// File: /workspace/github_cpp_makefile_star2_O3/millanek[P]evo/./process_vcf_coding_sequences.h
// Function: addN_S_Nd_Sd_SameIndividualsH1againstH2(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>>> const&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>>> const&, std::map<unsigned long, int, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, int>>>&, std::map<unsigned long, int, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, int>>>&, CDSComparisonMatrices&)
inline void addN_S_Nd_Sd_SameIndividualsH1againstH2(const std::vector<string>& altCodons, const std::vector<string>& altCodonsH2, std::map<std::vector<string>::size_type, int>& haveStop, std::map<std::vector<string>::size_type, int>& haveStopH2, CDSComparisonMatrices& p) {
    int numSamples = (int)altCodons.size();
    for (std::vector<std::string>::size_type j = 0; j != numSamples; j++) {
        if (haveStop[j] == 1 || getAminoAcid(altCodons[j]) == "Uncrecognised codon....")
            continue; // only consider this individual if it did not have a premature stop codon
        if (haveStopH2[j] == 1 || getAminoAcid(altCodonsH2[j]) == "Uncrecognised codon....")
            continue;
        
        int d = getCodonDistance(altCodons[j],altCodonsH2[j]);
        // Nd
        double n_d_ijk = calculateNd(altCodons[j],altCodonsH2[j], d);
        double s_d_ijk = d - n_d_ijk;
        p.N_d_jk[j][j] = p.N_d_jk[j][j] + n_d_ijk;
        p.S_d_jk[j][j] = p.S_d_jk[j][j] + s_d_ijk;
        // N
        double N_ijk = calculateN(altCodons[j],altCodonsH2[j], d, false);
        double S_ijk = (3 - N_ijk);
        p.N_jk[j][j] = p.N_jk[j][j] + N_ijk; p.S_jk[j][j] = p.S_jk[j][j] + S_ijk;
        // NtS -- for incorporating tS/tV mutation probabilities
        double N_tS = calculateNtS(altCodons[j],altCodonsH2[j], d, false);
        p.tS_N_jk[j][j] = p.tS_N_jk[j][j] + N_tS;
        p.tS_S_jk[j][j] = p.tS_S_jk[j][j] + (1 - N_tS);
        p.tV_N_jk[j][j] = p.tV_N_jk[j][j] + (N_ijk - N_tS);
        p.tV_S_jk[j][j] = p.tV_S_jk[j][j] + (2 - (N_ijk - N_tS));
    }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x58, %rsp
movq %r8, 0x20(%rsp)
movq %rcx, 0x30(%rsp)
movq 0x8(%rdi), %rax
subq (%rdi), %rax
movq %rsi, 0x8(%rsp)
movq %rax, %rcx
shlq $0x1b, %rcx
movq $0x0, (%rsp)
je 0x776e7
movq %rdx, %r15
movq %rdi, %r12
shrq $0x5, %rax
movslq %eax, %rbp
leaq 0x48(%rsp), %r14
movq %rsp, %r13
movq %rdi, 0x18(%rsp)
movq %rdx, 0x10(%rsp)
movq %r15, %rdi
movq %r13, %rsi
callq 0x761aa
cmpl $0x1, (%rax)
movq (%rsp), %rsi
je 0x776d7
movq %r13, %rbx
shlq $0x5, %rsi
addq (%r12), %rsi
leaq 0x38(%rsp), %r13
movq %r13, %rdi
callq 0x76360
movq %r13, %rdi
leaq 0x5f134(%rip), %rsi     # 0xd65ab
callq 0x8160
movl %eax, %r13d
movq 0x38(%rsp), %rdi
cmpq %r14, %rdi
je 0x77496
movq 0x48(%rsp), %rsi
incq %rsi
callq 0x8480
testl %r13d, %r13d
je 0x7755a
movq 0x30(%rsp), %rdi
movq %rbx, %r13
movq %rbx, %rsi
callq 0x761aa
cmpl $0x1, (%rax)
movq (%rsp), %rsi
je 0x776d7
shlq $0x5, %rsi
movq 0x8(%rsp), %rax
addq (%rax), %rsi
leaq 0x38(%rsp), %r13
movq %r13, %rdi
callq 0x76360
movq %r13, %rdi
leaq 0x5f0cc(%rip), %rsi     # 0xd65ab
callq 0x8160
movl %eax, %r13d
movq 0x38(%rsp), %rdi
cmpq %r14, %rdi
je 0x774fe
movq 0x48(%rsp), %rsi
incq %rsi
callq 0x8480
movq (%rsp), %rsi
testl %r13d, %r13d
je 0x7755e
movq (%r12), %rdi
shlq $0x5, %rsi
movq 0x8(%rsp), %rax
movq (%rax), %rax
movq 0x8(%rdi,%rsi), %rcx
cmpq 0x8(%rax,%rsi), %rcx
jne 0x776f6
addq %rsi, %rdi
addq %rsi, %rax
testq %rcx, %rcx
je 0x77566
movq (%rdi), %rdx
movq (%rax), %rsi
xorl %r8d, %r8d
xorl %r13d, %r13d
movb (%rdx,%r8), %r9b
xorl %r10d, %r10d
cmpb (%rsi,%r8), %r9b
setne %r10b
addl %r10d, %r13d
incq %r8
cmpq %r8, %rcx
jne 0x7753e
jmp 0x77569
movq (%rsp), %rsi
movq %rbx, %r13
jmp 0x776d7
xorl %r13d, %r13d
movq %rax, %rsi
movl %r13d, %edx
callq 0x777d5
cvtsi2sd %r13d, %xmm1
subsd %xmm0, %xmm1
movq (%rsp), %rsi
movq 0x20(%rsp), %r12
movq (%r12), %rax
leaq (,%rsi,8), %rcx
leaq (%rcx,%rcx,2), %rcx
movq (%rax,%rcx), %rax
addsd (%rax,%rsi,8), %xmm0
movsd %xmm0, (%rax,%rsi,8)
movq 0x30(%r12), %rax
movq (%rax,%rcx), %rax
addsd (%rax,%rsi,8), %xmm1
movsd %xmm1, (%rax,%rsi,8)
shlq $0x5, %rsi
movq 0x18(%rsp), %r15
movq (%r15), %rdi
addq %rsi, %rdi
movq 0x8(%rsp), %r14
addq (%r14), %rsi
movl %r13d, %edx
xorl %ecx, %ecx
callq 0x78251
movapd %xmm0, %xmm2
movsd %xmm0, 0x28(%rsp)
movsd 0x5e53e(%rip), %xmm0    # 0xd5b28
subsd %xmm2, %xmm0
movq (%rsp), %rsi
movq 0x18(%r12), %rax
leaq (,%rsi,8), %rcx
leaq (%rcx,%rcx,2), %rcx
movq (%rax,%rcx), %rax
movsd (%rax,%rsi,8), %xmm1
addsd %xmm2, %xmm1
movsd %xmm1, (%rax,%rsi,8)
movq 0x48(%r12), %rax
movq (%rax,%rcx), %rax
addsd (%rax,%rsi,8), %xmm0
movsd %xmm0, (%rax,%rsi,8)
shlq $0x5, %rsi
movq (%r15), %rdi
addq %rsi, %rdi
addq (%r14), %rsi
movl %r13d, %edx
xorl %ecx, %ecx
callq 0x78e29
movq (%rsp), %rsi
movq 0x60(%r12), %rax
leaq (,%rsi,8), %rcx
leaq (%rcx,%rcx,2), %rcx
movq (%rax,%rcx), %rax
movsd (%rax,%rsi,8), %xmm1
addsd %xmm0, %xmm1
movsd %xmm1, (%rax,%rsi,8)
movq 0x78(%r12), %rax
movq (%rax,%rcx), %rax
movsd 0x55099(%rip), %xmm1    # 0xcc710
subsd %xmm0, %xmm1
addsd (%rax,%rsi,8), %xmm1
movsd %xmm1, (%rax,%rsi,8)
movq 0x90(%r12), %rax
movq (%rax,%rcx), %rax
movsd 0x28(%rsp), %xmm1
subsd %xmm0, %xmm1
movsd 0x5e47d(%rip), %xmm0    # 0xd5b20
subsd %xmm1, %xmm0
addsd (%rax,%rsi,8), %xmm1
movsd %xmm1, (%rax,%rsi,8)
movq 0xa8(%r12), %rax
movq %r15, %r12
movq (%rax,%rcx), %rax
addsd (%rax,%rsi,8), %xmm0
movsd %xmm0, (%rax,%rsi,8)
leaq 0x48(%rsp), %r14
movq %rbx, %r13
movq 0x10(%rsp), %r15
incq %rsi
movq %rsi, (%rsp)
cmpq %rbp, %rsi
jne 0x7743d
addq $0x58, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
leaq 0x5eec6(%rip), %rdi     # 0xd65c3
leaq 0x566a8(%rip), %rsi     # 0xcddac
leaq 0x5effb(%rip), %rcx     # 0xd6706
movl $0x218, %edx            # imm = 0x218
callq 0x82c0