diff --git a/Process_Read.cpp b/Process_Read.cpp
index 2b4d3f4..e461714 100644
--- a/Process_Read.cpp
+++ b/Process_Read.cpp
@@ -81,7 +81,6 @@ void destory_All_reads(All_reads* r)
 	free(r->trio_flag);
 }
 
-
 void write_All_reads(All_reads* r, char* read_file_name)
 {
     fprintf(stderr, "Writing reads to disk... \n");
@@ -112,9 +111,6 @@ void write_All_reads(All_reads* r, char* read_file_name)
 		{
 			fwrite(&zero, sizeof(zero), 1, fp);
 		}
-		
-		
-		
 	}
 
 	fwrite(r->read_length, sizeof(uint64_t), r->total_reads, fp);
@@ -132,8 +128,6 @@ void write_All_reads(All_reads* r, char* read_file_name)
     fprintf(stderr, "Reads has been written.\n");
 }
 
-
-
 int load_All_reads(All_reads* r, char* read_file_name)
 {
     fprintf(stderr, "Loading reads from disk... \n");
@@ -164,7 +158,6 @@ int load_All_reads(All_reads* r, char* read_file_name)
 	r->N_site = (uint64_t**)malloc(sizeof(uint64_t*)*r->total_reads);
 	for (i = 0; i < r->total_reads; i++)
 	{
-
 		f_flag += fread(&zero, sizeof(zero), 1, fp);
 
 		if (zero)
@@ -233,32 +226,33 @@ int load_All_reads(All_reads* r, char* read_file_name)
 	return 1;
 }
 
-
-
-inline void insert_read(All_reads* r, kstring_t* read, kstring_t* name)
+void ha_insert_read_len(All_reads *r, int read_len, int name_len)
 {
 	r->total_reads++;
-	r->total_reads_bases = r->total_reads_bases + read->l;
-	r->total_name_length = r->total_name_length + name->l;
+	r->total_reads_bases += (uint64_t)read_len;
+	r->total_name_length += (uint64_t)name_len;
 
-	///must +1
-	if (r->index_size < r->total_reads + 2)
-	{
+	// must +1
+	if (r->index_size < r->total_reads + 2) {
 		r->index_size = r->index_size * 2 + 2;
-		r->read_length = (uint64_t*)realloc(r->read_length,sizeof(uint64_t)*(r->index_size));
+		r->read_length = (uint64_t*)realloc(r->read_length, sizeof(uint64_t) * r->index_size);
 		r->name_index_size = r->name_index_size * 2 + 2;
-		r->name_index = (uint64_t*)realloc(r->name_index,sizeof(uint64_t)*(r->name_index_size));
+		r->name_index = (uint64_t*)realloc(r->name_index, sizeof(uint64_t) * r->name_index_size);
 	}
 
-	r->read_length[r->total_reads - 1] = read->l;
-	r->name_index[r->total_reads] = r->name_index[r->total_reads-1] + name->l;
+	r->read_length[r->total_reads - 1] = read_len;
+	r->name_index[r->total_reads] = r->name_index[r->total_reads - 1] + name_len;
+}
+
+static inline void insert_read(All_reads* r, kstring_t* read, kstring_t* name)
+{
+	ha_insert_read_len(r, read->l, name->l);
 }
 
 void malloc_All_reads(All_reads* r)
 {
-
 	r->read_size = (uint64_t*)malloc(sizeof(uint64_t)*r->total_reads);
-	memcpy (r->read_size, r->read_length, sizeof(uint64_t)*r->total_reads);
+	memcpy(r->read_size, r->read_length, sizeof(uint64_t)*r->total_reads);
 
 	r->read_sperate = (uint8_t**)malloc(sizeof(uint8_t*)*r->total_reads);
 	long long i = 0;
@@ -313,7 +307,6 @@ void init_aux_table()
 			bit_t_seq_table_rc[i][2] = RC_CHAR(bit_t_seq_table[i][1]);
 			bit_t_seq_table_rc[i][3] = RC_CHAR(bit_t_seq_table[i][0]);
 		}
-		
 	}
 }
 
@@ -338,18 +331,12 @@ void init_UC_Read(UC_Read* r)
 			bit_t_seq_table_rc[i][2] = RC_CHAR(bit_t_seq_table[i][1]);
 			bit_t_seq_table_rc[i][3] = RC_CHAR(bit_t_seq_table[i][0]);
 		}
-		
 	}
-	
 }
 
-
-void recover_UC_Read_sub_region_begin_end
-(char* r, long long start_pos, long long length, uint8_t strand, All_reads* R_INF, long long ID, int extra_begin, int extra_end)
+void recover_UC_Read_sub_region_begin_end(char* r, long long start_pos, long long length, uint8_t strand,
+										  All_reads* R_INF, long long ID, int extra_begin, int extra_end)
 {
-
-
-
 	long long readLen = Get_READ_LENGTH((*R_INF), ID);
 	uint8_t* src = Get_READ((*R_INF), ID);
 
@@ -357,17 +344,11 @@ void recover_UC_Read_sub_region_begin_end
 	long long copyLen;
 	long long end_pos = start_pos + length - 1;
 
-
-	
-
 	if (strand == 0)
 	{
-		
 		i = start_pos;
 		copyLen = 0;
 
-
-
 		long long initLen = start_pos % 4;
 
 		if (initLen != 0)
@@ -376,8 +357,6 @@ void recover_UC_Read_sub_region_begin_end
 			copyLen = copyLen + 4 - initLen;
 			i = i + copyLen;
 		}
-		
-		
 		while (copyLen < length)
 		{
 			memcpy(r+copyLen, bit_t_seq_table[src[i>>2]], 4);
@@ -385,7 +364,6 @@ void recover_UC_Read_sub_region_begin_end
 			i = i + 4;
 		}
 
-		
 		if (R_INF->N_site[ID])
 		{
 			for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++)
@@ -400,17 +378,12 @@ void recover_UC_Read_sub_region_begin_end
 				}
 			}
 		}
-		
-		
 	}
 	else
 	{
-		
 		start_pos = readLen - start_pos - 1;
 		end_pos = readLen - end_pos - 1;
 
-
-
 		///start_pos > end_pos
 		i = start_pos;
 		copyLen = 0;
@@ -436,7 +409,6 @@ void recover_UC_Read_sub_region_begin_end
 
 			for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++)
 			{
-
 				if ((long long)R_INF->N_site[ID][i] >= end_pos && (long long)R_INF->N_site[ID][i] <= start_pos)
 				{
 					r[readLen - R_INF->N_site[ID][i] - 1 - offset] = 'N';
@@ -447,21 +419,11 @@ void recover_UC_Read_sub_region_begin_end
 				}
 			}
 		}
-		
-
-		
 	}
-		
 }
 
-
-
-
 void recover_UC_Read_sub_region(char* r, long long start_pos, long long length, uint8_t strand, All_reads* R_INF, long long ID)
 {
-
-
-
 	long long readLen = Get_READ_LENGTH((*R_INF), ID);
 	uint8_t* src = Get_READ((*R_INF), ID);
 
@@ -471,7 +433,6 @@ void recover_UC_Read_sub_region(char* r, long long start_pos, long long length,
 
 	if (strand == 0)
 	{
-		
 		i = start_pos;
 		copyLen = 0;
 
@@ -483,8 +444,7 @@ void recover_UC_Read_sub_region(char* r, long long start_pos, long long length,
 			copyLen = copyLen + 4 - initLen;
 			i = i + copyLen;
 		}
-		
-		
+
 		while (copyLen < length)
 		{
 			memcpy(r+copyLen, bit_t_seq_table[src[i>>2]], 4);
@@ -492,7 +452,6 @@ void recover_UC_Read_sub_region(char* r, long long start_pos, long long length,
 			i = i + 4;
 		}
 
-		
 		if (R_INF->N_site[ID])
 		{
 			for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++)
@@ -507,17 +466,12 @@ void recover_UC_Read_sub_region(char* r, long long start_pos, long long length,
 				}
 			}
 		}
-		
-		
 	}
 	else
 	{
-		
 		start_pos = readLen - start_pos - 1;
 		end_pos = readLen - end_pos - 1;
 
-
-
 		///start_pos > end_pos
 		i = start_pos;
 		copyLen = 0;
@@ -543,7 +497,6 @@ void recover_UC_Read_sub_region(char* r, long long start_pos, long long length,
 
 			for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++)
 			{
-
 				if ((long long)R_INF->N_site[ID][i] >= end_pos && (long long)R_INF->N_site[ID][i] <= start_pos)
 				{
 					r[readLen - R_INF->N_site[ID][i] - 1 - offset] = 'N';
@@ -554,11 +507,7 @@ void recover_UC_Read_sub_region(char* r, long long start_pos, long long length,
 				}
 			}
 		}
-		
-
-		
 	}
-		
 }
 
 
@@ -623,7 +572,6 @@ void recover_UC_Read_RC(UC_Read* r, All_reads* R_INF, uint64_t ID)
 		index = index + 4;
 	}
 
-
 	if (R_INF->N_site[ID])
 	{
 		for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++)
@@ -631,11 +579,8 @@ void recover_UC_Read_RC(UC_Read* r, All_reads* R_INF, uint64_t ID)
 			r->seq[r->length - R_INF->N_site[ID][i] - 1] = 'N';
 		}
 	}
-		
 }
 
-
-
 #define COMPRESS_BASE {c = seq_nt6_table[(uint8_t)src[i]];\
 		if (c >= 4)\
 		{\
@@ -647,7 +592,6 @@ void recover_UC_Read_RC(UC_Read* r, All_reads* R_INF, uint64_t ID)
 
 void compress_base(uint8_t* dest, char* src, uint64_t src_l, uint64_t** N_site_lis, uint64_t N_site_occ)
 {
-
 	///N_site_lis saves the pos of all Ns in this read
 	///N_site_lis[0] is the number of Ns
 	if (N_site_occ)
@@ -666,10 +610,8 @@ void compress_base(uint8_t* dest, char* src, uint64_t src_l, uint64_t** N_site_l
 	uint8_t tmp = 0;
 	uint8_t c = 0;
 
-
 	while (i + 4 <= src_l)
 	{
-
 		tmp = 0;
 
 		COMPRESS_BASE;
@@ -705,12 +647,8 @@ void compress_base(uint8_t* dest, char* src, uint64_t src_l, uint64_t** N_site_l
 		dest[dest_i] = tmp;
 		dest_i++;
 	}
-
 }
 
-
-
-
 void open_file(gz_files* nfps, char* name)
 {
 	nfps->fp = gzopen(name, "r");
@@ -722,7 +660,6 @@ void open_file(gz_files* nfps, char* name)
 	nfps->seq = kseq_init(nfps->fp);
 }
 
-
 void close_file(gz_files* nfps)
 {
 	kseq_destroy(nfps->seq);
@@ -774,11 +711,9 @@ inline void exchage_kstring_t(kstring_t* a, kstring_t* b)
 int get_read(kseq_t *s, int adapterLen)
 {
 	int l;
-	
 	///if ((l = kseq_read(seq)) >= 0)
 	if ((l = read_item()) >= 0)
 	{
-		
 		exchage_kstring_t(&(fps.seq->comment), &s->comment);
 		exchage_kstring_t(&(fps.seq->name), &s->name);
 		exchage_kstring_t(&(fps.seq->qual), &s->qual);
@@ -801,15 +736,12 @@ int get_read(kseq_t *s, int adapterLen)
 			} 
 			
 		}
-		
 		return 1;
 	}
 	else
 	{
 		return 0;
 	}
-	
-	
 }
 
 void init_R_buffer_block(R_buffer_block* curr_sub_block)
@@ -823,6 +755,7 @@ void clear_R_buffer()
 	RDB.all_read_end = 0;
 	RDB.num = 0;
 }
+
 void init_R_buffer(int thread_num)
 {
 	RDB.all_read_end = 0;
@@ -841,13 +774,11 @@ void init_R_buffer(int thread_num)
 	
 }
 
-
 void destory_R_buffer_block(R_buffer_block* curr_sub_block)
 {
 	kseq_destroy(curr_sub_block->read);
 }
 
-
 void destory_R_buffer()
 {
 	int i = 0;
@@ -858,7 +789,6 @@ void destory_R_buffer()
 	}
 
 	free(RDB.sub_block);
-	
 }
 
 
@@ -868,12 +798,8 @@ inline void load_read_block(R_buffer_block* read_batch, int batch_read_size,
 	int inner_i = 0;
 	int file_flag = 1;
 
-
-
-
 	while (inner_i<batch_read_size)
 	{
-
 		file_flag = get_read(&read_batch->read[inner_i], adapterLen);
 
 		if (file_flag == 1)
@@ -881,7 +807,6 @@ inline void load_read_block(R_buffer_block* read_batch, int batch_read_size,
 			read_batch->read[inner_i].ID = total_reads;
 			total_reads++;
 
-
 			if (is_insert)
 			{
 				insert_read(&R_INF, &read_batch->read[inner_i].seq, 
@@ -903,14 +828,11 @@ inline void load_read_block(R_buffer_block* read_batch, int batch_read_size,
 
 	*return_file_flag = file_flag;
 	read_batch->num = inner_i;
-
 }
 
 
 inline void push_R_block(R_buffer_block* tmp_sub_block)
 {
-	
-
 	///only exchange pointers
 	kseq_t *k1;
 	k1 = RDB.sub_block[RDB.num].read;
@@ -940,29 +862,20 @@ inline void pop_R_block(R_buffer_block* curr_sub_block)
 
 	curr_sub_block->num = RDB.sub_block[RDB.num].num;
 	RDB.sub_block[RDB.num].num = 0;
-
-
-
 }
 
-
-
 void* input_reads_muti_threads(void* arg)
 {
 	int is_insert = *((int*)arg);
 
-
 	total_reads = 0;
 
-
 	int file_flag = 1;
 
 	R_buffer_block tmp_buf;
 
 	init_R_buffer_block(&tmp_buf);
 
-
-
 	while (1)
 	{
 		load_read_block(&tmp_buf, RDB.block_inner_size, &file_flag, is_insert, asm_opt.adapterLen);
@@ -972,7 +885,6 @@ void* input_reads_muti_threads(void* arg)
 			break;
 		}
 
-
 		pthread_mutex_lock(&i_readinputMutex);
 		while (IS_FULL(RDB))
 		{
@@ -981,14 +893,12 @@ void* input_reads_muti_threads(void* arg)
 			pthread_cond_wait(&i_readinputflushCond, &i_readinputMutex);
 		}
 
-
 		push_R_block(&tmp_buf);
 
 		pthread_cond_signal(&i_readinputstallCond);
 		pthread_mutex_unlock(&i_readinputMutex);
 	}
 
-
 	pthread_mutex_lock(&i_readinputMutex);
 	RDB.all_read_end = 1;
 	pthread_cond_signal(&i_readinputstallCond);  //important
@@ -999,34 +909,25 @@ void* input_reads_muti_threads(void* arg)
 	fprintf(stderr, "Reads #: %lu\n", (unsigned long)total_reads);
 	fprintf(stderr, "Bases #: %lu\n", (unsigned long)R_INF.total_reads_bases);
 	
-
 	return NULL;
 }
 
-
-
 int get_reads_mul_thread(R_buffer_block* curr_sub_block)
 {
-
-
 	pthread_mutex_lock(&i_readinputMutex);
 
-
 	while (IS_EMPTY(RDB) && RDB.all_read_end == 0)
 	{
-
 		pthread_cond_signal(&i_readinputflushCond);
 		pthread_cond_wait(&i_readinputstallCond, &i_readinputMutex);
 	}
 
-
 	if (!IS_EMPTY(RDB))
 	{
 		pop_R_block(curr_sub_block);
 		pthread_cond_signal(&i_readinputflushCond);
 		pthread_mutex_unlock(&i_readinputMutex);
 
-
 		return 1;
 	}
 	else
@@ -1039,17 +940,8 @@ int get_reads_mul_thread(R_buffer_block* curr_sub_block)
 
 		return 0;
 	}
-	
-
 }
 
-
-
-
-
-
-
-
 void reverse_complement(char* pattern, uint64_t length)
 {
 	uint64_t i = 0;
@@ -1069,11 +961,8 @@ void reverse_complement(char* pattern, uint64_t length)
 	{
 		pattern[end] = RC_CHAR(pattern[end]);
 	}
-
 }
 
-
-
 typedef struct {
   char* tmp;
   long long tmpSize;
diff --git a/Process_Read.h b/Process_Read.h
index 23764e6..e359328 100644
--- a/Process_Read.h
+++ b/Process_Read.h
@@ -25,11 +25,9 @@
 #define Get_NAME(R_INF, ID) R_INF.name + R_INF.name_index[(ID)]
 
 
-
 KSEQ_INIT(gzFile, gzread)
 
 
-
 extern uint8_t seq_nt6_table[256];
 extern char bit_t_seq_table[256][4];
 extern char bit_t_seq_table_rc[256][4];
@@ -43,7 +41,6 @@ extern char rc_Table[5];
 void init_aux_table();
 int get_read(kseq_t *s, int adapterLen);
 
-
 typedef struct
 {
     uint64_t x_id;
@@ -76,7 +73,6 @@ inline void init_PAF_alloc(PAF_alloc* list)
     list->list = (PAF*)malloc(sizeof(PAF)*list->size);
 }
 
-
 inline void append_PAF_alloc(PAF_alloc* list, PAF* e)
 {
     if(list->length+1 > list->size)
@@ -89,9 +85,6 @@ inline void append_PAF_alloc(PAF_alloc* list, PAF* e)
     list->length++;
 }
 
-
-
-
 typedef struct
 {
     /**[0-1] bits are type:**/
@@ -104,7 +97,7 @@ typedef struct
     uint32_t lost_base_length;
 	uint32_t lost_base_size;
 	uint32_t new_length;
-}Compressed_Cigar_record;
+} Compressed_Cigar_record;
 
 #define AMBIGU 0
 #define FATHER 1
@@ -112,13 +105,13 @@ typedef struct
 #define MIX_TRIO 3
 #define NON_TRIO 4
 #define DROP 5
+
 typedef struct
 {
 	uint64_t** N_site;
 	///uint8_t* read;
 	char* name;
 
-
 	uint8_t** read_sperate;
 	uint64_t* read_length;
 	uint64_t* read_size;
@@ -129,7 +122,6 @@ typedef struct
 	///uint64_t* index;
 	uint64_t index_size;
 
-
     ///name start pos in char* name
 	uint64_t* name_index;
 	uint64_t name_index_size;
@@ -143,7 +135,6 @@ typedef struct
     ma_hit_t_alloc* paf;
     ma_hit_t_alloc* reverse_paf;
     ma_sub_t* coverage_cut;
-
 } All_reads;
 
 extern All_reads R_INF;
@@ -154,10 +145,8 @@ typedef struct
 {
 	kseq_t* read;
 	long long num;
-
 } R_buffer_block;
 
-
 typedef struct
 {
 	R_buffer_block* sub_block;
@@ -167,7 +156,6 @@ typedef struct
 	int all_read_end;
 } R_buffer;
 
-
 typedef struct
 {
 	char* seq;
@@ -208,5 +196,6 @@ void clear_R_buffer();
 void init_gz_files(hifiasm_opt_t* asm_opt);
 void destory_gz_files();
 
+void ha_insert_read_len(All_reads *r, int read_len, int name_len);
 
 #endif
diff --git a/htab.cpp b/htab.cpp
index 1a0f055..1de88d2 100644
--- a/htab.cpp
+++ b/htab.cpp
@@ -9,6 +9,7 @@
 #include "kseq.h"
 #include "ksort.h"
 #include "htab.h"
+#include "Process_Read.h"
 #include "CommandLines.h"
 
 #define YAK_COUNTER_BITS 12
@@ -308,7 +309,6 @@ static void worker_pt_gen(void *data, long i, int tid) // callback for kt_for()
 			b->n += kh_key(g, k) & YAK_MAX_COUNT;
 		}
 	}
-//	fprintf(stderr, "X\t%ld\t%d\t%ld\n", i, kh_size(g), (long)b->n);
 	yak_ct_destroy(g);
 	a->ct->h[i].h = 0;
 	CALLOC(b->a, b->n);
@@ -464,12 +464,15 @@ static void count_seq_buf_HPC(ch_buf_t *buf, int k, int p, int len, const char *
  * K-mer counting *
  ******************/
 
-KSEQ_INIT(gzFile, gzread)
+//KSEQ_INIT(gzFile, gzread)
+
+#define HAF_COUNT_EXACT  0x1
+#define HAF_COUNT_ALL    0x2
 
 typedef struct { // global data structure for kt_pipeline()
 	const yak_copt_t *opt;
 	const void *flt_tab;
-	int create_new, is_store;
+	int flag, create_new, is_store;
 	uint64_t batch_offset;
 	uint64_t n_base;
 	kseq_t *ks;
@@ -608,7 +611,7 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
 	return 0;
 }
 
-static ha_ct_t *yak_count(const char *fn, const yak_copt_t *opt, ha_pt_t *p0, ha_ct_t *c0, const void *flt_tab)
+static ha_ct_t *yak_count(const yak_copt_t *opt, const char *fn, int flag, ha_pt_t *p0, ha_ct_t *c0, const void *flt_tab)
 {
 	pl_data_t pl;
 	gzFile fp;
@@ -633,28 +636,28 @@ static ha_ct_t *yak_count(const char *fn, const yak_copt_t *opt, ha_pt_t *p0, ha
 	return pl.ct;
 }
 
-static ha_ct_t *yak_count_file(const yak_copt_t *opt, ha_pt_t *p0, int n_fn, char **fn, const void *flt_tab)
+static ha_ct_t *yak_count_file(const yak_copt_t *opt, int flag, ha_pt_t *p0, int n_fn, char **fn, const void *flt_tab)
 {
 	int i;
 	ha_ct_t *h = 0;
 	for (i = 0; i < n_fn; ++i)
-		h = yak_count(fn[i], opt, p0, h, flt_tab);
+		h = yak_count(opt, fn[i], flag, p0, h, flt_tab);
 	if (h && opt->bf_shift > 0)
 		ha_ct_destroy_bf(h);
 	return h;
 }
 
-ha_ct_t *ha_count(const hifiasm_opt_t *asm_opt, ha_pt_t *p0, int is_exact, int count_all, const void *flt_tab)
+ha_ct_t *ha_count(const hifiasm_opt_t *asm_opt, int flag, ha_pt_t *p0, const void *flt_tab)
 {
 	yak_copt_t opt;
 	ha_ct_t *h;
 	yak_copt_init(&opt);
 	opt.k = asm_opt->k_mer_length;
 	opt.is_HPC = !asm_opt->no_HPC;
-	opt.w = count_all? 1 : asm_opt->mz_win;
-	opt.bf_shift = is_exact? 0 : asm_opt->bf_shift;
+	opt.w = flag & HAF_COUNT_ALL? 1 : asm_opt->mz_win;
+	opt.bf_shift = flag & HAF_COUNT_EXACT? 0 : asm_opt->bf_shift;
 	opt.n_thread = asm_opt->thread_num;
-	h = yak_count_file(&opt, p0, asm_opt->num_reads, asm_opt->read_file_names, flt_tab);
+	h = yak_count_file(&opt, flag, p0, asm_opt->num_reads, asm_opt->read_file_names, flt_tab);
 	return h;
 }
 
@@ -707,7 +710,7 @@ void *ha_gen_flt_tab(const hifiasm_opt_t *asm_opt)
 	int64_t cnt[YAK_N_COUNTS];
 	int peak_hom, peak_het, cutoff;
 	ha_ct_t *h;
-	h = ha_count(asm_opt, 0, 0, 1, 0);
+	h = ha_count(asm_opt, HAF_COUNT_ALL, NULL, NULL);
 	ha_ct_hist(h, cnt, asm_opt->thread_num);
 	peak_hom = yak_analyze_count(YAK_N_COUNTS, cnt, &peak_het);
 	if (peak_hom > 0) fprintf(stderr, "[M::%s] peak_hom: %d; peak_het: %d\n", __func__, peak_hom, peak_het);
@@ -727,7 +730,7 @@ void *ha_gen_mzidx(const hifiasm_opt_t *asm_opt, const void *flt_tab)
 	int peak_hom, peak_het, i;
 	ha_ct_t *ct;
 	ha_pt_t *pt;
-	ct = ha_count(asm_opt, 0, 1, 0, flt_tab);
+	ct = ha_count(asm_opt, HAF_COUNT_EXACT, NULL, flt_tab);
 	fprintf(stderr, "[M::%s::%.3f*%.2f] ==> counted %ld distinct minimizer k-mers\n", __func__,
 			yak_realtime(), yak_cputime() / yak_realtime(), (long)ct->tot);
 	ha_ct_hist(ct, cnt, asm_opt->thread_num);
@@ -737,7 +740,7 @@ void *ha_gen_mzidx(const hifiasm_opt_t *asm_opt, const void *flt_tab)
 	ha_ct_shrink(ct, 2, YAK_MAX_COUNT - 1, asm_opt->thread_num);
 	for (i = 2, tot_cnt = 0; i <= YAK_MAX_COUNT - 1; ++i) tot_cnt += cnt[i] * i;
 	pt = ha_pt_gen(ct, asm_opt->thread_num);
-	ha_count(asm_opt, pt, 1, 0, flt_tab);
+	ha_count(asm_opt, HAF_COUNT_EXACT, pt, flt_tab);
 	assert((uint64_t)tot_cnt == pt->tot_pos);
 	ha_pt_sort(pt, asm_opt->thread_num);
 	fprintf(stderr, "[M::%s::%.3f*%.2f] ==> indexed %ld positions\n", __func__,