minimizer filtering apparently works

Assembly.h

@@ -9,6 +9,8 @@
 #define Get_Cigar_Length(RECORD) (RECORD>>2)
 
 void *ha_gen_flt_tab(const hifiasm_opt_t *asm_opt);
+void *ha_gen_mzidx(const hifiasm_opt_t *asm_opt, const void *flt_tab);
+
 void Counting_multiple_thr();
 void Build_hash_table_multiple_thr();
 void Overlap_calculate_multipe_thr();

CommandLines.cpp

@@ -65,6 +65,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
     asm_opt->mat_index = NULL;
     asm_opt->thread_num = 1;
     asm_opt->k_mer_length = 41;
+	asm_opt->mz_win = 41;
 	asm_opt->bf_shift = 37;
 	asm_opt->high_factor = 10.0f;
 	asm_opt->no_HPC = 0;

CommandLines.h

@@ -15,6 +15,7 @@ typedef struct {
     char* mat_index;
     int thread_num;
     int k_mer_length;
+	int mz_win;
 	int bf_shift;
 	float high_factor;
 	int no_HPC;

main.cpp

@@ -17,6 +17,7 @@ int main(int argc, char *argv[])
 
 	yak_reset_realtime();
 	flt_tab = ha_gen_flt_tab(&asm_opt);
+	ha_gen_mzidx(&asm_opt, flt_tab);
 	ha_hf_destroy(flt_tab);
 	if (0) {
 	    Correct_Reads(asm_opt.number_of_round);

yak-count.cpp

@@ -496,3 +496,24 @@ void ha_hf_destroy(void *h)
 {
 	yak_hh_destroy((yak_hh_t*)h);
 }
+
+void *ha_gen_mzidx(const hifiasm_opt_t *asm_opt, const void *flt_tab)
+{
+	int64_t cnt[YAK_N_COUNTS];
+	int peak_hom, peak_het;
+	yak_copt_t opt;
+	yak_ch_t *h;
+	yak_copt_init(&opt);
+	opt.is_HPC = !asm_opt->no_HPC;
+	opt.k = asm_opt->k_mer_length;
+	opt.w = asm_opt->mz_win;
+	opt.n_thread = asm_opt->thread_num;
+	opt.bf_shift = asm_opt->bf_shift;
+	h = yak_count_file(&opt, asm_opt->num_reads, asm_opt->read_file_names, flt_tab);
+	yak_ch_hist(h, cnt, opt.n_thread);
+	fprintf(stderr, "[M::%s] count[%d] = %ld (for sanity check)\n", __func__, YAK_MAX_COUNT, (long)cnt[YAK_MAX_COUNT]);
+	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);
+	yak_ch_destroy(h);
+	return 0;
+}