diff --git a/anchor.cpp b/anchor.cpp
index 3a07f95..bad4b55 100644
--- a/anchor.cpp
+++ b/anchor.cpp
@@ -265,130 +265,127 @@ void calculate_ug_chaining(Candidates_list* candidates, overlap_region_alloc* ov
     }
 }
 
-/**
-void ha_get_inter_candidates(ha_abufl_t *ab, int64_t uid, ma_utg_v *ua, overlap_region_alloc *ovlp, 
-Candidates_list *cl, double bw_thres, int max_n_chain, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* chain_idx, 
-void *ha_flt_tab, ha_pt_t *ha_idx, overlap_region* f_cigar, kvec_t_u64_warp* dbg_ct, st_mt_t *sp, 
-double chain_match_rate, uint32_t uk, uint32_t uw, uint32_t is_hpc, uint32_t h_occ)
-{
 
-	uint32_t i, rlen;
-    uint64_t k, l;
-	ma_utg_t *u = &(ua->a[uid]);
+void ha_get_inter_candidates(ha_abufl_t *ab, uint64_t id, char* r, uint64_t rlen, uint64_t rw, uint64_t rk, uint64_t is_hpc,
+        overlap_region_alloc *ol, Candidates_list *cl, double bw_thres, int max_n_chain, int keep_whole_chain,
+						    kvec_t_u8_warp* k_flag, kvec_t_u64_warp* chain_idx, void *ha_flt_tab, ha_pt_t *ha_idx, 
+                            overlap_region* f_cigar, kvec_t_u64_warp* dbg_ct, st_mt_t *sp)
+{
+	uint64_t i, k, l;
 	// prepare
     clear_Candidates_list(cl);
-    clear_overlap_region_alloc(ovlp);
+    clear_overlap_region_alloc(ol);
 	ab->mz.n = 0, ab->n_a = 0;
 
-	mz2_ha_sketch(u->s, u->len, uw, uk, uid, is_hpc, &ab->mz, ha_flt_tab, asm_opt.mz_sample_dist, k_flag, dbg_ct,	
-	NULL, -1, asm_opt.dp_min_len, -1, sp, asm_opt.mz_rewin, 1);
+	// get the list of anchors
+    mz2_ha_sketch(r, rlen, rw, rk, 0, is_hpc, &ab->mz, ha_flt_tab, asm_opt.mz_sample_dist, k_flag, dbg_ct,   
+    NULL, -1, asm_opt.dp_min_len, -1, sp, asm_opt.mz_rewin, 1);
+	
 	// minimizer of queried read
 	if (ab->mz.m > ab->old_mz_m) {
-        ab->old_mz_m = ab->mz.m;
-        REALLOC(ab->seed, ab->old_mz_m);
-    }
-    for (i = 0, ab->n_a = 0; i < ab->mz.n; ++i) {
-        int n;
-        ab->seed[i].a = ha_ptl_get(ha_idx, ab->mz.a[i].x, &n);
-        ab->seed[i].n = n;
-        ab->seed[i].cnt = ha_ft_cnt(ha_flt_tab, ab->mz.a[i].x);
-        ab->n_a += n;
-    }
-    if (ab->n_a > ab->m_a) {
-        ab->m_a = ab->n_a;
-        kroundup64(ab->m_a);
-        REALLOC(ab->a, ab->m_a);
-    }
-    for (i = 0, k = 0; i < ab->mz.n; ++i) {
-        int j;
-        ///z is one of the minimizer
-        ha_mzl_t *z = &ab->mz.a[i];
-        seedl_t *s = &ab->seed[i];
-        for (j = 0; j < s->n; ++j) {
-            const ha_idxposl_t *y = &s->a[j];
-            anchor1_t *an = &ab->a[k++];
-            uint8_t rev = z->rev == y->rev? 0 : 1;
-            an->other_off = y->pos;
-            an->self_off = rev? u->len - 1 - (z->pos + 1 - z->span) : z->pos;
-            an->cnt = s->cnt;
-            an->srt = (uint64_t)y->rid<<33 | (uint64_t)rev<<32 | an->other_off;
-        }
-    }
+		ab->old_mz_m = ab->mz.m;
+		REALLOC(ab->seed, ab->old_mz_m);
+	}
+	for (i = 0, ab->n_a = 0; i < ab->mz.n; ++i) {
+		int n;
+		ab->seed[i].a = ha_ptl_get(ha_idx, ab->mz.a[i].x, &n);
+		ab->seed[i].n = n;
+		ab->seed[i].cnt = ha_ft_cnt(ha_flt_tab, ab->mz.a[i].x);
+		ab->n_a += n;
+	}
+	if (ab->n_a > ab->m_a) {
+		ab->m_a = ab->n_a;
+		kroundup64(ab->m_a);
+		REALLOC(ab->a, ab->m_a);
+	}
+	for (i = 0, k = 0; i < ab->mz.n; ++i) {
+		int j;
+		///z is one of the minimizer
+		ha_mzl_t *z = &ab->mz.a[i];
+		seedl_t *s = &ab->seed[i];
+		for (j = 0; j < s->n; ++j) {
+			const ha_idxposl_t *y = &s->a[j];
+			anchor1_t *an = &ab->a[k++];
+			uint8_t rev = z->rev == y->rev? 0 : 1;
+			an->other_off = y->pos;
+			an->self_off = rev? rlen - 1 - (z->pos + 1 - z->span) : z->pos;
+			an->cnt = s->n;
+			an->srt = (uint64_t)y->rid<<33 | (uint64_t)rev<<32 | an->other_off;
+		}
+	}
 
-    // sort anchors
-    radix_sort_ha_an1(ab->a, ab->a + ab->n_a);
-    for (k = 1, l = 0; k <= ab->n_a; ++k) {
-        if (k == ab->n_a || ab->a[k].srt != ab->a[l].srt) {
-            if (k - l > 1)
-                radix_sort_ha_an2(ab->a + l, ab->a + k);
-            l = k;
-        }
-    }
+	// sort anchors
+	radix_sort_ha_an1(ab->a, ab->a + ab->n_a);
+	for (k = 1, l = 0; k <= ab->n_a; ++k) {
+		if (k == ab->n_a || ab->a[k].srt != ab->a[l].srt) {
+			if (k - l > 1)
+				radix_sort_ha_an2(ab->a + l, ab->a + k);
+			l = k;
+		}
+	}
 
 
-    // copy over to _cl_
-    if (ab->m_a >= (uint64_t)cl->size) {
-        cl->size = ab->m_a;
-        REALLOC(cl->list, cl->size);
-    }
-    for (k = 0; k < ab->n_a; ++k) {
-        k_mer_hit *p = &cl->list[k];
-        p->readID = ab->a[k].srt >> 33;
-        p->strand = ab->a[k].srt >> 32 & 1;
-        p->offset = ab->a[k].other_off;
-        p->self_offset = ab->a[k].self_off;
-        p->cnt = (ab->a[k].cnt == 1? 1 : 16);
-    }
-    cl->length = ab->n_a;
-    // calculate_overlap_region_by_chaining(cl, ovlp, chain_idx, rid, ucr->length, &R_INF, bw_thres, keep_whole_chain, f_cigar);
-	// calculate_ug_chaining(cl, overlap_list, chain_idx, rid, ua, bw_thres, keep_whole_chain, f_cigar, ab->mz.n, chain_match_rate);
+	// copy over to _cl_
+	if (ab->m_a >= (uint64_t)cl->size) {
+		cl->size = ab->m_a;
+		REALLOC(cl->list, cl->size);
+	}
+	for (k = 0; k < ab->n_a; ++k) {
+		k_mer_hit *p = &cl->list[k];
+		p->readID = ab->a[k].srt >> 33;
+		p->strand = ab->a[k].srt >> 32 & 1;
+		p->offset = ab->a[k].other_off;
+		p->self_offset = ab->a[k].self_off;
+		p->cnt = (ab->a[k].cnt == 1? 1 : 16);
+	}
+	cl->length = ab->n_a;
 
+	calculate_overlap_region_by_chaining(cl, ol, chain_idx, id, rlen, &R_INF, bw_thres, keep_whole_chain, f_cigar);
 
-    #if 0
-    if (overlap_list->length > 0) {
-        fprintf(stderr, "B\t%ld\t%ld\t%d\n", (long)rid, (long)overlap_list->length, rlen);
-        for (int i = 0; i < (int)overlap_list->length; ++i) {
-            overlap_region *r = &overlap_list->list[i];
-            fprintf(stderr, "C\t%d\t%d\t%d\t%c\t%d\t%ld\t%d\t%d\t%c\t%d\t%d\n", (int)r->x_id, (int)r->x_pos_s, (int)r->x_pos_e, "+-"[r->x_pos_strand],
-                    (int)r->y_id, (long)Get_READ_LENGTH(R_INF, r->y_id), (int)r->y_pos_s, (int)r->y_pos_e, "+-"[r->y_pos_strand], (int)r->shared_seed, ha_ov_type(r, rlen));
-        }
-    }
-    #endif
-    
-    if ((int)ovlp->length > max_n_chain) {
-        int32_t w, n[4], s[4];
-        n[0] = n[1] = n[2] = n[3] = 0, s[0] = s[1] = s[2] = s[3] = 0;
-        ks_introsort_or_ss(ovlp->length, ovlp->list);
-        for (i = 0; i < (uint32_t)ovlp->length; ++i) {
-            const overlap_region *r = &ovlp->list[i];
-            w = ha_ov_type(r, rlen);
-            ++n[w];
-            if ((int)n[w] == max_n_chain) s[w] = r->shared_seed;
-        }
-        if (s[0] > 0 || s[1] > 0 || s[2] > 0 || s[3] > 0) {
-            // n[0] = n[1] = n[2] = n[3] = 0;
-            for (i = 0, k = 0; i < (uint32_t)ovlp->length; ++i) {
-                overlap_region *r = &ovlp->list[i];
-                w = ha_ov_type(r, rlen);
-                // ++n[w];
-                // if (((int)n[w] <= max_n_chain) || (r->shared_seed >= s[w] && s[w] >= (asm_opt.k_mer_length<<1))) {
-                if (r->shared_seed >= s[w]) {
-                    if ((uint32_t)k != i) {
-                        overlap_region t;
-                        t = ovlp->list[k];
-                        ovlp->list[k] = ovlp->list[i];
-                        ovlp->list[i] = t;
-                    }
-                    ++k;
-                }
-            }
-            ovlp->length = k;
-        }
-    }
-    ///ks_introsort_or_xs(overlap_list->length, overlap_list->list);
-}
-**/
+	#if 0
+	if (ol->length > 0) {
+		fprintf(stderr, "B\t%ld\t%ld\t%d\n", (long)rid, (long)ol->length, rlen);
+		for (int i = 0; i < (int)ol->length; ++i) {
+			overlap_region *r = &ol->list[i];
+			fprintf(stderr, "C\t%d\t%d\t%d\t%c\t%d\t%ld\t%d\t%d\t%c\t%d\t%d\n", (int)r->x_id, (int)r->x_pos_s, (int)r->x_pos_e, "+-"[r->x_pos_strand],
+					(int)r->y_id, (long)Get_READ_LENGTH(R_INF, r->y_id), (int)r->y_pos_s, (int)r->y_pos_e, "+-"[r->y_pos_strand], (int)r->shared_seed, ha_ov_type(r, rlen));
+		}
+	}
+	#endif
+	
+	if ((int)ol->length > max_n_chain) {
+		int32_t w, n[4], s[4];
+		n[0] = n[1] = n[2] = n[3] = 0, s[0] = s[1] = s[2] = s[3] = 0;
+		ks_introsort_or_ss(ol->length, ol->list);
+		for (i = 0; i < (uint32_t)ol->length; ++i) {
+			const overlap_region *r = &ol->list[i];
+			w = ha_ov_type(r, rlen);
+			++n[w];
+			if ((int)n[w] == max_n_chain) s[w] = r->shared_seed;
+		}
+		if (s[0] > 0 || s[1] > 0 || s[2] > 0 || s[3] > 0) {
+			// n[0] = n[1] = n[2] = n[3] = 0;
+			for (i = 0, k = 0; i < (uint32_t)ol->length; ++i) {
+				overlap_region *r = &ol->list[i];
+				w = ha_ov_type(r, rlen);
+				// ++n[w];
+				// if (((int)n[w] <= max_n_chain) || (r->shared_seed >= s[w] && s[w] >= (asm_opt.k_mer_length<<1))) {
+				if (r->shared_seed >= s[w]) {
+					if ((uint32_t)k != i) {
+						overlap_region t;
+						t = ol->list[k];
+						ol->list[k] = ol->list[i];
+						ol->list[i] = t;
+					}
+					++k;
+				}
+			}
+			ol->length = k;
+		}
+	}
 
+	///ks_introsort_or_xs(overlap_list->length, overlap_list->list);
+}
 
 void ha_get_ug_candidates(ha_abuf_t *ab, int64_t rid, ma_utg_t *u, ma_utg_v *ua, overlap_region_alloc *overlap_list, Candidates_list *cl, double bw_thres, int max_n_chain, int keep_whole_chain, kvec_t_u8_warp* k_flag,
 kvec_t_u64_warp* chain_idx, void *ha_flt_tab, ha_pt_t *ha_idx, overlap_region* f_cigar, kvec_t_u64_warp* dbg_ct, double chain_match_rate)
diff --git a/inter.cpp b/inter.cpp
index ce6b2d5..e4d6315 100644
--- a/inter.cpp
+++ b/inter.cpp
@@ -8,12 +8,20 @@
 #include "Overlaps.h"
 #include "CommandLines.h"
 #include "htab.h"
+#include "Hash_Table.h"
 KSEQ_INIT(gzFile, gzread)
 
 typedef struct {
 	int w, k, bw, max_gap, is_HPC, hap_n;
 } mg_idxopt_t;
 
+typedef struct {
+    ha_abufl_t *abl;
+    st_mt_t sp;
+    Candidates_list clist;
+    overlap_region_alloc olist;
+} ma_ov_buf_t;
+
 typedef struct { // global data structure for kt_pipeline()
     const void *ha_flt_tab;
     const ha_pt_t *ha_idx;
@@ -25,6 +33,39 @@ typedef struct { // global data structure for kt_pipeline()
     uint64_t total_pair;
 } uldat_t;
 
+typedef struct { // data structure for each step in kt_pipeline()
+    const void *ha_flt_tab;
+    const ha_pt_t *ha_idx;
+	int n, m, sum_len;
+	uint64_t *len, id;
+	char **seq;
+    ma_ov_buf_t **mo;
+} utepdat_t;
+
+ma_ov_buf_t **init_ma_ov_buf_t_arr(uint64_t n)
+{
+    uint64_t i;
+    ma_ov_buf_t **p = NULL; CALLOC(p, 1); CALLOC(*p, n);
+    for (i = 0; i < n; i++){
+        kv_init((*p)[i].sp); (*p)[i].abl = ha_abufl_init();
+        init_Candidates_list(&((*p)[i].clist));
+	    init_overlap_region_alloc(&((*p)[i].olist));
+    }
+    return p;
+}
+
+void destory_ma_ov_buf_t_arr(ma_ov_buf_t ***p, uint64_t n)
+{
+    uint64_t i;
+    for (i = 0; i < n; i++){
+        kv_destroy((**p)[i].sp); ha_abufl_destroy((**p)[i].abl);
+        destory_Candidates_list(&((**p)[i].clist));
+	    destory_overlap_region_alloc(&((**p)[i].olist));
+    }
+    free((**p)); free((*p));
+}
+
+
 void init_mg_opt(mg_idxopt_t *opt, int is_HPC, int k, int w, int hap_n)
 {
     opt->k = k; 
@@ -50,33 +91,39 @@ void uidx_destory()
     ha_pt_destroy(ha_idx);
 }
 
+static void worker_for_ul_alignment(void *data, long i, int tid) // callback for kt_for()
+{
+    utepdat_t *s = (utepdat_t*)data;
+    ma_ov_buf_t *b = s->mo[tid];
+    uint64_t len = s->len[i];
+    char *r = s->seq[i];
+
+
+}
+
 static void *worker_ul_pipeline(void *data, int step, void *in) // callback for kt_pipeline()
 {
-    /**
     uldat_t *p = (uldat_t*)data;
     ///uint64_t total_base = 0, total_pair = 0;
     if (step == 0) { // step 1: read a block of sequences
-        int ret1, ret2;
-        uint64_t l1, l2;
-		stepdat_t *s;
+        int ret;
+        uint64_t l;
+		utepdat_t *s;
 		CALLOC(s, 1);
-        s->idx = p->idx; s->id = p->total_pair; s->t_ch = p->t_ch;
-        while (((ret1 = kseq_read(p->ks1)) >= 0)&&((ret2 = kseq_read(p->ks2)) >= 0)) 
+        s->ha_flt_tab = p->ha_flt_tab; s->ha_idx = p->ha_idx; s->id = p->total_pair; 
+        while ((ret = kseq_read(p->ks)) >= 0) 
         {
-            if (p->ks1->seq.l < p->idx->k || p->ks2->seq.l < p->idx->k) continue;
+            if (p->ks->seq.l < (uint64_t)p->opt->k) continue;
             if (s->n == s->m) {
                 s->m = s->m < 16? 16 : s->m + (s->n>>1);
                 REALLOC(s->len, s->m);
                 REALLOC(s->seq, s->m);
             }
-
-            l1 = p->ks1->seq.l; l2 = p->ks2->seq.l;
-            MALLOC(s->seq[s->n], l1+l2);
-            s->sum_len += l1+l2;
-            memcpy(s->seq[s->n], p->ks1->seq.s, l1);
-            memcpy(s->seq[s->n]+l1, p->ks2->seq.s, l2);
-            s->len[s->n++] = (uint64_t)(l1<<32)|(uint64_t)l2;
-
+            l = p->ks->seq.l;
+            MALLOC(s->seq[s->n], l);
+            s->sum_len += l;
+            memcpy(s->seq[s->n], p->ks->seq.s, l);
+            s->len[s->n++] = l;
             if (s->sum_len >= p->chunk_size) break;            
         }
         p->total_pair += s->n;
@@ -84,25 +131,24 @@ static void *worker_ul_pipeline(void *data, int step, void *in) // callback for
 		else return s;
     }
     else if (step == 1) { // step 2: alignment
-        stepdat_t *s = (stepdat_t*)in;
-        CALLOC(s->pos_buf, p->n_thread);
+        utepdat_t *s = (utepdat_t*)in;
+        s->mo = init_ma_ov_buf_t_arr(p->n_thread);
+        /**
         CALLOC(s->pos, s->n);
+        **/
         int i;
-        kt_for(p->n_thread, worker_for_alignment, s, s->n);
+        kt_for(p->n_thread, worker_for_ul_alignment, s, s->n);
         for (i = 0; i < s->n; ++i) {
             free(s->seq[i]);
-            p->total_base += (s->len[i]>>32) + (uint32_t)s->len[i];
+            p->total_base += s->len[i];
         }
-        
         free(s->seq); free(s->len);
-        for (i = 0; i < (int)p->n_thread; ++i) {
-            free(s->pos_buf[i].a.a);
-        }
-        free(s->pos_buf);
+        destory_ma_ov_buf_t_arr(&(s->mo), p->n_thread);
 		return s;
     }
     else if (step == 2) { // step 3: dump
-        stepdat_t *s = (stepdat_t*)in;
+        utepdat_t *s = (utepdat_t*)in;
+        /**
         int i;
         for (i = 0; i < s->n; ++i) {
             // if(s->pos[i].a == NULL) continue;
@@ -111,9 +157,9 @@ static void *worker_ul_pipeline(void *data, int step, void *in) // callback for
             kv_push(pe_hit, p->hits.a, s->pos[i]);
         }
         free(s->pos);
+        **/
         free(s);
     }
-    **/
     return 0;
 }