// File: /workspace/github_cpp_makefile_star2_O3/medvedevgroup[P]varmatch/src/wholegenome.cpp
// Function: WholeGenome::ReadDirectRef(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>)
void WholeGenome::ReadDirectRef(string genome_seq, string ref_vcf){

    for(int i = 0; i < 22; i++){
        chrid_by_chrname[to_string(i+1)] = i;
        chrname_by_chrid[i] = to_string(i+1);
    }
    chrid_by_chrname["X"] = 22;
    chrname_by_chrid[22] = "X";
    chrid_by_chrname["Y"] = 23;
    chrname_by_chrid[23]="Y";
    baseline_variant_total_num = ReadReferenceVariants(ref_vcf);
    ref_vcf_filename = ref_vcf;

}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x78, %rsp
movq %rdx, 0x48(%rsp)
leaq 0x88(%rdi), %rax
movq %rax, 0x38(%rsp)
leaq 0x20(%rsp), %rdx
leaq 0xc(%rsp), %rax
movl $0x0, (%rax)
movq %rdi, 0x40(%rsp)
leaq 0xb8(%rdi), %rax
movq %rax, 0x30(%rsp)
xorl %esi, %esi
leaq 0x10(%rsp), %rbp
movl $0xd1b71759, %r12d      # imm = 0xD1B71759
leal 0x1(%rsi), %r14d
movl %r14d, %ebx
negl %ebx
cmovsl %r14d, %ebx
movl $0x1, %r13d
cmpl $0xa, %ebx
jb 0x26a6c
movl $0x4, %r13d
movl %ebx, %eax
cmpl $0x63, %eax
jbe 0x26a63
cmpl $0x3e7, %eax            # imm = 0x3E7
jbe 0x26a69
cmpl $0x2710, %eax           # imm = 0x2710
jb 0x26a6c
movl %eax, %ecx
imulq %r12, %rcx
shrq $0x2d, %rcx
addl $0x4, %r13d
cmpl $0x1869f, %eax          # imm = 0x1869F
movl %ecx, %eax
ja 0x26a33
addl $-0x3, %r13d
jmp 0x26a6c
addl $-0x2, %r13d
jmp 0x26a6c
decl %r13d
movq %rsi, 0x50(%rsp)
shrl $0x1f, %r14d
leal (%r14,%r13), %esi
movq %rdx, 0x10(%rsp)
movq %rbp, %rdi
movq %rbp, %r12
movq %rdx, %rbp
movl $0x2d, %edx
callq 0x53b0
addq 0x10(%rsp), %r14
movq %r14, %rdi
movl %r13d, %esi
movl %ebx, %edx
callq 0xe33a
movq 0x38(%rsp), %rdi
movq %r12, %r15
movq %r12, %rsi
callq 0x2841c
movq 0x50(%rsp), %rcx
movl %ecx, (%rax)
movq 0x10(%rsp), %rdi
cmpq %rbp, %rdi
movq %rbp, %rdx
je 0x26ad9
movq 0x20(%rsp), %rsi
incq %rsi
callq 0x5340
leaq 0x20(%rsp), %rdx
movl 0xc(%rsp), %ebx
incl %ebx
movl %ebx, %r14d
negl %r14d
cmovsl %ebx, %r14d
movl $0x1, %r13d
cmpl $0xa, %r14d
movq %r15, %rbp
movl $0xd1b71759, %r12d      # imm = 0xD1B71759
jb 0x26b40
movl $0x4, %r13d
movl %r14d, %eax
cmpl $0x63, %eax
jbe 0x26b37
cmpl $0x3e7, %eax            # imm = 0x3E7
jbe 0x26b3d
cmpl $0x2710, %eax           # imm = 0x2710
jb 0x26b40
movl %eax, %ecx
imulq %r12, %rcx
shrq $0x2d, %rcx
addl $0x4, %r13d
cmpl $0x1869f, %eax          # imm = 0x1869F
movl %ecx, %eax
ja 0x26b07
addl $-0x3, %r13d
jmp 0x26b40
addl $-0x2, %r13d
jmp 0x26b40
decl %r13d
shrl $0x1f, %ebx
leal (%rbx,%r13), %esi
movq %rdx, 0x10(%rsp)
movq %rbp, %rdi
movq %rdx, %r15
movl $0x2d, %edx
callq 0x53b0
addq 0x10(%rsp), %rbx
movq %rbx, %rdi
movl %r13d, %esi
movl %r14d, %edx
callq 0xe33a
movq 0x30(%rsp), %rdi
leaq 0xc(%rsp), %rsi
callq 0x2851c
movq %rax, %rdi
movq %rbp, %rsi
callq 0x53e0
movq 0x10(%rsp), %rdi
cmpq %r15, %rdi
movq %r15, %rdx
je 0x26ba8
movq 0x20(%rsp), %rsi
incq %rsi
callq 0x5340
leaq 0x20(%rsp), %rdx
movl 0xc(%rsp), %eax
leal 0x1(%rax), %esi
movl %esi, 0xc(%rsp)
cmpl $0x15, %eax
jl 0x26a13
leaq 0x10(%rsp), %rdi
movq %rdx, (%rdi)
leaq 0xa744(%rip), %rsi      # 0x3130f
leaq 0xa73e(%rip), %rdx      # 0x31310
callq 0xc3da
leaq 0x10(%rsp), %rsi
movq 0x38(%rsp), %rdi
callq 0x2841c
movq 0x48(%rsp), %r15
movq 0x40(%rsp), %r12
movl $0x16, (%rax)
movq 0x10(%rsp), %rdi
leaq 0x20(%rsp), %rax
cmpq %rax, %rdi
je 0x26c12
movq 0x20(%rsp), %rsi
incq %rsi
callq 0x5340
leaq 0x10(%rsp), %rbx
movl $0x16, (%rbx)
movq 0x30(%rsp), %rdi
movq %rbx, %rsi
callq 0x2958c
movq 0x8(%rax), %rdx
leaq 0xa6da(%rip), %rcx      # 0x3130f
movl $0x1, %r8d
movq %rax, %rdi
xorl %esi, %esi
callq 0x54b0
leaq 0x20(%rsp), %rax
movq %rax, (%rbx)
leaq 0xa6c0(%rip), %rsi      # 0x31314
leaq 0xa6ba(%rip), %rdx      # 0x31315
leaq 0x10(%rsp), %rdi
callq 0xc3da
leaq 0x10(%rsp), %rsi
movq 0x38(%rsp), %rdi
callq 0x2841c
movl $0x17, (%rax)
movq 0x10(%rsp), %rdi
leaq 0x20(%rsp), %rax
cmpq %rax, %rdi
je 0x26c96
movq 0x20(%rsp), %rsi
incq %rsi
callq 0x5340
leaq 0x10(%rsp), %rsi
movl $0x17, (%rsi)
movq 0x30(%rsp), %rdi
callq 0x2958c
movq 0x8(%rax), %rdx
leaq 0xa65e(%rip), %rcx      # 0x31314
movl $0x1, %r8d
movq %rax, %rdi
xorl %esi, %esi
callq 0x54b0
leaq 0x68(%rsp), %r14
movq %r14, -0x10(%r14)
movq (%r15), %rsi
movq 0x8(%r15), %rdx
addq %rsi, %rdx
leaq 0x58(%rsp), %rbx
movq %rbx, %rdi
callq 0x1123c
movq %r12, %rdi
movq %rbx, %rsi
callq 0x267e0
movl %eax, 0x48(%r12)
movq 0x58(%rsp), %rdi
cmpq %r14, %rdi
je 0x26d0d
movq 0x68(%rsp), %rsi
incq %rsi
callq 0x5340
addq $0x8, %r12
movq %r12, %rdi
movq %r15, %rsi
callq 0x51c0
addq $0x78, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %rbx
movq 0x58(%rsp), %rdi
cmpq %r14, %rdi
je 0x26d85
movq 0x68(%rsp), %rsi
jmp 0x26d7d
jmp 0x26d43
jmp 0x26d57
movq %rax, %rbx
movq 0x10(%rsp), %rdi
leaq 0x20(%rsp), %rax
cmpq %rax, %rdi
jne 0x26d78
jmp 0x26d85
movq %rax, %rbx
jmp 0x26d85
movq %rax, %rbx
movq 0x10(%rsp), %rdi
cmpq %rbp, %rdi
jne 0x26d78
jmp 0x26d85
movq %rax, %rbx
movq 0x10(%rsp), %rdi
cmpq %r15, %rdi
je 0x26d85
movq 0x20(%rsp), %rsi
incq %rsi
callq 0x5340
movq %rbx, %rdi
callq 0x55c0
nop