resolve conflicts

CommandLines.h

@@ -4,7 +4,7 @@
 #include <pthread.h>
 #include <stdint.h>
 
-#define HA_VERSION "0.15.5-r351"
+#define HA_VERSION "0.15.5-r352"
 
 #define VERBOSE 0
 

anchor.cpp

@@ -255,7 +255,8 @@ kvec_t_u64_warp* chain_idx, void *ha_flt_tab, ha_pt_t *ha_idx, overlap_region* f
 	ab->mz.n = 0, ab->n_a = 0;
 
 	// get the list of anchors
-	ha_sketch_query(u->s, u->len, asm_opt.mz_win, asm_opt.k_mer_length, 0, !(asm_opt.flag & HA_F_NO_HPC), &ab->mz, ha_flt_tab, k_flag, dbg_ct);
+	//should use the new version...
+	///ha_sketch_query(u->s, u->len, asm_opt.mz_win, asm_opt.k_mer_length, 0, !(asm_opt.flag & HA_F_NO_HPC), &ab->mz, ha_flt_tab, k_flag, dbg_ct);
 	// minimizer of queried read
 	if (ab->mz.m > ab->old_mz_m) {
 		ab->old_mz_m = ab->mz.m;

htab.cpp

@@ -954,7 +954,7 @@ void *ha_ft_ug_gen(const hifiasm_opt_t *asm_opt, ma_utg_v *us, int hap_n)
 	print_hist_lines(YAK_N_COUNTS, 1, cnt);
 	
 	ha_ct_shrink(h, cutoff, YAK_MAX_COUNT, asm_opt->thread_num);
-	flt_tab = gen_hh(h);
+	flt_tab = gen_hh(h, asm_opt->max_kmer_cnt);
 	ha_ct_destroy(h);
 	fprintf(stderr, "[M::%s::%.3f*%.2f@%.3fGB] ==> filtered out %ld k-mers occurring %d or more times\n", __func__,
 			yak_realtime(), yak_cpu_usage(), yak_peakrss_in_gb(), (long)kh_size(flt_tab), cutoff);

sketch.cpp

@@ -9,25 +9,6 @@
 #define MAX_HIGH_OCC     8   // TODO: don't hard code if we need to tune this parameter
 #define MAX_MAX_HIGH_OCC 16
 
-typedef struct { // a simplified version of kdq
-	int front, count;
-	int a[64];
-} tiny_queue_t;
-
-static inline void tq_push(tiny_queue_t *q, int x)
-{
-	q->a[((q->count++) + q->front) & 0x3f] = x;
-}
-
-static inline int tq_shift(tiny_queue_t *q)
-{
-	int x;
-	if (q->count == 0) return -1;
-	x = q->a[q->front++];
-	q->front &= 0x3f;
-	--q->count;
-	return x;
-}
 
 static inline int mzcmp(const ha_mz1_t *a, const ha_mz1_t *b)
 {