anchor.cpp

#include <stdio.h>
#include <math.h>
#include <assert.h>
#include "htab.h"
#include "ksort.h"
#include "Hash_Table.h"
#include "kalloc.h"
#include "Overlaps.h"

#define HA_KMER_GOOD_RATIO 0.333
#define OFL 0.95
#define CH_OCC 4
#define CH_SC 16

typedef struct { // this struct is not strictly necessary; we can use k_mer_pos instead, with modifications
	uint64_t srt;
	uint32_t self_off;
	uint32_t other_off;
	uint32_t cnt;
} anchor1_t;

#define an_key1(a) ((a).srt)
#define an_key2(a) ((a).self_off)
#define an_key3(a) ((a).other_off)
KRADIX_SORT_INIT(ha_an1, anchor1_t, an_key1, 8)
KRADIX_SORT_INIT(ha_an2, anchor1_t, an_key2, 4)
KRADIX_SORT_INIT(ha_an3, anchor1_t, an_key3, 4)
#define generic_key(x) (x)
KRADIX_SORT_INIT(anc64, uint64_t, generic_key, 8)

#define oreg_xs_lt(a, b) (((uint64_t)(a).x_pos_s<<32|(a).x_pos_e) < ((uint64_t)(b).x_pos_s<<32|(b).x_pos_e))
KSORT_INIT(or_xs, overlap_region, oreg_xs_lt)

#define oreg_ss_lt(a, b) ((a).shared_seed > (b).shared_seed) // in the decending order
KSORT_INIT(or_ss, overlap_region, oreg_ss_lt)

#define oreg_occ_lt(a, b) ((a).align_length > (b).align_length) // in the decending order
KSORT_INIT(or_occ, overlap_region, oreg_occ_lt)

#define oreg_id_lt(a, b) ((a).y_id < (b).y_id)
KSORT_INIT(or_id, overlap_region, oreg_id_lt)

typedef struct {
	int n;
	const ha_idxpos_t *a;
} seed1_t;

typedef struct {
	int n, cnt;
	const ha_idxposl_t *a;
} seedl_t;

struct ha_abuf_s {
	uint64_t n_a, m_a;///number of anchors (seed positions)
	uint32_t old_mz_m;///number of seeds
	ha_mz1_v mz;
	seed1_t *seed;
	anchor1_t *a;
};

struct ha_abufl_s {
	uint64_t n_a, m_a;///number of anchors (seed positions)
	uint32_t old_mz_m;///number of seeds
	ha_mzl_v mz;
	seedl_t *seed;
	anchor1_t *a;
};

#define HA_ABUF_INIT(HType, MZType, SDType, sf) \
HType *sf##_init_buf(void *km){HType *b = NULL; KCALLOC((km), b, 1); return b;}\
HType *sf##_init(void){return (HType*)calloc(1, sizeof(HType));}\
void sf##_free_buf(void *km, HType *ab, int is_z){if(ab){kfree(km, ab->seed); kfree(km, ab->a); kfree(km, ab->mz.a); if((is_z)){memset(ab, 0, sizeof(*ab));}}}\
void sf##_destroy_buf(void *km, HType *ab){if(ab){kfree(km, ab->seed); kfree(km, ab->a); kfree(km, ab->mz.a); kfree(km, ab);}}\
void sf##_destroy(HType *ab){if(ab){free(ab->seed); free(ab->a); free(ab->mz.a); free(ab);}}\
uint64_t sf##_mem(const HType *ab){\
	return ab->m_a * sizeof(anchor1_t) + ab->mz.m * (sizeof(MZType) + sizeof(SDType)) + sizeof(HType);\
}

HA_ABUF_INIT(ha_abuf_s, ha_mz1_t, seed1_t, ha_abuf)
HA_ABUF_INIT(ha_abufl_s, ha_mzl_t, seedl_t, ha_abufl)

int ha_ov_type(const overlap_region *r, uint32_t len)
{
	if (r->x_pos_s == 0 && r->x_pos_e == len - 1) return 2; // contained in a longer read
	else if (r->x_pos_s > 0 && r->x_pos_e < len - 1) return 3; // containing a shorter read
	else return r->x_pos_s == 0? 0 : 1;
}

void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, 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, st_mt_t *sp)
{
	uint32_t i, rlen;
	uint64_t k, l;
	uint32_t low_occ = asm_opt.hom_cov * HA_KMER_GOOD_RATIO;
	uint32_t high_occ = asm_opt.hom_cov * (2.0 - HA_KMER_GOOD_RATIO);
	if(low_occ < 2) low_occ = 2;

	// prepare
    clear_Candidates_list(cl);
    clear_overlap_region_alloc(overlap_list);
	recover_UC_Read(ucr, &R_INF, rid);
	ab->mz.n = 0, ab->n_a = 0;
	rlen = Get_READ_LENGTH(R_INF, rid); // read length

	// get the list of anchors
	mz1_ha_sketch(ucr->seq, ucr->length, asm_opt.mz_win, asm_opt.k_mer_length, 0, !(asm_opt.flag & HA_F_NO_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, 0, NULL);
	// 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_pt_get(ha_idx, ab->mz.a[i].x, &n);
		ab->seed[i].n = n;
		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_mz1_t *z = &ab->mz.a[i];
		seed1_t *s = &ab->seed[i];
		for (j = 0; j < s->n; ++j) {
			const ha_idxpos_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? ucr->length - 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;
		}
	}


	// 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;
		if(ab->a[k].cnt > low_occ && ab->a[k].cnt < high_occ){
			p->cnt = 1;
		}
		else if(ab->a[k].cnt <= low_occ){
			p->cnt = 2;
		}
		else{
			p->cnt = 1 + ((ab->a[k].cnt + (high_occ<<1) - 1)/(high_occ<<1));
			p->cnt = pow(p->cnt, 1.1);
		}
	}
	cl->length = ab->n_a;

	calculate_overlap_region_by_chaining(cl, overlap_list, chain_idx, rid, ucr->length, &R_INF, NULL, bw_thres, keep_whole_chain, f_cigar, NULL);

	#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)overlap_list->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(overlap_list->length, overlap_list->list);
		for (i = 0; i < (uint32_t)overlap_list->length; ++i) {
			const overlap_region *r = &overlap_list->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)overlap_list->length; ++i) {
				overlap_region *r = &overlap_list->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 = overlap_list->list[k];
						overlap_list->list[k] = overlap_list->list[i];
						overlap_list->list[i] = t;
					}
					++k;
				}
			}
			overlap_list->length = k;
		}
	}

	///ks_introsort_or_xs(overlap_list->length, overlap_list->list);
}

void ha_get_new_ul_candidates(ha_abufl_t *ab, int64_t rid, char* rs, int64_t rl, uint64_t mz_w, uint64_t mz_k, const ul_idx_t *uref, 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, st_mt_t *sp, uint32_t high_occ, void *km)
{
	uint32_t i;
	uint64_t k, l;
	if(high_occ < 1) high_occ = 1;
	// uint32_t high_occ = asm_opt.hom_cov >= 1?asm_opt.hom_cov:1;

	// prepare
    clear_Candidates_list(cl);
    clear_overlap_region_alloc(overlap_list);
	ab->mz.n = 0, ab->n_a = 0;

	// get the list of anchors
	mz2_ha_sketch(rs, rl, mz_w, mz_k, 0, !(asm_opt.flag & HA_F_NO_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, 0, km);
	
	// minimizer of queried read
	if (ab->mz.m > ab->old_mz_m) {
		ab->old_mz_m = ab->mz.m;
		KREALLOC(km, 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->n_a += n;
	}
	if (ab->n_a > ab->m_a) {
		ab->m_a = ab->n_a;
		KREALLOC(km, 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? rl - 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;
		}
	}

	
	// copy over to _cl_
	if (ab->m_a >= (uint64_t)cl->size) {
		cl->size = ab->m_a;
		KREALLOC(km, 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;
		if(ab->a[k].cnt <= high_occ){
			p->cnt = 1;
		}
		else{
			p->cnt = 1 + ((ab->a[k].cnt + (high_occ<<1) - 1)/(high_occ<<1));
			p->cnt = pow(p->cnt, 1.1);
		}
	}
	cl->length = ab->n_a;

	calculate_overlap_region_by_chaining(cl, overlap_list, chain_idx, rid, rl, NULL, uref, bw_thres, keep_whole_chain, f_cigar, km);
	
	#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)overlap_list->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(overlap_list->length, overlap_list->list);
		for (i = 0; i < (uint32_t)overlap_list->length; ++i) {
			const overlap_region *r = &overlap_list->list[i];
			w = ha_ov_type(r, rl);
			++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)overlap_list->length; ++i) {
				overlap_region *r = &overlap_list->list[i];
				w = ha_ov_type(r, rl);
				// ++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 = overlap_list->list[k];
						overlap_list->list[k] = overlap_list->list[i];
						overlap_list->list[i] = t;
					}
					++k;
				}
			}
			overlap_list->length = k;
		}
	}

	///ks_introsort_or_xs(overlap_list->length, overlap_list->list);
}


void calculate_ug_chaining(Candidates_list* candidates, overlap_region_alloc* overlap_list, kvec_t_u64_warp* chain_idx,
                                          uint64_t readID, ma_utg_v *ua, double band_width_threshold, int add_beg_end, overlap_region* f_cigar, long long mz_occ, double mz_rate)
{
    long long i = 0;
    uint64_t current_ID;
    uint64_t current_stand;

    if (candidates->length == 0)
    {
        return;
    }

    long long sub_region_beg;
    long long sub_region_end;
	long long chain_len;

    clear_fake_cigar(&((*f_cigar).f_cigar));

    i = 0;
    while (i < candidates->length)
    {
        chain_idx->a.n = 0;
        current_ID = candidates->list[i].readID;
        current_stand = candidates->list[i].strand;

        ///reference read
        (*f_cigar).x_id = readID;
        (*f_cigar).x_pos_strand = current_stand;
        ///query read
        (*f_cigar).y_id = current_ID;
        ///here the strand of query is always 0
        (*f_cigar).y_pos_strand = 0;  

        sub_region_beg = i;
        sub_region_end = i;
        i++;

        while (i < candidates->length 
        && 
        current_ID == candidates->list[i].readID
        &&
        current_stand == candidates->list[i].strand)
        {
            sub_region_end = i;
            i++;
        }

        if ((*f_cigar).x_id == (*f_cigar).y_id)
        {
            continue;
        }

		chain_len = chain_DP(candidates->list + sub_region_beg,
				sub_region_end - sub_region_beg + 1, &(candidates->chainDP), f_cigar, band_width_threshold,
				50, ua->a[(*f_cigar).x_id].len, ua->a[(*f_cigar).y_id].len, NULL);
		
		
		// if ((*f_cigar).x_id != (*f_cigar).y_id)
		if ((*f_cigar).x_id != (*f_cigar).y_id && chain_len > mz_occ*mz_rate)
        {
			append_utg_inexact_overlap_region_alloc(overlap_list, f_cigar, ua, add_beg_end, NULL);
        }
    }
}


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(ol);
	ab->mz.n = 0, ab->n_a = 0;

	// 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, NULL);
	
	// 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? 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;
		}
	}


	// 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**/NULL, NULL, bw_thres, keep_whole_chain, f_cigar, NULL);

	#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)
{
    uint32_t i;
    uint64_t k, l;

    // prepare
    clear_Candidates_list(cl);
    clear_overlap_region_alloc(overlap_list);
    ab->mz.n = 0, ab->n_a = 0;

    // get the list of anchors
    //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;
        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_pt_get(ha_idx, ab->mz.a[i].x, &n);
        ab->seed[i].n = n;
        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_mz1_t *z = &ab->mz.a[i];
        seed1_t *s = &ab->seed[i];
        for (j = 0; j < s->n; ++j) {
            const ha_idxpos_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 = 1;
            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;
        }
    }


    // 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 = 1;
    }
    cl->length = ab->n_a;

    calculate_ug_chaining(cl, overlap_list, chain_idx, rid, ua, bw_thres, keep_whole_chain, f_cigar, ab->mz.n, chain_match_rate);

    #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)overlap_list->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(overlap_list->length, overlap_list->list);
        for (i = 0; i < (uint32_t)overlap_list->length; ++i) {
            const overlap_region *r = &overlap_list->list[i];
            w = ha_ov_type(r, u->len);
            ++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) {
            for (i = 0, k = 0; i < (uint32_t)overlap_list->length; ++i) {
                overlap_region *r = &overlap_list->list[i];
                w = ha_ov_type(r, u->len);
                if (r->shared_seed >= s[w]) {
                    if ((uint32_t)k != i) {
                        overlap_region t;
                        t = overlap_list->list[k];
                        overlap_list->list[k] = overlap_list->list[i];
                        overlap_list->list[i] = t;
                    }
                    ++k;
                }
            }
            overlap_list->length = k;
        }
    }

    ///ks_introsort_or_xs(overlap_list->length, overlap_list->list);
}


void lable_matched_ovlp(overlap_region_alloc* overlap_list, ma_hit_t_alloc* paf)
{
	uint64_t j = 0, inner_j = 0;
	while (j < overlap_list->length && inner_j < paf->length)
    {
        if(overlap_list->list[j].y_id < paf->buffer[inner_j].tn)
        {
            j++;
        }
        else if(overlap_list->list[j].y_id > paf->buffer[inner_j].tn)
        {
            inner_j++;
        }
        else
        {
            if(overlap_list->list[j].y_pos_strand == paf->buffer[inner_j].rev)
            {
				overlap_list->list[j].is_match = 1;
            }
            j++;
            inner_j++;
        }
    }
}


void ha_get_candidates_interface(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, overlap_region_alloc *overlap_list_hp, 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, ma_hit_t_alloc* paf, ma_hit_t_alloc* rev_paf, overlap_region* f_cigar,
								 kvec_t_u64_warp* dbg_ct, st_mt_t *sp)
{
	extern void *ha_flt_tab;
	extern ha_pt_t *ha_idx;
	extern void *ha_flt_tab_hp;
	extern ha_pt_t *ha_idx_hp;

	ha_get_new_candidates(ab, rid, ucr, overlap_list, cl, bw_thres, max_n_chain, keep_whole_chain, k_flag, chain_idx, ha_flt_tab, ha_idx, f_cigar, dbg_ct, sp);

	if(ha_idx_hp)
	{
		uint32_t i, k, y_id, overlapLen, max_i;
		int shared_seed;
		overlap_region t;
		overlap_region_sort_y_id(overlap_list->list, overlap_list->length);
		ma_hit_sort_tn(paf->buffer, paf->length);
		ma_hit_sort_tn(rev_paf->buffer, rev_paf->length);
		lable_matched_ovlp(overlap_list, paf);
		lable_matched_ovlp(overlap_list, rev_paf);

		for (i = 0, k = 0; i < overlap_list->length; ++i) 
		{
			if(overlap_list->list[i].is_match == 1)
			{
				if(k != i)
				{
					t = overlap_list->list[k];
					overlap_list->list[k] = overlap_list->list[i];
					overlap_list->list[i] = t;
					overlap_list->list[k].is_match = 0;
				}
				k++;
			}
		}
		overlap_list->length = k;


		ha_get_new_candidates(ab, rid, ucr, overlap_list_hp, cl, bw_thres, max_n_chain, keep_whole_chain, k_flag, chain_idx, ha_flt_tab_hp, ha_idx_hp, f_cigar, dbg_ct, sp);	
		
		if(overlap_list->length + overlap_list_hp->length > overlap_list->size)
		{
			overlap_list->list = (overlap_region*)realloc(overlap_list->list, 
				sizeof(overlap_region)*(overlap_list->length + overlap_list_hp->length));
			memset(overlap_list->list + overlap_list->size, 0, sizeof(overlap_region)*
				(overlap_list->length + overlap_list_hp->length - overlap_list->size));
			overlap_list->size = overlap_list->length + overlap_list_hp->length;
		}
		
		for (i = 0, k = overlap_list->length; i < overlap_list_hp->length; i++, k++)
		{
			t = overlap_list->list[k];
			overlap_list->list[k] = overlap_list_hp->list[i];
			overlap_list_hp->list[i] = t;
		}
		overlap_list->length = k;
		
		overlap_region_sort_y_id(overlap_list->list, overlap_list->length);

		i = k = 0;
		while (i < overlap_list->length)
		{
			y_id = overlap_list->list[i].y_id;
			shared_seed = overlap_list->list[i].shared_seed;
			overlapLen = overlap_list->list[i].overlapLen;
			max_i = i;
			i++;
			while (i < overlap_list->length && overlap_list->list[i].y_id == y_id)
			{
				if((overlap_list->list[i].shared_seed > shared_seed) || 
				  ((overlap_list->list[i].shared_seed == shared_seed) && (overlap_list->list[i].overlapLen <= overlapLen)))
				{
					y_id = overlap_list->list[i].y_id;
					shared_seed = overlap_list->list[i].shared_seed;
					overlapLen = overlap_list->list[i].overlapLen;
					max_i = i;
				}
				i++;
			}

			if(k != max_i)
			{
				t = overlap_list->list[k];
				overlap_list->list[k] = overlap_list->list[max_i];
				overlap_list->list[max_i] = t;
			}
			k++;
		}

		overlap_list->length = k;
	}
	
	ks_introsort_or_xs(overlap_list->length, overlap_list->list);
}


void ha_get_ul_candidates_interface(ha_abufl_t *ab, int64_t rid, char* rs, uint64_t rl, uint64_t mz_w, uint64_t mz_k, const ul_idx_t *uref, overlap_region_alloc *overlap_list, overlap_region_alloc *overlap_list_hp, 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, overlap_region* f_cigar, kvec_t_u64_warp* dbg_ct, st_mt_t *sp, uint32_t high_occ, void *km)
{
	extern void *ha_flt_tab;
	extern ha_pt_t *ha_idx;

	ha_get_new_ul_candidates(ab, rid, rs, rl, mz_w, mz_k, uref, overlap_list, cl, bw_thres, max_n_chain, keep_whole_chain, k_flag, chain_idx, ha_flt_tab, ha_idx, f_cigar, dbg_ct, sp, high_occ, km);
	if(km) {
		ha_abufl_free_buf(km, ab, 1); 
		destory_Candidates_list_buf(km, cl, 1); 
	}
	ks_introsort_or_xs(overlap_list->length, overlap_list->list);
}



void ha_sort_list_by_anchor(overlap_region_alloc *overlap_list)
{
	ks_introsort_or_xs(overlap_list->length, overlap_list->list);
}


void minimizers_gen(ha_abufl_t *ab, char* rs, int64_t rl, uint64_t mz_w, uint64_t mz_k, Candidates_list *cl, kvec_t_u8_warp* k_flag, 
void *ha_flt_tab, ha_pt_t *ha_idx, kvec_t_u64_warp* dbg_ct, st_mt_t *sp, uint32_t *high_occ, uint32_t *low_occ)
{
	// fprintf(stderr, "+[M::%s]\n", __func__);
	uint64_t i, k, l, max_cnt = UINT32_MAX, min_cnt = 0; int n, j; ha_mzl_t *z; seedl_t *s; 
	if(high_occ) {
		max_cnt = (*high_occ);
		if(max_cnt < 2) max_cnt = 2;
	}
	if(low_occ) {
		min_cnt = (*low_occ);
		if(min_cnt < 2) min_cnt = 2;
	}
	clear_Candidates_list(cl); ab->mz.n = 0, ab->n_a = 0;
	
	// get the list of anchors
	mz2_ha_sketch(rs, rl, mz_w, mz_k, 0, !(asm_opt.flag & HA_F_NO_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, 0, NULL);

	// 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) {
		ab->seed[i].a = ha_ptl_get(ha_idx, ab->mz.a[i].x, &n);
		ab->seed[i].n = n;
		ab->n_a += n;
	}

	if (ab->n_a > ab->m_a) {
		ab->m_a = ab->n_a;
		REALLOC(ab->a, ab->m_a);
	}

	for (i = 0, k = 0; i < ab->mz.n; ++i) {
		///z is one of the minimizer
		z = &ab->mz.a[i]; 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? rl - 1 - (z->pos + 1 - z->span) : z->pos;
			///an->cnt: cnt<<8|span
			an->cnt = s->n; if(an->cnt > ((uint32_t)(0xffffffu))) an->cnt = 0xffffffu;
			an->cnt <<= 8; an->cnt |= ((z->span <= ((uint32_t)(0xffu)))?z->span:((uint32_t)(0xffu)));
			an->srt = (uint64_t)y->rid<<33 | (uint64_t)rev<<32 | an->other_off;
		}
	}

	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;
		if(((ab->a[k].cnt>>8) < max_cnt) && ((ab->a[k].cnt>>8) > min_cnt)){
			p->cnt = 1;
		} else if((ab->a[k].cnt>>8) <= min_cnt) {
			p->cnt = 2;
		} else{
			p->cnt = 1 + (((ab->a[k].cnt>>8) + (max_cnt<<1) - 1)/(max_cnt<<1));
			p->cnt = pow(p->cnt, 1.1);
		}
		if(p->cnt > ((uint32_t)(0xffffffu))) p->cnt = 0xffffffu;
		p->cnt <<= 8; p->cnt |= (((uint32_t)(0xffu))&(ab->a[k].cnt));
	}
	cl->length = ab->n_a;
}


void minimizers_qgen(ha_abufl_t *ab, char* rs, int64_t rl, uint64_t mz_w, uint64_t mz_k, Candidates_list *cl, kvec_t_u8_warp* k_flag, 
void *ha_flt_tab, ha_pt_t *ha_idx, All_reads* rdb, const ul_idx_t *udb, kvec_t_u64_warp* dbg_ct, st_mt_t *sp, uint32_t *high_occ, 
uint32_t *low_occ)
{
	// fprintf(stderr, "+[M::%s]\n", __func__);
	uint64_t i, k, l, max_cnt = UINT32_MAX, min_cnt = 0; int n, j; ha_mzl_t *z; seedl_t *s; 
	if(high_occ) {
		max_cnt = (*high_occ);
		if(max_cnt < 2) max_cnt = 2;
	}
	if(low_occ) {
		min_cnt = (*low_occ);
		if(min_cnt < 2) min_cnt = 2;
	}
	clear_Candidates_list(cl); ab->mz.n = 0, ab->n_a = 0;
	
	// get the list of anchors
	mz2_ha_sketch(rs, rl, mz_w, mz_k, 0, !(asm_opt.flag & HA_F_NO_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, 0, NULL);

	// 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) {
		ab->seed[i].a = ha_ptl_get(ha_idx, ab->mz.a[i].x, &n);
		ab->seed[i].n = n;
		ab->n_a += n;
	}

	if (ab->n_a > ab->m_a) {
		ab->m_a = ab->n_a;
		REALLOC(ab->a, ab->m_a);
	}

	for (i = 0, k = 0; i < ab->mz.n; ++i) {
		///z is one of the minimizer
		z = &ab->mz.a[i]; 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 = rev?((uint32_t)-1)-1-(y->pos+1-y->span):y->pos;
			an->self_off = z->pos;
			///an->cnt: cnt<<8|span
			an->cnt = s->n; if(an->cnt > ((uint32_t)(0xffffffu))) an->cnt = 0xffffffu;
			an->cnt <<= 8; an->cnt |= ((z->span <= ((uint32_t)(0xffu)))?z->span:((uint32_t)(0xffu)));
			an->srt = (uint64_t)y->rid<<33 | (uint64_t)rev<<32 | an->self_off;
		}
	}

	// copy over to _cl_
	if (ab->m_a >= (uint64_t)cl->size) {
		cl->size = ab->m_a;
		REALLOC(cl->list, cl->size);
	}

	k_mer_hit *p; uint64_t tid = (uint64_t)-1, tl = (uint64_t)-1;
	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_an3(ab->a+l, ab->a+k);
			if((ab->a[l].srt>>33)!=tid) {
				tid = ab->a[l].srt>>33;
				tl = rdb?Get_READ_LENGTH((*rdb), tid):udb->ug->u.a[tid].len;
			} 
			for (i = l; i < k; i++) {
				p = &cl->list[i];
				p->readID = ab->a[i].srt>>33;
				p->strand = (ab->a[i].srt>>32)&1;
				if(!(p->strand)) {
					p->offset = ab->a[i].other_off;
				} else {
					p->offset = ((uint32_t)-1)-ab->a[i].other_off;
					p->offset = tl-p->offset;
				}
				p->self_offset = ab->a[i].self_off;
				if(((ab->a[i].cnt>>8) < max_cnt) && ((ab->a[i].cnt>>8) > min_cnt)){
					p->cnt = 1;
				} else if((ab->a[i].cnt>>8) <= min_cnt) {
					p->cnt = 2;
				} else{
					p->cnt = 1 + (((ab->a[i].cnt>>8) + (max_cnt<<1) - 1)/(max_cnt<<1));
					p->cnt = pow(p->cnt, 1.1);
				}
				if(p->cnt > ((uint32_t)(0xffffffu))) p->cnt = 0xffffffu;
				p->cnt <<= 8; p->cnt |= (((uint32_t)(0xffu))&(ab->a[i].cnt));
			}
			l = k;
		}
	}
	cl->length = ab->n_a;
}

void gen_pair_chain(ha_abufl_t *ab, uint64_t rid, st_mt_t *tid, uint64_t tid_n, ha_mzl_t *in, uint64_t in_n, ha_mzl_t *idx, int64_t idx_n, uint64_t mzl_cutoff)
{
	if(!tid_n) return;
	uint64_t i, l, k, n, m, rev, x, tn, kn; ha_mzl_t *z, *p, *y; int64_t zi, ns, ne; anchor1_t *an;
	for (i = tn = 0; i < in_n; ++i) {
		///z is one of the minimizer
		z = &in[i]; p = &(idx[z->x]); n = 0;
		assert(z->pos == p->pos && z->rid == p->rid && z->span == p->span && z->rev == p->rev);
		for (zi = z->x+1; zi < idx_n && idx[zi].x == p->x && n < mzl_cutoff; zi++) {
			if(idx[zi].rid == rid) continue; 
			x = idx[zi].rid; x <<= 1; x |= ((uint64_t)((z->rev == idx[zi].rev)?0:1));
			for (m = 0; m < tid_n; m++) {
				if(tid->a[m] == x) {
					n++; break;
				}
			}
		}
		for (zi = ((int64_t)z->x)-1; zi >= 0 && idx[zi].x == p->x && n < mzl_cutoff; zi--) {
			if(idx[zi].rid == rid) continue; 
			x = idx[zi].rid; x <<= 1; x |= ((uint64_t)((z->rev == idx[zi].rev)?0:1));
			for (m = 0; m < tid_n; m++) {
				if(tid->a[m] == x) {
					n++; break;
				}
			}
		}
		if((!n) || (n >= mzl_cutoff)) continue;
		tn += n;
	}
	if(!tn) return;
	ab->n_a += tn;
	if (ab->n_a > ab->m_a) {
		ab->m_a = ab->n_a;
		REALLOC(ab->a, ab->m_a);
	}


	for (i = 0, k = ab->n_a - tn; i < in_n; ++i) {
		///z is one of the minimizer
		z = &in[i]; p = &(idx[z->x]); n = 0; ns = 0; ne = -1;
		for (zi = z->x+1; zi < idx_n && idx[zi].x == p->x && n < mzl_cutoff; zi++) {
			if(idx[zi].rid == rid) continue; 
			x = idx[zi].rid; x <<= 1; x |= ((uint64_t)((z->rev == idx[zi].rev)?0:1));
			for (m = 0; m < tid_n; m++) {
				if(tid->a[m] == x) {
					n++; break;
				}
			}
		}
		ne = zi;
		for (zi = ((int64_t)z->x)-1; zi >= 0 && idx[zi].x == p->x && n < mzl_cutoff; zi--) {
			if(idx[zi].rid == rid) continue; 
			x = idx[zi].rid; x <<= 1; x |= ((uint64_t)((z->rev == idx[zi].rev)?0:1));
			for (m = 0; m < tid_n; m++) {
				if(tid->a[m] == x) {
					n++; break;
				}
			}
		}
		ns = zi + 1; 
		if((!n) || (n >= mzl_cutoff)) continue;
		n = ne - ns; if(n > ((uint32_t)(0xffffffu))) n = 0xffffffu; n<<=8;

		for (zi = z->x+1; zi < idx_n && idx[zi].x == p->x; zi++) {
			if(idx[zi].rid == rid) continue; 
			x = idx[zi].rid; x <<= 1; x |= ((uint64_t)((z->rev == idx[zi].rev)?0:1));
			for (m = 0; m < tid_n; m++) {
				if(tid->a[m] == x) break;
			}
			if(m >= tid_n) continue; 


			y = &(idx[zi]); an = &ab->a[k++];
			rev = z->rev == y->rev? 0 : 1;
			an->other_off = rev?((uint32_t)-1)-1-(y->pos+1-y->span):y->pos;
			an->self_off = z->pos;
			///an->cnt: cnt<<8|span
			an->cnt = ((z->span <= ((uint32_t)(0xffu)))?z->span:((uint32_t)(0xffu))); an->cnt |= n;
			an->srt = (uint64_t)y->rid<<33 | (uint64_t)rev<<32 | an->self_off;
		}
		for (zi = ((int64_t)z->x)-1; zi >= 0 && idx[zi].x == p->x; zi--) {
			if(idx[zi].rid == rid) continue; 
			x = idx[zi].rid; x <<= 1; x |= ((uint64_t)((z->rev == idx[zi].rev)?0:1));
			for (m = 0; m < tid_n; m++) {
				if(tid->a[m] == x) break;
			}
			if(m >= tid_n) continue; 



			y = &(idx[zi]); an = &ab->a[k++];
			rev = z->rev == y->rev? 0 : 1;
			an->other_off = rev?((uint32_t)-1)-1-(y->pos+1-y->span):y->pos;
			an->self_off = z->pos;
			///an->cnt: cnt<<8|span
			an->cnt = ((z->span <= ((uint32_t)(0xffu)))?z->span:((uint32_t)(0xffu))); an->cnt |= n;
			an->srt = (uint64_t)y->rid<<33 | (uint64_t)rev<<32 | an->self_off;
		}
	}
	assert(k == ab->n_a);
	radix_sort_ha_an1(ab->a + ab->n_a - tn, ab->a + ab->n_a); kn = 0;
	for (k = ab->n_a - tn + 1, l = ab->n_a - tn; k <= ab->n_a; ++k) {
		if (k == ab->n_a || (ab->a[k].srt>>32) != (ab->a[l].srt>>32)) {
			for (; kn < tid_n && tid->a[kn] < (ab->a[l].srt>>32); kn++);
			if(kn < tid_n && tid->a[kn] == (ab->a[l].srt>>32)) kv_push(uint64_t, *tid, l);
			for (; kn < tid_n && tid->a[kn] == (ab->a[l].srt>>32); kn++);
			l = k;
		}
	}
}

void minimizers_qgen_input(ha_abufl_t *ab, uint64_t rid, char* rs, int64_t rl, uint64_t mz_w, uint64_t mz_k, Candidates_list *cl, kvec_t_u8_warp* k_flag, 
void *ha_flt_tab, ha_pt_t *ha_idx, All_reads* rdb, const ul_idx_t *udb, kvec_t_u64_warp* dbg_ct, st_mt_t *sp, uint32_t *high_occ, 
uint32_t *low_occ, ha_mzl_t *in, uint64_t in_n, ha_mzl_t *idx, int64_t idx_n, uint64_t mzl_cutoff, uint64_t chain_cutoff, kv_u_trans_t *kov)
{
	// fprintf(stderr, "+[M::%s]\n", __func__);
	uint64_t i, k, l, max_cnt = UINT32_MAX, min_cnt = 0, n; ha_mzl_t *z, *p, *y; anchor1_t *an;
	int64_t zi, ns, ne; uint8_t rev; k_mer_hit *s;
	if(high_occ) {
		max_cnt = (*high_occ);
		if(max_cnt < 2) max_cnt = 2;
	}
	if(low_occ) {
		min_cnt = (*low_occ);
		if(min_cnt < 2) min_cnt = 2;
	}
	clear_Candidates_list(cl); 

	for (i = 0, ab->n_a = 0; i < in_n; ++i) {
		///z is one of the minimizer
		z = &in[i]; p = &(idx[z->x]); n = 0;
		assert(z->pos == p->pos && z->rid == p->rid && z->span == p->span && z->rev == p->rev);
		for (zi = z->x+1; zi < idx_n && idx[zi].x == p->x && n < mzl_cutoff; zi++) {
			if(idx[zi].rid == rid) continue; n++;
		}
		for (zi = ((int64_t)z->x)-1; zi >= 0 && idx[zi].x == p->x && n < mzl_cutoff; zi--) {
			if(idx[zi].rid == rid) continue; n++;
		}
		if((!n) || (n >= mzl_cutoff)) continue;
		ab->n_a += n;
	}
	// if(rid == 0) {
	// 	fprintf(stderr, "-0-[M::%s] ab->n_a::%lu, in_n::%lu\n", __func__, ab->n_a, in_n);
	// }

	if (ab->n_a > ab->m_a) {
		ab->m_a = ab->n_a;
		REALLOC(ab->a, ab->m_a);
	}

	for (i = 0, k = 0; i < in_n; ++i) {
		///z is one of the minimizer
		z = &in[i]; p = &(idx[z->x]); n = 0; ns = 0; ne = -1;
		for (zi = z->x+1; zi < idx_n && idx[zi].x == p->x && n < mzl_cutoff; zi++) {
			if(idx[zi].rid == rid) continue; n++;
		}
		ne = zi;
		for (zi = ((int64_t)z->x)-1; zi >= 0 && idx[zi].x == p->x && n < mzl_cutoff; zi--) {
			if(idx[zi].rid == rid) continue; n++;
		}
		ns = zi + 1; 
		if((!n) || (n >= mzl_cutoff)) continue;
		n = ne - ns; if(n > ((uint32_t)(0xffffffu))) n = 0xffffffu; n<<=8;

		for (zi = z->x+1; zi < idx_n && idx[zi].x == p->x; zi++) {
			if(idx[zi].rid == rid) continue; 
			y = &(idx[zi]); an = &ab->a[k++];
			rev = z->rev == y->rev? 0 : 1;
			an->other_off = rev?((uint32_t)-1)-1-(y->pos+1-y->span):y->pos;
			an->self_off = z->pos;
			///an->cnt: cnt<<8|span
			an->cnt = ((z->span <= ((uint32_t)(0xffu)))?z->span:((uint32_t)(0xffu))); an->cnt |= n;
			an->srt = (uint64_t)y->rid<<33 | (uint64_t)rev<<32 | an->self_off;
		}
		for (zi = ((int64_t)z->x)-1; zi >= 0 && idx[zi].x == p->x; zi--) {
			if(idx[zi].rid == rid) continue; 
			y = &(idx[zi]); an = &ab->a[k++];
			rev = z->rev == y->rev? 0 : 1;
			an->other_off = rev?((uint32_t)-1)-1-(y->pos+1-y->span):y->pos;
			an->self_off = z->pos;
			///an->cnt: cnt<<8|span
			an->cnt = ((z->span <= ((uint32_t)(0xffu)))?z->span:((uint32_t)(0xffu))); an->cnt |= n;
			an->srt = (uint64_t)y->rid<<33 | (uint64_t)rev<<32 | an->self_off;
		}
	}
	assert(k == ab->n_a);

	uint64_t kn, spn; u_trans_t *ka; 
	kn = spn = 0; ka = NULL; sp->n = 0;
	if(kov) {
		kn = u_trans_n(*kov, rid); ka = u_trans_a(*kov, rid); 
	}
	if(kn > 0) {
		kv_resize(uint64_t, *sp, kn);
		for (k = 0; k < kn; ++k) {
			if(ka[k].del) continue;
			l = ka[k].tn; l <<= 1; l |= ka[k].rev; 
			kv_push(uint64_t, *sp, l);
		}
		if(sp->n > 1) radix_sort_anc64(sp->a, sp->a + sp->n);
	}

	radix_sort_ha_an1(ab->a, ab->a + ab->n_a); kn = 0;
	for (k = 1, l = n = 0, spn = sp->n; k <= ab->n_a; ++k) {
		if (k == ab->n_a || (ab->a[k].srt>>32) != (ab->a[l].srt>>32)) {
			if(k - l >= chain_cutoff) {
				for (; kn < spn && sp->a[kn] < (ab->a[l].srt>>32); kn++);
				if(kn < spn && sp->a[kn] == (ab->a[l].srt>>32)) kv_push(uint64_t, *sp, n);
				for (; kn < spn && sp->a[kn] == (ab->a[l].srt>>32); kn++) sp->a[kn] = (uint64_t)-1;
				for (i = l; i < k; i++) ab->a[n++] = ab->a[i];
			}
			l = k;
		}
	}
	ab->n_a = n;
	for (k = kn = 0; k < spn; k++) {
		if(sp->a[k] == (uint64_t)-1) continue;
		sp->a[kn++] = sp->a[k];
	}
	// sp->n = kn;
	if(kn > 0) gen_pair_chain(ab, rid, sp, kn, in, in_n, idx, idx_n, mzl_cutoff);
	if(spn > 0) {
		for (k = spn, kn = 0; k < sp->n; k++) sp->a[kn++] = sp->a[k];
		sp->n = kn;
	}
	

	// copy over to _cl_
	if (ab->n_a >= (uint64_t)cl->size) {
		cl->size = ab->n_a;
		REALLOC(cl->list, cl->size);
	}

    uint64_t tid = (uint64_t)-1, tl = (uint64_t)-1;
    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_an3(ab->a+l, ab->a+k);
            if((ab->a[l].srt>>33)!=tid) {
                tid = ab->a[l].srt>>33;
                tl = rdb?Get_READ_LENGTH((*rdb), tid):udb->ug->u.a[tid].len;
            } 
            for (i = l; i < k; i++) {
                s = &cl->list[i];
                s->readID = ab->a[i].srt>>33;
                s->strand = (ab->a[i].srt>>32)&1;
                if(!(s->strand)) {
                    s->offset = ab->a[i].other_off;
                } else {
                    s->offset = ((uint32_t)-1)-ab->a[i].other_off;
                    s->offset = tl-s->offset;
                }
                s->self_offset = ab->a[i].self_off;
                if(((ab->a[i].cnt>>8) < max_cnt) && ((ab->a[i].cnt>>8) > min_cnt)){
                    s->cnt = 1;
                } else if((ab->a[i].cnt>>8) <= min_cnt) {
                    s->cnt = 2;
                } else{
                    s->cnt = 1 + (((ab->a[i].cnt>>8) + (max_cnt<<1) - 1)/(max_cnt<<1));
                    s->cnt = pow(s->cnt, 1.1);
                }
                if(s->cnt > ((uint32_t)(0xffffffu))) s->cnt = 0xffffffu;
                s->cnt <<= 8; s->cnt |= (((uint32_t)(0xffu))&(ab->a[i].cnt));
            }
            l = k;
        }
    }
	cl->length = ab->n_a;
}

void inline reverse_k_mer_hit(k_mer_hit *a, uint64_t a_n, uint64_t xl, uint64_t yl)
{
	uint64_t z, han = a_n>>1; k_mer_hit *ai, *aj, ka;
	for (z = 0; z < han; z++) {
		ai = &(a[z]); aj = &(a[a_n-z-1]);
		ka = (*ai); (*ai) = (*aj); (*aj) = ka;

		ai->self_offset = xl-ai->self_offset-1;
		ai->offset = yl-ai->offset-1;

		aj->self_offset = xl-aj->self_offset-1;
		aj->offset = yl-aj->offset-1;
	}
	if(a_n&1) {
		a[z].self_offset = xl-a[z].self_offset-1;
		a[z].offset = yl-a[z].offset-1;
	}
}


void inline reset_k_mer_hit(k_mer_hit *a, uint64_t a_n, uint64_t xl, uint64_t yl, uint64_t rev, uint64_t *nid)
{
	uint64_t z, han = a_n>>1; k_mer_hit *ai, *aj, ka;
	if(rev) {
		for (z = 0; z < han; z++) {
			ai = &(a[z]); aj = &(a[a_n-z-1]); 
			ka = (*ai); (*ai) = (*aj); (*aj) = ka;

			ai->self_offset = xl-ai->self_offset-1;
			ai->offset = yl-ai->offset-1;

			aj->self_offset = xl-aj->self_offset-1;
			aj->offset = yl-aj->offset-1;
			if(nid) ai->readID = aj->readID = (*nid);
		}
		if(a_n&1) {
			a[z].self_offset = xl-a[z].self_offset-1;
			a[z].offset = yl-a[z].offset-1;
			if(nid) a[z].readID = (*nid);
		}
	} else if(nid) {
		for (z = 0; z < a_n; z++) a[z].readID = (*nid);
	}
}

void lchain_gen(Candidates_list* cl, overlap_region_alloc* ol, uint32_t rid, uint64_t rl, All_reads* rdb, 
				const ul_idx_t *udb, uint32_t apend_be, overlap_region* tf, uint64_t max_n_chain,
				int64_t max_skip, int64_t max_iter, int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate, int64_t quick_check, uint32_t gen_off)
{
	// fprintf(stderr, "+[M::%s]\n", __func__);
	uint64_t i, k, l, m, sm, cn = cl->length; overlap_region *r; ///srt = 0
	clear_overlap_region_alloc(ol);
	clear_fake_cigar(&(tf->f_cigar));

	for (l = 0, k = 1, m = 0; k <= cn; k++) {
		if((k == cn) || (cl->list[k].readID != cl->list[l].readID) 
													|| (cl->list[k].strand != cl->list[l].strand)) {
			if(cl->list[l].readID != rid) {
				tf->x_id = rid; 
				tf->x_pos_strand = cl->list[l].strand;
				tf->y_id = cl->list[l].readID; 
				tf->y_pos_strand = 0;///always 0
				// fprintf(stderr, "+[M::%s] l::%lu, k::%lu\n", __func__, l, k);
				sm = lchain_dp(cl->list+l, k-l, cl->list+m, &(cl->chainDP), tf, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_rate, 
              	rl, rdb?Get_READ_LENGTH((*rdb), (*tf).y_id):udb->ug->u.a[(*tf).y_id].len, quick_check);
				// assert(sm > 0);
				if(ovlp_chain_gen(ol, tf, rl, rdb?Get_READ_LENGTH((*rdb), (*tf).y_id):udb->ug->u.a[(*tf).y_id].len, apend_be, cl->list+m, sm)) {
					r = &(ol->list[ol->length-1]); r->non_homopolymer_errors = m; 
					// if(r->y_pos_strand) {
					// 	reverse_k_mer_hit(cl->list+m, sm, rl, rdb?Get_READ_LENGTH((*rdb), r->y_id):udb->ug->u.a[r->y_id].len);
					// }
					reset_k_mer_hit(cl->list+m, sm, rl, rdb?Get_READ_LENGTH((*rdb), r->y_id):udb->ug->u.a[r->y_id].len, r->y_pos_strand, &(ol->length));
					if(gen_off) gen_fake_cigar(&(r->f_cigar), r, apend_be, cl->list+m, sm);
					m += sm;
				}
			}
			l = k;
		}
	}
	cl->length = m;


	k = ol->length;
	if (ol->length > max_n_chain) {
		int32_t w, n[4], s[4]; overlap_region t;
		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); ///srt = 1;
		for (i = 0; i < ol->length; ++i) {
			r = &(ol->list[i]);
			w = ha_ov_type(r, rl);
			++n[w];
			if (((uint64_t)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 < ol->length; ++i) {
				r = &(ol->list[i]);
				w = ha_ov_type(r, rl);
				// ++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 (k != i) {
						t = ol->list[k];
						ol->list[k] = ol->list[i];
						ol->list[i] = t;
					}
					++k;
				}
			}
			ol->length = k;
		}
	}
	/**
	if(!gen_off) {
		if(srt) ks_introsort_or_id(ol->length, ol->list);
		uint64_t cln = cl->length;
		for (i = k = m = 0; i < ol->length; ++i) {
			r = &(ol->list[i]);
			for (;(k<cln)&&((cl->list[k].readID!=r->y_id)||(cl->list[k].strand!=r->y_pos_strand)); k++);
			// assert(k<cln);
			for (cn = m; k < cln; k++, m++) {
				if((cl->list[k].readID!=r->y_id)||(cl->list[k].strand!=r->y_pos_strand)) break;
				if(m != k) cl->list[m] = cl->list[k];
			}
			// assert(m - cn > 0);
			if(r->y_pos_strand) {
				reverse_k_mer_hit(cl->list+cn, m-cn, rl, rdb?Get_READ_LENGTH((*rdb), r->y_id):udb->ug->u.a[r->y_id].len);
			}
			// gen_fake_cigar(&(r->f_cigar), r, apend_be, cl->list+cn, m-cn);
		}
		cl->length = m;
	}
	**/

	ks_introsort_or_xs(ol->length, ol->list);
}

void lchain_qgen(Candidates_list* cl, overlap_region_alloc* ol, uint32_t rid, uint64_t rl, All_reads* rdb, 
				const ul_idx_t *udb, uint32_t apend_be, overlap_region* tf, uint64_t max_n_chain,
				int64_t max_skip, int64_t max_iter, int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate, int64_t quick_check, uint32_t gen_off)
{
	uint64_t i, k, l, m, sm, cn = cl->length; overlap_region *r; ///srt = 0
	clear_overlap_region_alloc(ol);
	clear_fake_cigar(&(tf->f_cigar));

	for (l = 0, k = 1, m = 0; k <= cn; k++) {
		if((k == cn) || (cl->list[k].readID != cl->list[l].readID) 
													|| (cl->list[k].strand != cl->list[l].strand)) {
			if(cl->list[l].readID != rid) {
				tf->x_id = rid; 
				tf->x_pos_strand = cl->list[l].strand;
				tf->y_id = cl->list[l].readID; 
				tf->y_pos_strand = 0;///always 0
				// fprintf(stderr, "+[M::%s] l::%lu, k::%lu\n", __func__, l, k);
				sm = lchain_qdp(cl->list+l, k-l, cl->list+m, &(cl->chainDP), tf, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_rate, 
              	rl, rdb?Get_READ_LENGTH((*rdb), (*tf).y_id):udb->ug->u.a[(*tf).y_id].len, quick_check);
				// assert(sm > 0);
				if(ovlp_chain_qgen(ol, tf, rl, rdb?Get_READ_LENGTH((*rdb), (*tf).y_id):udb->ug->u.a[(*tf).y_id].len, apend_be, cl->list+m, sm)) {
					r = &(ol->list[ol->length-1]); r->non_homopolymer_errors = m; 
					// if(tf->y_id == 66 || tf->y_id == 66) {
					// 	fprintf(stderr, "\n[M::%s::] utg%.6dl(%c), i::%lu\n", 
        			// 			__func__, (int32_t)tf->y_id+1, "+-"[tf->x_pos_strand], m);
					// }
					// reset_k_mer_hit(cl->list+m, sm, rl, rdb?Get_READ_LENGTH((*rdb), r->y_id):udb->ug->u.a[r->y_id].len, r->y_pos_strand, &(ol->length));
					for (i = 0; i < sm; i++) {
						cl->list[m+i].readID = ol->length;
						// if(tf->y_id == 126) fprintf(stderr, "[M::%s::qoff->%u::toff->%u]\n", __func__, cl->list[m+i].self_offset, cl->list[m+i].offset);
					}
					if(gen_off) gen_fake_cigar(&(r->f_cigar), r, apend_be, cl->list+m, sm);
					m += sm;
				}
			}
			l = k;
		}
	}
	cl->length = m;
	// fprintf(stderr, "+[M::%s] cn::%lu, m::%lu, ol->length::%lu\n", __func__, cn, m, ol->length);
	// 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);
	// }


	k = ol->length;
	if (ol->length > max_n_chain) {
		int32_t w, n[4], s[4]; overlap_region t;
		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); ///srt = 1;
		for (i = 0; i < ol->length; ++i) {
			r = &(ol->list[i]);
			w = ha_ov_type(r, rl);
			++n[w];
			if (((uint64_t)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 < ol->length; ++i) {
				r = &(ol->list[i]);
				w = ha_ov_type(r, rl);
				// ++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 (k != i) {
						t = ol->list[k];
						ol->list[k] = ol->list[i];
						ol->list[i] = t;
					}
					++k;
				}
			}
			ol->length = k;
		}
	}
	ks_introsort_or_xs(ol->length, ol->list);
}


void lchain_qgen_mcopy(Candidates_list* cl, overlap_region_alloc* ol, uint32_t rid, uint64_t rl, All_reads* rdb, 
				const ul_idx_t *udb, uint32_t apend_be, uint64_t max_n_chain, int64_t max_skip, int64_t max_iter, 
				int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate, int64_t quick_check, 
				uint32_t gen_off, double mcopy_rate, uint32_t chain_cutoff, uint32_t mcopy_khit_cut, st_mt_t *sp)
{
	// fprintf(stderr, "+[M::%s]\n", __func__);
	uint64_t i, k, l, m, cn = cl->length, yid, ol0, lch; overlap_region *r, t; ///srt = 0
	clear_overlap_region_alloc(ol);

	for (l = 0, k = 1, m = 0, lch = 0; k <= cn; k++) {
		if((k == cn) || (cl->list[k].readID != cl->list[l].readID)) {
			if(cl->list[l].readID != rid) {
				yid = cl->list[l].readID; ol0 = ol->length;
				m += lchain_qdp_mcopy(cl, l, k-l, m, &(cl->chainDP), ol, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_rate, 
				rid, rl, rdb?Get_READ_LENGTH((*rdb), yid):udb->ug->u.a[yid].len, quick_check, apend_be, gen_off, 1, mcopy_rate, mcopy_khit_cut, 1);
				if((chain_cutoff >= 2) && (!lch)) {
					for (i = ol0; (i<ol->length) && (!lch); i++) {
						if(ol->list[i].align_length < chain_cutoff) lch = 1;
					}
				}
			}
			l = k;
		}
	}
	cl->length = m;

	// 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);
	// }

	k = ol->length;
	if (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 < ol->length; ++i) {
			r = &(ol->list[i]);
			w = ha_ov_type(r, rl);
			++n[w];
			if (((uint64_t)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, lch = 0; i < ol->length; ++i) {
				r = &(ol->list[i]);
				w = ha_ov_type(r, rl);
				// ++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 (k != i) {
						t = ol->list[k];
						ol->list[k] = ol->list[i];
						ol->list[i] = t;
					}
					if(ol->list[k].align_length < chain_cutoff) lch = 1;
					++k;
				}
			}
			ol->length = k;
		}
	} 
	
	ks_introsort_or_xs(ol->length, ol->list);
	if(lch) {
		//@brief r485
		uint64_t zs, ze, rs, re, ob, os, oe, ocn, pp, kn, ms, me; int64_t osc;
		for (i = l = 0, cn = cl->length; i < ol->length; ++i) {
			if(ol->list[i].align_length < chain_cutoff) {
				zs = ol->list[i].x_pos_s; ze = ol->list[i].x_pos_e + 1;
				ob = (ze - zs)*OFL; if(ob < 16) ob = 16;
				osc = ol->list[i].shared_seed*CH_SC;
				ocn = ol->list[i].align_length<<CH_OCC;
				for (k = 0; (k < ol->length) && (ze > ol->list[k].x_pos_s); k++) {
					if(ol->list[k].align_length < chain_cutoff) continue;
					if(ol->list[k].align_length < ocn) continue;
					if(ol->list[k].shared_seed < osc) continue;
					rs = ol->list[k].x_pos_s; re = ol->list[k].x_pos_e + 1;
					os = ((rs>=zs)?rs:zs); oe = ((re<=ze)?re:ze);
					if((oe > os) && (oe - os) >= ob) {
						m = ol->list[k].non_homopolymer_errors;
						pp = cl->list[m].readID; kn = 0;
						for (; (m < cn) && (cl->list[m].readID == pp) && (kn < ocn); m++) {
							me = cl->list[m].self_offset; ms = me - (cl->list[m].cnt&(0xffu)); 
							if((ms >= os) && (me <= oe)) kn++;
						}
						if(kn >= ocn) break;
					}
				}
				if((k < ol->length) && (ze > ol->list[k].x_pos_s)) continue;
			}
			if (l != i) {
				t = ol->list[l];
				ol->list[l] = ol->list[i];
				ol->list[i] = t;
			}
			l++;
		}
		// fprintf(stderr, "+[M::%s] rid::%u, ol->length0::%lu, ol->length1::%lu\n", __func__, rid, ol->length, l);
		ol->length = l;


		/**
		//@brief r484
		for (i = sp->n = 0; i < ol->length; ++i) {
			if(ol->list[i].align_length < chain_cutoff) continue;
			os = ol->list[i].x_pos_s; oe = ol->list[i].x_pos_e + 1;
			if((sp->n) && (((uint32_t)sp->a[sp->n-1]) >= os)) {
				if(oe > ((uint32_t)sp->a[sp->n-1])) {
					oe = oe - ((uint32_t)sp->a[sp->n-1]);
					sp->a[sp->n-1] += oe; 
				}
			} else {
				os = (os<<32)|oe; kv_push(uint64_t, *sp, os);
			}
		}

		for (i = k = 0; i < ol->length; ++i) {
			if(ol->list[i].align_length < chain_cutoff) {///ol has been sorted by x_pos_s
				r = &(ol->list[i]); rs = r->x_pos_s; re = r->x_pos_e + 1;
				rl = re - rs; ovl = 0;
				for (m = 0; (m < sp->n) && (re > (sp->a[m]>>32)); m++) {
					os = ((rs>=(sp->a[m]>>32))? rs:(sp->a[m]>>32));
            		oe = ((re<=((uint32_t)sp->a[m]))? re:((uint32_t)sp->a[m]));
					if(oe > os) {
						ovl += (oe - os); if(ovl >= (rl*0.95)) break;
					}
				}
				if(ovl >= (rl*0.95)) continue;
			}
			if (k != i) {
				t = ol->list[k];
				ol->list[k] = ol->list[i];
				ol->list[i] = t;
			}
			ol->list[k++].align_length = 0;
		}
		// fprintf(stderr, "+[M::%s] ol->length0::%lu, ol->length1::%lu\n", __func__, ol->length, k);
		ol->length = k;
		**/
	} 
	/**else {
		for (i = 0; i < ol->length; ++i) ol->list[i].align_length = 0;
	}
	**/
	for (i = 0; i < ol->length; ++i) ol->list[i].align_length = 0;
}

inline uint64_t special_lchain(Candidates_list* cl, overlap_region_alloc* ol, uint32_t rid, uint64_t rl, All_reads* rdb, 
				const ul_idx_t *udb, uint32_t apend_be, int64_t max_skip, int64_t max_iter, int64_t max_dis, double chn_pen_gap, 
				double chn_pen_skip, double bw_rate, int64_t quick_check, uint32_t gen_off, double mcopy_rate, uint32_t mcopy_khit_cut, 
				st_mt_t *sp, uint64_t *si, uint64_t m, uint64_t l, uint64_t k)
{
	uint64_t z, s, e, yid, ol0 = ol->length, ol1, m0 = m; 
	if(l >= k) return m;
	yid = cl->list[l].readID;
	for (z = l; z < k && cl->list[z].strand == cl->list[l].strand; z++);
	if(z > l) {
		s = l; e = z; ol1 = ol->length; // m0 = m;
		m += lchain_qdp_mcopy(cl, s, e-s, m, &(cl->chainDP), ol, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_rate, 
						rid, rl, rdb?Get_READ_LENGTH((*rdb), yid):udb->ug->u.a[yid].len, quick_check, apend_be, gen_off, 0, mcopy_rate, mcopy_khit_cut, 0);
		// if(rid == 7) {
		// 	fprintf(stderr, "+[M::%s::utg%.6ul] inn::[%lu, %lu), (*si)::%lu, ol1::%lu, ol->length::%lu\n", 
		// 	__func__, rid+1, s, e, (*si), ol1, ol->length);
		// }
		if(((*si) < sp->n) && (sp->a[(*si)] == s) && (ol->length > ol1)) {
			ol->list[ol->length-1].x_pos_strand = 1;
			// fprintf(stderr, "+[M::%s] utg%.6u%c -> utg%.6u%c, n_khits0::%lu, n_khits::%lu\n", __func__, rid+1, "lc"[udb->ug->u.a[rid].circ], 
			// ol->list[ol->length-1].y_id+1, "lc"[udb->ug->u.a[ol->list[ol->length-1].y_id].circ], e-s, m-m0);
		}
		for (; (*si) < sp->n && sp->a[(*si)] == s; (*si)++);
	}

	if(z < k) {
		s = z; e = k; ol1 = ol->length;	// m0 = m;
		m += lchain_qdp_mcopy(cl, s, e-s, m, &(cl->chainDP), ol, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_rate, 
						rid, rl, rdb?Get_READ_LENGTH((*rdb), yid):udb->ug->u.a[yid].len, quick_check, apend_be, gen_off, 0, mcopy_rate, mcopy_khit_cut, 0);
		// if(rid == 7) {
		// 	fprintf(stderr, "-[M::%s::utg%.6ul] inn::[%lu, %lu), (*si)::%lu, ol1::%lu, ol->length::%lu\n", 
		// 	__func__, rid+1, s, e, (*si), ol1, ol->length);
		// }
		if(((*si) < sp->n) && (sp->a[(*si)] == s) && (ol->length > ol1)) {
			ol->list[ol->length-1].x_pos_strand = 1;
			// fprintf(stderr, "-[M::%s] utg%.6u%c -> utg%.6u%c, n_khits0::%lu, n_khits::%lu\n", __func__, rid+1, "lc"[udb->ug->u.a[rid].circ], 
			// ol->list[ol->length-1].y_id+1, "lc"[udb->ug->u.a[ol->list[ol->length-1].y_id].circ], e-s, m-m0);
		}
		for (; (*si) < sp->n && sp->a[(*si)] == s; (*si)++);
	}
	if(ol->length > ol0) {
		overlap_region *p = &(ol->list[ol0]); uint64_t pi = ol0; overlap_region t;
		for (z = ol0; z < ol->length; z++) {
			if((p->shared_seed < ol->list[z].shared_seed) || 
				((p->shared_seed == ol->list[z].shared_seed) && (ol->list[z].x_pos_strand == 1))) {
				p = &(ol->list[z]); pi = z;
			}
		}

		// if(rid == 7) {
		// 	fprintf(stderr, ">[M::%s::] utg%.6ul\t->\tutg%.6ul\tflag::%u\n", 
		// 	__func__, p->x_id+1, p->y_id+1, p->x_pos_strand);
		// }

		for (z = s = ol0; z < ol->length; z++) {
			if((ol->list[z].x_pos_strand == 0) && (z != pi)) continue;
			if(s != z) {
				t = ol->list[s];
    			ol->list[s] = ol->list[z];
    			ol->list[z] = t;
			}
			s++;
		}

		if(s != ol->length) {
			ol->length = s;
			for (z = ol0; z < ol->length; z++) {
				s = ol->list[z].non_homopolymer_errors;
				pi = cl->list[s].readID;
				ol->list[z].non_homopolymer_errors = m0;
				for (; s < m && cl->list[s].readID == pi; s++) {
					cl->list[m0] = cl->list[s];
					cl->list[m0].readID = z; m0++;
				}
			}
			m = m0;
		}
		
	}
	return m;
}

void lchain_qgen_mcopy_input(Candidates_list* cl, overlap_region_alloc* ol, uint32_t rid, uint64_t rl, All_reads* rdb, 
				const ul_idx_t *udb, uint32_t apend_be, uint64_t max_n_chain, int64_t max_skip, int64_t max_iter, 
				int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate, double bw_thres_sec, 
				int64_t quick_check, uint32_t gen_off, double mcopy_rate, uint32_t mcopy_khit_cut, st_mt_t *sp)
{
	// fprintf(stderr, "+[M::%s]\n", __func__);
	uint64_t i, k, l, m, cn = cl->length, yid, si; overlap_region *r; ///srt = 0
	clear_overlap_region_alloc(ol);

	// if(rid == 160) {
	// 	fprintf(stderr, "[M::%s::utg%.6ul] sp->n::%u\n", __func__, rid+1, (uint32_t)sp->n);
	// }
	for (l = 0, k = 1, m = 0, si = 0; k <= cn; k++) {
		if((k == cn) || (cl->list[k].readID != cl->list[l].readID)) {
			if(cl->list[l].readID != rid) {
				yid = cl->list[l].readID;
				// if(rid == 160) {
				// 	fprintf(stderr, "+[M::%s::utg%.6lul] [%lu, %lu), m::%lu, ol->length::%lu\n", __func__, yid+1, l, k, m, ol->length);
				// }
				for (; si < sp->n && sp->a[si] < l; si++);
				if(si >= sp->n || sp->a[si] >= k) {///might be unmatched
					m += lchain_qdp_mcopy(cl, l, k-l, m, &(cl->chainDP), ol, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_rate, 
						rid, rl, rdb?Get_READ_LENGTH((*rdb), yid):udb->ug->u.a[yid].len, quick_check, apend_be, gen_off, 0, mcopy_rate, mcopy_khit_cut, 0);
				} else {
					m = special_lchain(cl, ol, rid, rl, rdb, udb, apend_be, max_skip, max_iter, max_dis, chn_pen_gap, 
					chn_pen_skip, bw_thres_sec, quick_check, gen_off, mcopy_rate, mcopy_khit_cut, sp, &si, m, l, k);
				}
				// if(rid == 160) {
				// 	fprintf(stderr, "-[M::%s::utg%.6lul] [%lu, %lu), m::%lu, ol->length::%lu\n", __func__, yid+1, l, k, m, ol->length);
				// }
			}
			l = k;
		}
	}
	cl->length = m;

	// 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);
	// }

	k = ol->length;
	if (ol->length > max_n_chain) {
		int32_t w, n[4], s[4]; overlap_region t;
		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); ///srt = 1;
		for (i = 0; i < ol->length; ++i) {
			r = &(ol->list[i]);
			w = ha_ov_type(r, rl);
			++n[w];
			if (((uint64_t)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 < ol->length; ++i) {
				r = &(ol->list[i]);
				w = ha_ov_type(r, rl);
				// ++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]) || (r->x_pos_strand == 1)) {
					if (k != i) {
						t = ol->list[k];
						ol->list[k] = ol->list[i];
						ol->list[i] = t;
					}
					++k;
				}
			}
			ol->length = k;
		}
	}
	ks_introsort_or_xs(ol->length, ol->list);
}

void set_lchain_dp_op(uint32_t is_accurate, uint32_t mz_k, int64_t *max_skip, int64_t *max_iter, int64_t *max_dis, double *chn_pen_gap, double *chn_pen_skip, int64_t *quick_check)
{
	double div, pen_gap, pen_skip, tmp;
	if(is_accurate) {
		(*quick_check) = 1; (*max_skip) = 25; (*max_iter) = 5000; (*max_dis) = 5000; div = 0.01; pen_gap = 0.5f; pen_skip = 0.0005f; 
	} else {
		(*quick_check) = 0; (*max_skip) = 25; (*max_iter) = 5000; (*max_dis) = 5000; div = 0.1; pen_gap = 0.5f; pen_skip = 0.0005f;
	}
	tmp = expf(-div * (double)mz_k);///0.60049557881 -> HiFi; 0.18268352405 -> ont
	*chn_pen_gap = pen_gap * tmp;///0.300247789405 -> HiFi; 0.091341762025 -> ont
	///0.000300247789405 -> HiFi (>3330 will be negative);
	//0.000091341762025 -> ont (>10947 will be negative);
	*chn_pen_skip = pen_skip * tmp; 
}

void ul_map_lchain(ha_abufl_t *ab, uint32_t rid, char* rs, uint64_t rl, uint64_t mz_w, uint64_t mz_k, const ul_idx_t *uref, overlap_region_alloc *overlap_list, Candidates_list *cl, double bw_thres, 
								 int max_n_chain, int apend_be, kvec_t_u8_warp* k_flag, overlap_region* f_cigar, kvec_t_u64_warp* dbg_ct, st_mt_t *sp, uint32_t *high_occ, uint32_t *low_occ, uint32_t is_accurate, uint32_t gen_off, double mcopy_rate, uint32_t chain_cutoff, uint32_t mcopy_khit_cut)
{
	extern void *ha_flt_tab;
	extern ha_pt_t *ha_idx;
	int64_t max_skip, max_iter, max_dis, quick_check; double chn_pen_gap, chn_pen_skip;
	set_lchain_dp_op(is_accurate, mz_k, &max_skip, &max_iter, &max_dis, &chn_pen_gap, &chn_pen_skip, &quick_check);
	// minimizers_gen(ab, rs, rl, mz_w, mz_k, cl, k_flag, ha_flt_tab, ha_idx, dbg_ct, sp, high_occ, low_occ);
	minimizers_qgen(ab, rs, rl, mz_w, mz_k, cl, k_flag, ha_flt_tab, ha_idx, NULL, uref, dbg_ct, sp, high_occ, low_occ);
	// lchain_gen(cl, overlap_list, rid, rl, NULL, uref, apend_be, f_cigar, max_n_chain, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_thres, quick_check, gen_off);
	// lchain_qgen(cl, overlap_list, rid, rl, NULL, uref, apend_be, f_cigar, max_n_chain, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_thres, quick_check, gen_off);
	///no need to sort here, overlap_list has been sorted at lchain_gen
	lchain_qgen_mcopy(cl, overlap_list, rid, rl, NULL, uref, apend_be, max_n_chain, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_thres, quick_check, gen_off, mcopy_rate, chain_cutoff, mcopy_khit_cut, sp);
}

int64_t ug_map_lchain(ha_abufl_t *ab, uint32_t rid, char* rs, uint64_t rl, uint64_t mz_w, uint64_t mz_k, const ul_idx_t *uref, overlap_region_alloc *overlap_list, Candidates_list *cl, double bw_thres, double bw_thres_sec,
								 int max_n_chain, int apend_be, kvec_t_u8_warp* k_flag, overlap_region* f_cigar, kvec_t_u64_warp* dbg_ct, st_mt_t *sp, uint32_t *high_occ, uint32_t *low_occ, uint32_t is_accurate, 
								 uint32_t gen_off, double mcopy_rate, uint32_t mcopy_khit_cut, uint32_t is_hpc, ha_mzl_t *res, uint64_t res_n, ha_mzl_t *idx, uint64_t idx_n, uint64_t mzl_cutoff, uint64_t chain_cutoff, kv_u_trans_t *kov)
{
	int64_t max_skip, max_iter, max_dis, quick_check; double chn_pen_gap, chn_pen_skip;
	set_lchain_dp_op(is_accurate, mz_k, &max_skip, &max_iter, &max_dis, &chn_pen_gap, &chn_pen_skip, &quick_check);
	if((!overlap_list) || (!cl)) {
		ab->mz.n = 0;
		mz2_ha_sketch(rs, rl, mz_w, mz_k, rid, is_hpc, &ab->mz, NULL, asm_opt.mz_sample_dist, k_flag, dbg_ct, NULL, -1, asm_opt.dp_min_len, -1, sp, asm_opt.mz_rewin, 0, NULL);
		if(res) memcpy(res, ab->mz.a, ab->mz.n * (sizeof((*(ab->mz.a)))));
		return ab->mz.n;
	} else {
		sp->n = 0;
		minimizers_qgen_input(ab, rid, rs, rl, mz_w, mz_k, cl, k_flag, ha_flt_tab, ha_idx, NULL, uref, dbg_ct, sp, high_occ, low_occ, res, res_n, idx, idx_n, mzl_cutoff, chain_cutoff, kov);
		lchain_qgen_mcopy_input(cl, overlap_list, rid, rl, NULL, uref, apend_be, max_n_chain, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_thres, bw_thres_sec, quick_check, gen_off, mcopy_rate, mcopy_khit_cut, sp);
		return 0;
	}
}

int64_t ug_map_lchain_simple(ha_abufl_t *ab, uint32_t rid, char* rs, uint64_t rl, uint64_t mz_w, uint64_t mz_k, const ul_idx_t *uref, overlap_region_alloc *overlap_list, Candidates_list *cl, double bw_thres,
								 int max_n_chain, int apend_be, kvec_t_u8_warp* k_flag, overlap_region* f_cigar, kvec_t_u64_warp* dbg_ct, st_mt_t *sp, uint32_t *high_occ, uint32_t *low_occ, uint32_t is_accurate, 
								 uint32_t gen_off, double mcopy_rate, uint32_t mcopy_khit_cut, uint32_t is_hpc, ha_mzl_t *res, uint64_t res_n, ha_mzl_t *idx, uint64_t idx_n, uint64_t mzl_cutoff, uint64_t chain_cutoff)
{
	int64_t max_skip, max_iter, max_dis, quick_check; double chn_pen_gap, chn_pen_skip;
	set_lchain_dp_op(is_accurate, mz_k, &max_skip, &max_iter, &max_dis, &chn_pen_gap, &chn_pen_skip, &quick_check);
	if((!overlap_list) || (!cl)) {
		ab->mz.n = 0;
		mz2_ha_sketch(rs, rl, mz_w, mz_k, rid, is_hpc, &ab->mz, NULL, asm_opt.mz_sample_dist, k_flag, dbg_ct, NULL, -1, asm_opt.dp_min_len, -1, sp, asm_opt.mz_rewin, 0, NULL);
		if(res) memcpy(res, ab->mz.a, ab->mz.n * (sizeof((*(ab->mz.a)))));
		return ab->mz.n;
	} else {
		sp->n = 0;
		minimizers_qgen_input(ab, rid, rs, rl, mz_w, mz_k, cl, k_flag, ha_flt_tab, ha_idx, NULL, uref, dbg_ct, sp, high_occ, low_occ, res, res_n, idx, idx_n, mzl_cutoff, chain_cutoff, NULL);
		// lchain_qgen_mcopy_input(cl, overlap_list, rid, rl, NULL, uref, apend_be, max_n_chain, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_thres, bw_thres_sec, quick_check, gen_off, mcopy_rate, mcopy_khit_cut, sp);
		lchain_qgen_mcopy(cl, overlap_list, rid, rl, NULL, uref, apend_be, max_n_chain, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_thres, quick_check, gen_off, mcopy_rate, chain_cutoff, mcopy_khit_cut, sp);
		return 0;
	}
}