// File: /workspace/github_cpp_makefile_star2_O2/readmapping[P]alfalfa/src/ksw.c
// Function: ksw_i16
kswr_t ksw_i16(kswq_t *q, int tlen, const uint8_t *target, int _gapo, int _gape, int xtra) // the first gap costs -(_o+_e)
{
	int slen, i, m_b, n_b, te = -1, gmax = 0, minsc, endsc;
	uint64_t *b;
	__m128i zero, gapoe, gape, *H0, *H1, *E, *Hmax;
	kswr_t r;

#define __max_8(ret, xx) do { \
		(xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 8)); \
		(xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 4)); \
		(xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 2)); \
    	(ret) = _mm_extract_epi16((xx), 0); \
	} while (0)

	// initialization
	r = g_defr;
	minsc = (xtra&KSW_XSUBO)? xtra&0xffff : 0x10000;
	endsc = (xtra&KSW_XSTOP)? xtra&0xffff : 0x10000;
	m_b = n_b = 0; b = 0;
	zero = _mm_set1_epi32(0);
	gapoe = _mm_set1_epi16(_gapo + _gape);
	gape = _mm_set1_epi16(_gape);
	H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax;
	slen = q->slen;
	for (i = 0; i < slen; ++i) {
		_mm_store_si128(E + i, zero);
		_mm_store_si128(H0 + i, zero);
		_mm_store_si128(Hmax + i, zero);
	}
	// the core loop
	for (i = 0; i < tlen; ++i) {
		int j, k, imax;
		__m128i e, h, f = zero, max = zero, *S = q->qp + target[i] * slen; // s is the 1st score vector
		h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example
		h = _mm_slli_si128(h, 2);
		for (j = 0; LIKELY(j < slen); ++j) {
			h = _mm_adds_epi16(h, *S++);
			e = _mm_load_si128(E + j);
			h = _mm_max_epi16(h, e);
			h = _mm_max_epi16(h, f);
			max = _mm_max_epi16(max, h);
			_mm_store_si128(H1 + j, h);
			h = _mm_subs_epu16(h, gapoe);
			e = _mm_subs_epu16(e, gape);
			e = _mm_max_epi16(e, h);
			_mm_store_si128(E + j, e);
			f = _mm_subs_epu16(f, gape);
			f = _mm_max_epi16(f, h);
			h = _mm_load_si128(H0 + j);
		}
		for (k = 0; LIKELY(k < 16); ++k) {
			f = _mm_slli_si128(f, 2);
			for (j = 0; LIKELY(j < slen); ++j) {
				h = _mm_load_si128(H1 + j);
				h = _mm_max_epi16(h, f);
				_mm_store_si128(H1 + j, h);
				h = _mm_subs_epu16(h, gapoe);
				f = _mm_subs_epu16(f, gape);
				if(UNLIKELY(!_mm_movemask_epi8(_mm_cmpgt_epi16(f, h)))) goto end_loop8;
			}
		}
end_loop8:
		__max_8(imax, max);
		if (imax >= minsc) {
			if (n_b == 0 || (int32_t)b[n_b-1] + 1 != i) {
				if (n_b == m_b) {
					m_b = m_b? m_b<<1 : 8;
					b = (uint64_t*)realloc(b, 8 * m_b);
				}
				b[n_b++] = (uint64_t)imax<<32 | i;
			} else if ((int)(b[n_b-1]>>32) < imax) b[n_b-1] = (uint64_t)imax<<32 | i; // modify the last
		}
		if (imax > gmax) {
			gmax = imax; te = i;
			for (j = 0; LIKELY(j < slen); ++j)
				_mm_store_si128(Hmax + j, _mm_load_si128(H1 + j));
			if (gmax >= endsc) break;
		}
		S = H1; H1 = H0; H0 = S;
	}
	r.score = gmax; r.te = te;
	{
		int max = -1, low, high, qlen = slen * 8;
		uint16_t *t = (uint16_t*)Hmax;
		for (i = 0, r.qe = -1; i < qlen; ++i, ++t)
			if ((int)*t > max) max = *t, r.qe = i / 8 + i % 8 * slen;
		if (b) {
			i = (r.score + q->max - 1) / q->max;
			low = te - i; high = te + i;
			for (i = 0; i < n_b; ++i) {
				int e = (int32_t)b[i];
				if ((e < low || e > high) && (int)(b[i]>>32) > r.score2)
					r.score2 = b[i]>>32, r.te2 = e;
			}
		}
	}
	free(b);
	return r;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x98, %rsp
movl %edx, %r10d
movups 0x924b(%rip), %xmm0     # 0x39a14
movups %xmm0, 0xc(%rdi)
movups 0x9234(%rip), %xmm0     # 0x39a08
movups %xmm0, (%rdi)
addl %r9d, %r8d
movd %r8d, %xmm1
movd %r9d, %xmm0
movq 0x18(%rsi), %r13
movq 0x20(%rsi), %rax
movq 0x28(%rsi), %r15
movq 0x30(%rsi), %rbp
movq %rsi, 0x38(%rsp)
movslq 0x4(%rsi), %rbx
xorl %edx, %edx
testl %ebx, %ebx
movl $0x0, %r12d
cmovgl %ebx, %r12d
shlq $0x4, %r12
pxor %xmm2, %xmm2
cmpq %rdx, %r12
je 0x30831
movdqa %xmm2, (%r15,%rdx)
movdqa %xmm2, (%r13,%rdx)
movdqa %xmm2, (%rbp,%rdx)
addq $0x10, %rdx
jmp 0x30813
movq %rdi, 0x40(%rsp)
movl 0xd0(%rsp), %r9d
movzwl %r9w, %edx
movl %edx, 0x1c(%rsp)
pshuflw $0x0, %xmm1, %xmm1      # xmm1 = xmm1[0,0,0,0,4,5,6,7]
pshufd $0x0, %xmm1, %xmm5      # xmm5 = xmm1[0,0,0,0]
pshuflw $0x0, %xmm0, %xmm0      # xmm0 = xmm0[0,0,0,0,4,5,6,7]
pshufd $0x0, %xmm0, %xmm6      # xmm6 = xmm0[0,0,0,0]
xorl %esi, %esi
testl %r10d, %r10d
cmovlel %esi, %r10d
pushq $-0x1
popq %rdx
movl %edx, 0xc(%rsp)
movq %rbx, %rdx
shlq $0x4, %rdx
movq %rdx, 0x68(%rsp)
xorl %edi, %edi
movq $0x0, 0x10(%rsp)
xorl %r8d, %r8d
movq $0x0, 0x28(%rsp)
movq %rbx, 0x30(%rsp)
movq %rcx, 0x50(%rsp)
movq %r10, 0x48(%rsp)
movdqa %xmm5, 0x80(%rsp)
movdqa %xmm6, 0x70(%rsp)
cmpq %r10, %rsi
je 0x30ac7
movq %rax, %r14
movzbl (%rcx,%rsi), %eax
imull %ebx, %eax
cltq
shlq $0x4, %rax
movq 0x38(%rsp), %rdx
addq 0x10(%rdx), %rax
movq 0x68(%rsp), %rdx
movdqa -0x10(%r13,%rdx), %xmm2
pslldq $0x2, %xmm2             # xmm2 = zero,zero,xmm2[0,1,2,3,4,5,6,7,8,9,10,11,12,13]
pxor %xmm1, %xmm1
xorl %edx, %edx
pxor %xmm0, %xmm0
cmpq %rdx, %r12
je 0x30935
paddsw (%rax,%rdx), %xmm2
movdqa (%r15,%rdx), %xmm3
movdqa %xmm3, %xmm4
pmaxsw %xmm1, %xmm4
pmaxsw %xmm2, %xmm4
pmaxsw %xmm4, %xmm0
movdqa %xmm4, (%r14,%rdx)
psubusw %xmm5, %xmm4
psubusw %xmm6, %xmm3
pmaxsw %xmm4, %xmm3
movdqa %xmm3, (%r15,%rdx)
psubusw %xmm6, %xmm1
pmaxsw %xmm4, %xmm1
movdqa (%r13,%rdx), %xmm2
addq $0x10, %rdx
jmp 0x308e8
movq %rsi, 0x20(%rsp)
xorl %eax, %eax
cmpl $0x10, %eax
je 0x3097f
pslldq $0x2, %xmm1             # xmm1 = zero,zero,xmm1[0,1,2,3,4,5,6,7,8,9,10,11,12,13]
xorl %esi, %esi
cmpq %rsi, %r12
je 0x3097b
movdqa (%r14,%rsi), %xmm2
pmaxsw %xmm1, %xmm2
movdqa %xmm2, (%r14,%rsi)
psubusw %xmm5, %xmm2
psubusw %xmm6, %xmm1
movdqa %xmm1, %xmm3
pcmpgtw %xmm2, %xmm3
pmovmskb %xmm3, %edx
testl %edx, %edx
je 0x3097f
addq $0x10, %rsi
jmp 0x30948
incl %eax
jmp 0x3093c
btl $0x12, %r9d
movdqa %xmm0, %xmm1
psrldq $0x8, %xmm1             # xmm1 = xmm1[8,9,10,11,12,13,14,15],zero,zero,zero,zero,zero,zero,zero,zero
pmaxsw %xmm0, %xmm1
movdqa %xmm1, %xmm0
psrldq $0x4, %xmm0             # xmm0 = xmm0[4,5,6,7,8,9,10,11,12,13,14,15],zero,zero,zero,zero
pmaxsw %xmm1, %xmm0
movdqa %xmm0, %xmm1
psrldq $0x2, %xmm1             # xmm1 = xmm1[2,3,4,5,6,7,8,9,10,11,12,13,14,15],zero,zero
pmaxsw %xmm0, %xmm1
pextrw $0x0, %xmm1, %ebx
jae 0x30a6d
cmpl %ebx, 0x1c(%rsp)
movq 0x20(%rsp), %rsi
ja 0x30a72
movslq %r8d, %r11
testl %r8d, %r8d
je 0x309f5
movq -0x8(%rdi,%r11,8), %rax
leal 0x1(%rax), %edx
cmpq %rsi, %rdx
jne 0x309f5
shrq $0x20, %rax
cmpl %ebx, %eax
jge 0x30a72
decq %r11
movq %rbx, %rax
shlq $0x20, %rax
orq %rsi, %rax
jmp 0x30a67
cmpl 0x28(%rsp), %r8d
jne 0x30a5a
movq %r11, 0x58(%rsp)
leal (%r8,%r8), %edx
testl %r8d, %r8d
pushq $0x8
popq %rax
cmovel %eax, %edx
movq %rdx, 0x28(%rsp)
leal (,%rdx,8), %eax
movslq %eax, %rsi
movq %r8, 0x60(%rsp)
callq 0x7590
movq 0x58(%rsp), %r11
movdqa 0x70(%rsp), %xmm6
movdqa 0x80(%rsp), %xmm5
movq 0x20(%rsp), %rsi
movl 0xd0(%rsp), %r9d
movq 0x48(%rsp), %r10
movq 0x50(%rsp), %rcx
movq 0x60(%rsp), %r8
movq %rax, %rdi
movq %rbx, %rax
shlq $0x20, %rax
orq %rsi, %rax
incl %r8d
movq %rax, (%rdi,%r11,8)
jmp 0x30a72
movq 0x20(%rsp), %rsi
cmpl %ebx, 0x10(%rsp)
jae 0x30ab4
xorl %eax, %eax
cmpq %rax, %r12
je 0x30a91
movdqa (%r14,%rax), %xmm0
movdqa %xmm0, (%rbp,%rax)
addq $0x10, %rax
jmp 0x30a7a
btl $0x11, %r9d
jae 0x30aab
movl %ebx, %eax
movq %rax, 0x10(%rsp)
movl %esi, 0xc(%rsp)
cmpl %ebx, 0x1c(%rsp)
ja 0x30ab4
jmp 0x30ad1
movq %rbx, 0x10(%rsp)
movl %esi, 0xc(%rsp)
incq %rsi
movq %r13, %rax
movq %r14, %r13
movq 0x30(%rsp), %rbx
jmp 0x308ab
movq %r8, %r15
movl 0xc(%rsp), %r12d
jmp 0x30ae1
movq %r8, %r15
movq %rbx, 0x10(%rsp)
movl %esi, %r12d
movq 0x30(%rsp), %rbx
movq 0x40(%rsp), %r14
movq 0x10(%rsp), %rax
movl %eax, (%r14)
movl %r12d, 0x4(%r14)
leal (,%rbx,8), %eax
xorl %ecx, %ecx
testl %eax, %eax
cmovlel %ecx, %eax
pushq $-0x1
popq %rdx
movl %edx, %esi
cmpl %ecx, %eax
je 0x30b34
movzwl (%rbp,%rcx,2), %r8d
movl %ecx, %r9d
shrl $0x3, %r9d
movl %ecx, %r10d
andl $0x7, %r10d
imull %ebx, %r10d
addl %r9d, %r10d
cmpl %r8d, %esi
cmovll %r10d, %edx
cmovlel %r8d, %esi
incq %rcx
jmp 0x30b05
movl %edx, 0x8(%r14)
testq %rdi, %rdi
je 0x30bb3
movq 0x38(%rsp), %rax
movzbl 0xa(%rax), %ecx
movq 0x10(%rsp), %rax
addl %ecx, %eax
decl %eax
cltd
idivl %ecx
movl %r12d, %ecx
subl %eax, %ecx
addl %r12d, %eax
movl 0xc(%r14), %r8d
movl 0x10(%r14), %edx
xorl %esi, %esi
testl %r15d, %r15d
cmovlel %esi, %r15d
cmpq %rsi, %r15
je 0x30bab
movq (%rdi,%rsi,8), %r9
cmpl %r9d, %ecx
setg %r10b
cmpl %r9d, %eax
setl %r11b
orb %r10b, %r11b
movq %r9, %r10
shrq $0x20, %r10
cmpl %r10d, %r8d
cmovgl %r8d, %r10d
movl %edx, %ebx
cmovll %r9d, %ebx
testb %r11b, %r11b
cmovnel %ebx, %edx
cmovel %r8d, %r10d
incq %rsi
movl %r10d, %r8d
jmp 0x30b6b
movl %r8d, 0xc(%r14)
movl %edx, 0x10(%r14)
callq 0x7360
movq %r14, %rax
addq $0x98, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq