// File: /workspace/github_cpp_makefile_star2_O2/chhylp123[P]hifiasm/inter.cpp
// Function: gl_chain_refine_advance_combine_with_trans(mg_tbuf_s*, ul_vec_t*, overlap_region_alloc*, Correct_dumy*, haplotype_evdience_alloc*, st_mt_t*, glchain_t*, gdpchain_t*, ul_idx_t const*, double, long, long, ug_opt_t const*, long, long, void*)
int64_t gl_chain_refine_advance_combine_with_trans(mg_tbuf_t *b, ul_vec_t *rch, overlap_region_alloc* olist, Correct_dumy* dumy, haplotype_evdience_alloc *hap, st_mt_t *sps, glchain_t *ll, gdpchain_t *gdp, const ul_idx_t *uref, double diff_ec_ul, int64_t winLen, int64_t qlen, const ug_opt_t *uopt, 
int64_t debug_i, int64_t tid, void *km)
{
	ll->tk.n = ll->lo.n = 0;
	kv_ul_ov_t *idx = &(ll->lo);
	uint64_t o2 = gl_chain_gen(olist, uref, idx, 0, hap, km);
	if(idx->n == 0) return 0;
	// fprintf(stderr, "(beg0) [M::%s::tid:%ld] debug_i:%ld, qlen:%ld, # cis:%lu, # trans:%lu\n", __func__, tid, debug_i, qlen, (uint64_t)idx->n, o2);
	int64_t max_idx, occ = 0, f = 0;

	kv_resize_km(km, uint64_t, ll->srt.a, idx->n);
    kv_resize_km(km, uint64_t, hap->snp_srt, idx->n);
	kv_resize_km(km, ul_ov_t, ll->tk, idx->n);
	///chain exact U-matches
	occ = gl_chain_advance(idx, ll->tk.a, uref, uopt, G_CHAIN_BW, /**diff_ec_ul**/N_GCHAIN_RATE, qlen, UG_SKIP, dumy->overlapID, ll->srt.a.a, hap->snp_srt.a, G_CHAIN_TRANS_WEIGHT, 0, NULL, uref->ug, debug_i, km);
	if(occ) {
		if(ff_chain(idx, qlen, 0.99/**P_CHAIN_COV**/, -1/**G_CHAIN_TRANS_RATE**/, ll->tk.a, NULL, NULL, NULL, diff_ec_ul, winLen, km)) {
			f = l2g_res_chain(uref->ug, ll->tk.a+idx->a[idx->n-1].ts, idx->a[idx->n-1].te-idx->a[idx->n-1].ts, &(gdp->swap), -1/**N_GCHAIN_RATE**/);
		} else if(o2) {///means there are trans overlaps
			gl_chain_gen(olist, uref, idx, 1, hap, km);
			kv_resize_km(km, uint64_t, ll->srt.a, idx->n);
    		kv_resize_km(km, uint64_t, hap->snp_srt, idx->n);
			kv_resize_km(km, ul_ov_t, ll->tk, idx->n);
			///chain all U-matches
			occ = gl_chain_advance(idx, ll->tk.a, uref, uopt, G_CHAIN_BW, /**diff_ec_ul**/N_GCHAIN_RATE, qlen, UG_SKIP, dumy->overlapID, ll->srt.a.a, hap->snp_srt.a, G_CHAIN_TRANS_WEIGHT, 0, NULL, uref->ug, debug_i, km);
			if(ff_chain(idx, qlen, 0.99/**P_CHAIN_COV**/, G_CHAIN_TRANS_RATE, ll->tk.a, olist, hap, uref, diff_ec_ul, winLen, km)) {
				f = l2g_res_chain(uref->ug, ll->tk.a+idx->a[idx->n-1].ts, idx->a[idx->n-1].te-idx->a[idx->n-1].ts, &(gdp->swap), -1/**N_GCHAIN_RATE**/);
			}
		}
	}
	// fprintf(stderr, "(beg1) [M::%s] debug_i:%ld, qlen:%ld\n", __func__, debug_i, qlen);
	if(!f) {
		gl_chain_gen(olist, uref, idx, 1, hap, km);
		l2g_chain(uref, idx, &(gdp->l)); ll->tk.n = 0;
		///buffer
		kv_resize(uint64_t, ll->srt.a, gdp->l.n); kv_resize(uint64_t, hap->snp_srt, gdp->l.n);
		kv_resize(uint64_t, gdp->v, gdp->l.n); kv_resize(int64_t, gdp->f, gdp->l.n);
		max_idx = hc_gchain1_dp(b->km, uref, uref->ug, &(gdp->l), &(gdp->swap), &(gdp->dst), &(gdp->out), &(gdp->path), rch->rlen,
		uopt, G_CHAIN_BW, diff_ec_ul, -1, ll->srt.a.a, sps, gdp->f.a, hap->snp_srt.a, gdp->v.a);
		if(max_idx >= 0 && gen_max_gchain_adv(b->km, uref, debug_i, sps, &(gdp->l), &(ll->tk), NULL, rch->rlen, P_CHAIN_COV, 0.3/**P_FRAGEMENT_PRIMARY_CHAIN_COV**/, 
			0.1/**P_FRAGEMENT_PRIMARY_SECOND_COV**/, PRIMARY_UL_CHAIN_MIN, uref->ug->g, &(gdp->dst_done), &(gdp->out), &(gdp->path), ll->srt.a.a, &(gdp->swap))) {
			// print_raw_chains(&(gdp->swap), debug_i);
			f = check_trans_rate_gap(&(gdp->swap), &(ll->tk), olist, hap, uref, diff_ec_ul, winLen, G_CHAIN_TRANS_RATE);
		}
	}
	// if(debug_i == 1756) fprintf(stderr, "[M::%s] ulid:%ld, qlen:%ld, f:%ld\n", __func__, debug_i, qlen, f);
	if(f) update_ul_vec_t_ug(uref, rch, &(gdp->swap), debug_i);
	// debug_ul_vec_t_chain(km, uref->ug->g, rch, &(gdp->dst_done), &(gdp->out));
	// fprintf(stderr, "(beg3) [M::%s::tid:%ld] debug_i:%ld, qlen:%ld\n", __func__, tid, debug_i, qlen);
	return 1;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x38, %rsp
movsd %xmm0, 0x10(%rsp)
movq %r9, %rbx
movq %rcx, 0x28(%rsp)
movq %rsi, 0x18(%rsp)
movq %rdi, 0x20(%rsp)
movq 0xb0(%rsp), %r9
movq 0x70(%rsp), %rbp
andq $0x0, 0x8(%rbp)
movq 0x80(%rsp), %r14
andq $0x0, 0x20(%rbp)
xorl %r15d, %r15d
movq %rdx, 0x8(%rsp)
movq %rdx, %rdi
movq %r14, %rsi
movq %rbp, %rdx
xorl %ecx, %ecx
movq %r8, (%rsp)
callq 0x1604c4
movq %rax, %r12
movq 0x8(%rbp), %rax
testq %rax, %rax
je 0x16952e
cmpq %rax, 0x50(%rbp)
movq %rbx, 0x30(%rsp)
jae 0x168e0c
decq %rax
movq %rax, %rcx
shrq %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x2, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x4, %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x8, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x10, %rcx
orq %rax, %rcx
leaq 0x1(%rcx), %rax
movq %rax, 0x50(%rbp)
movq 0x58(%rbp), %rsi
leaq 0x8(,%rcx,8), %rdx
movq 0xb0(%rsp), %rdi
callq 0x1a3acc
movq %rax, 0x58(%rbp)
movq 0x8(%rbp), %rax
movq (%rsp), %rbx
cmpq %rax, 0x240(%rbx)
jae 0x168e7f
decq %rax
movq %rax, %rcx
shrq %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x2, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x4, %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x8, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x10, %rcx
orq %rax, %rcx
leaq 0x1(%rcx), %rax
movq %rax, 0x240(%rbx)
movq 0x248(%rbx), %rsi
leaq 0x8(,%rcx,8), %rdx
movq 0xb0(%rsp), %rdi
callq 0x1a3acc
movq %rax, 0x248(%rbx)
movq 0x8(%rbp), %rax
movq 0x98(%rsp), %r15
movq 0x90(%rsp), %r13
movq 0x18(%rbp), %rsi
cmpq %rax, 0x28(%rbp)
jae 0x168eec
decq %rax
movq %rax, %rcx
shrq %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x2, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x4, %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x8, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x10, %rcx
orq %rax, %rcx
incq %rcx
movq %rcx, 0x28(%rbp)
imulq $0x1c, %rcx, %rdx
movq 0xb0(%rsp), %rdi
callq 0x1a3acc
movq %rax, %rsi
movq %rax, 0x18(%rbp)
movq 0x78(%rsp), %rbx
movq 0x28(%rsp), %rax
movq 0x28(%rax), %rax
movq 0x58(%rbp), %rcx
movq (%rsp), %rdx
movq 0x248(%rdx), %rdx
movq (%r14), %rdi
subq $0x50, %rsp
movq %rdi, 0x38(%rsp)
xorps %xmm0, %xmm0
movups %xmm0, 0x28(%rsp)
movq %rdx, 0x18(%rsp)
movq %rcx, 0x10(%rsp)
movq %rax, 0x8(%rsp)
orq $-0x1, 0x20(%rsp)
pushq $0x10
popq %r8
movsd 0x7a5fa(%rip), %xmm0    # 0x1e3538
movq %rbp, %rdi
movq %r14, %rdx
movq %r15, %rcx
movq %r13, %r9
callq 0x1637c6
addq $0x50, %rsp
pushq $0x1
popq %r15
testq %rax, %rax
je 0x1691f1
movq 0x18(%rbp), %rdx
movss 0x88b14(%rip), %xmm0    # 0x1f1a80
movss 0x83b2c(%rip), %xmm1    # 0x1ecaa0
movq %rbp, %rdi
movq %r13, %rsi
xorl %ecx, %ecx
xorl %r8d, %r8d
xorl %r9d, %r9d
movsd 0x10(%rsp), %xmm2
pushq 0xb0(%rsp)
pushq 0x90(%rsp)
callq 0x164670
popq %rcx
popq %rdx
testl %eax, %eax
je 0x168fe0
movq (%r14), %rdi
imulq $0x1c, 0x8(%rbp), %rax
movq (%rbp), %rcx
movl -0xc(%rcx,%rax), %r8d
movl -0x8(%rcx,%rax), %edx
imulq $0x1c, %r8, %rsi
addq 0x18(%rbp), %rsi
subl %r8d, %edx
leaq 0x18(%rbx), %rcx
movsd 0x7a5b3(%rip), %xmm0    # 0x1e3580
callq 0x166780
testq %rax, %rax
jne 0x169514
jmp 0x1691f1
testq %r12, %r12
je 0x1691f1
pushq $0x1
popq %rcx
movq 0x8(%rsp), %rdi
movq %r14, %rsi
movq %rbp, %rdx
movq (%rsp), %r8
movq 0xb0(%rsp), %r12
movq %r12, %r9
callq 0x1604c4
movq 0x8(%rbp), %rax
cmpq %rax, 0x50(%rbp)
jae 0x16906d
decq %rax
movq %rax, %rcx
shrq %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x2, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x4, %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x8, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x10, %rcx
orq %rax, %rcx
leaq 0x1(%rcx), %rax
movq %rax, 0x50(%rbp)
movq 0x58(%rbp), %rsi
leaq 0x8(,%rcx,8), %rdx
movq %r12, %rdi
callq 0x1a3acc
movq %rax, 0x58(%rbp)
movq 0x8(%rbp), %rax
movq (%rsp), %r12
cmpq %rax, 0x240(%r12)
jae 0x1690e4
decq %rax
movq %rax, %rcx
shrq %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x2, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x4, %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x8, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x10, %rcx
orq %rax, %rcx
leaq 0x1(%rcx), %rax
movq %rax, 0x240(%r12)
movq 0x248(%r12), %rsi
leaq 0x8(,%rcx,8), %rdx
movq 0xb0(%rsp), %rdi
callq 0x1a3acc
movq %rax, 0x248(%r12)
movq 0x8(%rbp), %rax
movq 0x18(%rbp), %rsi
cmpq %rax, 0x28(%rbp)
jae 0x169141
decq %rax
movq %rax, %rcx
shrq %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x2, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x4, %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x8, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x10, %rcx
orq %rax, %rcx
incq %rcx
movq %rcx, 0x28(%rbp)
imulq $0x1c, %rcx, %rdx
movq 0xb0(%rsp), %rdi
callq 0x1a3acc
movq %rax, %rsi
movq %rax, 0x18(%rbp)
movq 0x28(%rsp), %rax
movq 0x28(%rax), %rax
movq 0x58(%rbp), %rcx
movq (%rsp), %r12
movq 0x248(%r12), %rdx
movq (%r14), %rdi
subq $0x50, %rsp
movq %rdi, 0x38(%rsp)
xorps %xmm0, %xmm0
movups %xmm0, 0x28(%rsp)
movq %rdx, 0x18(%rsp)
movq %rcx, 0x10(%rsp)
movq %rax, 0x8(%rsp)
orq $-0x1, 0x20(%rsp)
pushq $0x10
popq %r8
movsd 0x7a3a9(%rip), %xmm0    # 0x1e3538
movq %rbp, %rdi
movq %r14, %rdx
movq 0xe8(%rsp), %rcx
movq %r13, %r9
callq 0x1637c6
addq $0x50, %rsp
movq 0x18(%rbp), %rdx
movss 0x888cb(%rip), %xmm0    # 0x1f1a80
movss 0x888bb(%rip), %xmm1    # 0x1f1a78
movq %rbp, %rdi
movq %r13, %rsi
movq 0x8(%rsp), %rcx
movq %r12, %r8
movq %r14, %r9
movsd 0x10(%rsp), %xmm2
pushq 0xb0(%rsp)
pushq 0x90(%rsp)
callq 0x164670
popq %rcx
popq %rdx
testl %eax, %eax
jne 0x168fa1
pushq $0x1
popq %rcx
movq 0x8(%rsp), %rdi
movq %r14, %rsi
movq %rbp, %rdx
movq (%rsp), %r13
movq %r13, %r8
movq 0xb0(%rsp), %r9
callq 0x1604c4
movq %r14, %rdi
movq %rbp, %rsi
movq %rbx, %rdx
callq 0x166640
andq $0x0, 0x20(%rbp)
movq 0x8(%rbx), %rax
cmpq %rax, 0x50(%rbp)
jae 0x169285
decq %rax
movq %rax, %rcx
shrq %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x2, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x4, %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x8, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x10, %rcx
orq %rax, %rcx
leaq 0x1(%rcx), %rax
movq %rax, 0x50(%rbp)
movq 0x58(%rbp), %rdi
leaq 0x8(,%rcx,8), %rsi
callq 0x2370
movq %rax, 0x58(%rbp)
movq 0x8(%rbx), %rax
cmpq %rax, 0x240(%r13)
jae 0x1692ec
decq %rax
movq %rax, %rcx
shrq %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x2, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x4, %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x8, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x10, %rcx
orq %rax, %rcx
leaq 0x1(%rcx), %rax
movq %rax, 0x240(%r13)
movq 0x248(%r13), %rdi
leaq 0x8(,%rcx,8), %rsi
callq 0x2370
movq %rax, 0x248(%r13)
movq 0x8(%rbx), %rax
cmpq %rax, 0x80(%rbx)
jae 0x169353
decq %rax
movq %rax, %rcx
shrq %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x2, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x4, %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x8, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x10, %rcx
orq %rax, %rcx
leaq 0x1(%rcx), %rax
movq %rax, 0x80(%rbx)
movq 0x88(%rbx), %rdi
leaq 0x8(,%rcx,8), %rsi
callq 0x2370
movq %rax, 0x88(%rbx)
movq 0x8(%rbx), %rax
cmpq %rax, 0x98(%rbx)
jae 0x1693b8
decq %rax
movq %rax, %rcx
shrq %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x2, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x4, %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x8, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x10, %rcx
orq %rax, %rcx
leaq 0x1(%rcx), %rax
movq %rax, 0x98(%rbx)
movq 0xa0(%rbx), %rdi
leaq 0x8(,%rcx,8), %rsi
callq 0x2370
movq %rax, 0xa0(%rbx)
jmp 0x1693bf
movq 0xa0(%rbx), %rax
movq 0x20(%rsp), %r15
movq (%r15), %rdi
movq (%r14), %rdx
leaq 0x18(%rbx), %r12
leaq 0x30(%rbx), %r9
movq %r14, %rsi
leaq 0x48(%rbx), %r14
movq 0x18(%rsp), %rcx
movl 0x18(%rcx), %ecx
movq 0x58(%rbp), %r11
movq 0x248(%r13), %r8
movq 0x88(%rbx), %r10
subq $0x50, %rsp
movq %r10, 0x48(%rsp)
movq %r8, 0x40(%rsp)
movq %rax, 0x38(%rsp)
movq 0x80(%rsp), %r13
movq %r13, 0x30(%rsp)
movq %r11, 0x28(%rsp)
movq 0xe8(%rsp), %rax
movq %rax, 0x18(%rsp)
movq %rcx, 0x10(%rsp)
movq %r14, (%rsp)
movq $0x10, 0x20(%rsp)
movsd 0x7a141(%rip), %xmm1    # 0x1e3580
movq %rbx, %rcx
movq %r12, %r8
movsd 0x60(%rsp), %xmm0
callq 0x169540
addq $0x50, %rsp
testq %rax, %rax
js 0x16952a
movq 0xa0(%rsp), %rdx
leaq 0x18(%rbp), %r8
leaq 0x60(%rbx), %r10
movq (%r15), %rdi
movq 0x18(%rsp), %rax
movl 0x18(%rax), %eax
movq 0x80(%rsp), %rsi
movq (%rsi), %r11
leaq 0xa8(%rbx), %r15
subq $0x8, %rsp
movss 0x885de(%rip), %xmm0    # 0x1f1a74
movss 0x885e6(%rip), %xmm1    # 0x1f1a84
movss 0x7e80a(%rip), %xmm2    # 0x1e7cb0
movq %r13, %rcx
movq %r8, %r13
movq %rbx, %r8
movq %r13, %r9
pushq %r12
pushq 0x58(%rbp)
pushq %r10
pushq %r14
pushq %r15
pushq 0x18(%r11)
pushq $0x124f8                # imm = 0x124F8
pushq %rax
pushq $0x0
callq 0x16a23d
addq $0x50, %rsp
testl %eax, %eax
je 0x16952a
movss 0x8859a(%rip), %xmm1    # 0x1f1a78
movq %r12, %rdi
movq %r13, %rsi
movq 0x8(%rsp), %rdx
movq (%rsp), %rcx
movq 0x80(%rsp), %r14
movq %r14, %r8
movsd 0x10(%rsp), %xmm0
movq 0x88(%rsp), %r9
callq 0x166f2f
testq %rax, %rax
pushq $0x1
popq %r15
je 0x16952e
addq $0x18, %rbx
movq %r14, %rdi
movq 0x18(%rsp), %rsi
movq %rbx, %rdx
callq 0x167b9e
jmp 0x16952e
pushq $0x1
popq %r15
movq %r15, %rax
addq $0x38, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq