) = &((v).list[(v).length++]); \
+	} while (0)
+
 #endif

Overlaps.cpp

@@ -17664,6 +17664,7 @@ long long gap_fuzz, ug_opt_t *opt)
     set_trio_flag_by_cov(ug, sg, cov);
     // print_r_het(cov, R_INF.trio_flag, "out-1");
     // print_debug_gfa(ug, sg, coverage_cut, output_file_name, sources, ruIndex);
+    // exit(1);
 
     destory_hap_cov_t(&cov);
     ma_ug_destroy(ug);

anchor.cpp

@@ -1943,10 +1943,11 @@ void lchain_qgen_mcopy_fast(Candidates_list* cl, overlap_region_alloc* ol, uint3
 	}
 	cl->length = m;
 
+	// fprintf(stderr, "[M::%s::] rn::%lu\tmax_n_chain::%lu\n", __func__, ol->length, max_n_chain);
 	// for (k = 0; k < ol->length; k++) {
-	// 	fprintf(stderr, "---[M::%s::utg%.6dl] q[%d, %d), t[%d, %d), khit_off::%u\n", __func__, 
-    //     (int32_t)ol->list[k].y_id+1, ol->list[k].x_pos_s, ol->list[k].x_pos_e+1,
-	// 	ol->list[k].y_pos_s, ol->list[k].y_pos_e+1, ol->list[k].non_homopolymer_errors);
+	// 	fprintf(stderr, "---[M::%s::%.*s(qid::%u)] q[%d, %d), t[%d, %d), khit_off::%u\n", __func__, 
+	// 	(int32_t)Get_NAME_LENGTH(R_INF, ol->list[k].y_id), Get_NAME(R_INF, ol->list[k].y_id), ol->list[k].y_id,
+	// 	ol->list[k].x_pos_s, ol->list[k].x_pos_e+1, ol->list[k].y_pos_s, ol->list[k].y_pos_e+1, ol->list[k].non_homopolymer_errors);
 	// }
 
 	k = ol->length;

ecovlp.cpp

@@ -3220,7 +3220,7 @@ static void worker_hap_ec(void *data, long i, int tid)
     // if(i != 1124) return;
     // if(i != 700) return;
     // if(i != 2243244) return;
-    // if(i != 19350) return;
+    // if(i != 15139) return;
 
     // debug_retrive_bqual(D, &b->v8t, i, 256); return;
 
@@ -3233,6 +3233,8 @@ static void worker_hap_ec(void *data, long i, int tid)
 
     aux_o = fetch_aux_ovlp(&b->olist);///must be here
 
+    // stderr_phase_ovlp(&b->olist);
+
     ///debug for memory
     // snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
 
@@ -4849,7 +4851,12 @@ void h_ec_lchain_fast_new(ha_abuf_t *ab, uint32_t rid, UC_Read *qu, UC_Read *tu,
     oa = in0->buffer; on = in0->length;
     for (k = 0; k < on; k++) {
         if(oa[k].el) {
-            z = &(ol->list[ol->length++]);
+            // z = &(ol->list[ol->length++]);
+            kv_pushp_ol(overlap_region, (*ol), &z);
+            clear_fake_cigar(&(z->f_cigar));
+            clear_window_list_alloc(&(z->w_list));
+            clear_window_list_alloc(&(z->boundary_cigars));
+            
             z->x_id = rid; z->y_id = oa[k].tn;
             z->x_pos_strand = 0; z->y_pos_strand = oa[k].rev;
             z->x_pos_s = (uint32_t)oa[k].qns;