// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/fasta.cpp
// Function: fastqInputReader::nextRead(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>&)
bool fastqInputReader::nextRead(string& meta, string& sequence, string& qualities){
    l = kseq_read(seq);
    if(l < 0)
        return false;
    else{
        meta = seq->name.s;
        sequence = seq->seq.s;
        for(size_t i = 0; i <= sequence.length(); i++) {
            char c = std::tolower(sequence[i]);
            if(nucleotidesOnly) {
                switch(c) {
                    case 'a': case 't': case 'g': case 'c': break;
                    default:
                        c = '~';
                }
            }
            sequence[i] = c;
        }
        
        if (seq->qual.l)
            qualities = seq->qual.s;
        
        return true;
    }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq %rcx, %r12
movq %rdx, %r15
movq %rsi, 0x20(%rsp)
movq %rdi, 0x18(%rsp)
movq 0x8(%rdi), %r13
movq 0x68(%r13), %rbp
cmpl $0x0, 0x60(%r13)
jne 0x19e07
movl 0x8(%rbp), %ecx
movl 0xc(%rbp), %eax
movl $0xffffffff, %r14d      # imm = 0xFFFFFFFF
cmpl $0x0, 0x10(%rbp)
je 0x19dad
cmpl %eax, %ecx
jge 0x19f4d
cmpl %eax, %ecx
jl 0x19de3
movl $0x0, 0x8(%rbp)
movq (%rbp), %rsi
movq 0x18(%rbp), %rdi
movl $0x4000, %edx           # imm = 0x4000
callq 0x7660
movl %eax, 0xc(%rbp)
cmpl $0x3fff, %eax           # imm = 0x3FFF
jg 0x19de3
movl $0x1, 0x10(%rbp)
testl %eax, %eax
je 0x19f4d
movq (%rbp), %rdx
movslq 0x8(%rbp), %rsi
leal 0x1(%rsi), %ecx
movl %ecx, 0x8(%rbp)
movzbl (%rdx,%rsi), %edx
movl %edx, 0xc(%rsp)
cmpl $0x40, %edx
je 0x19e03
cmpl $0x3e, %edx
jne 0x19d9f
movl %edx, 0x60(%r13)
xorl %eax, %eax
movq %rax, 0x48(%r13)
movq %rax, 0x30(%r13)
movq %rax, 0x18(%r13)
leaq 0xc(%rsp), %rcx
movq %rbp, %rdi
xorl %esi, %esi
movq %r13, %rdx
xorl %r8d, %r8d
callq 0x1a18f
testl %eax, %eax
js 0x19f47
cmpl $0xa, 0xc(%rsp)
je 0x19e4f
leaq 0x18(%r13), %rdx
movq %rbp, %rdi
movl $0x2, %esi
xorl %ecx, %ecx
xorl %r8d, %r8d
callq 0x1a18f
cmpq $0x0, 0x40(%r13)
jne 0x19e6c
movq $0x100, 0x38(%r13)      # imm = 0x100
movl $0x100, %edi            # imm = 0x100
callq 0x7430
movq %rax, 0x40(%r13)
cmpl $0x0, 0x10(%rbp)
sete %dl
movl 0xc(%rbp), %eax
cmpl %eax, 0x8(%rbp)
leaq 0x30(%r13), %rbx
setl %cl
orb %cl, %dl
testb $0x1, %dl
je 0x19f3d
testb $0x1, %cl
jne 0x19ebe
movl $0x0, 0x8(%rbp)
movq (%rbp), %rsi
movq 0x18(%rbp), %rdi
movl $0x4000, %edx           # imm = 0x4000
callq 0x7660
movl %eax, 0xc(%rbp)
cmpl $0x3fff, %eax           # imm = 0x3FFF
jg 0x19ebe
movl $0x1, 0x10(%rbp)
testl %eax, %eax
je 0x19f3d
movq (%rbp), %rcx
movslq 0x8(%rbp), %rsi
leal 0x1(%rsi), %edx
movl %edx, 0x8(%rbp)
movb (%rcx,%rsi), %cl
movzbl %cl, %esi
movl %esi, 0xc(%rsp)
cmpl $0x2a, %esi
jg 0x19ee2
cmpl $0xa, %esi
je 0x19f26
jmp 0x19ef5
cmpl $0x2b, %esi
je 0x19f6d
cmpl $0x3e, %esi
je 0x19f69
cmpl $0x40, %esi
je 0x19f69
movq 0x30(%r13), %rax
movq 0x40(%r13), %rdx
leaq 0x1(%rax), %rsi
movq %rsi, 0x30(%r13)
movb %cl, (%rdx,%rax)
movq %rbp, %rdi
movl $0x2, %esi
movq %rbx, %rdx
xorl %ecx, %ecx
movl $0x1, %r8d
callq 0x1a18f
movl 0x8(%rbp), %edx
movl 0xc(%rbp), %eax
cmpl %eax, %edx
setl %cl
cmpl $0x0, 0x10(%rbp)
je 0x19e8b
cmpl %eax, %edx
jl 0x19e8b
movl $0xffffffff, 0xc(%rsp)  # imm = 0xFFFFFFFF
jmp 0x19f6d
movl $0xffffffff, %r14d      # imm = 0xFFFFFFFF
movq 0x18(%rsp), %rax
movl %r14d, 0x10(%rax)
xorl %ebx, %ebx
movl %ebx, %eax
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movl %esi, 0x60(%r13)
movq 0x30(%r13), %rcx
movq 0x40(%r13), %rax
leaq 0x1(%rcx), %rdx
cmpq 0x38(%r13), %rdx
jb 0x19fc7
movq %rdx, %rcx
shrq %rcx
orq %rdx, %rcx
movq %rcx, %rdx
shrq $0x2, %rdx
orq %rcx, %rdx
movq %rdx, %rcx
shrq $0x4, %rcx
orq %rdx, %rcx
movq %rcx, %rdx
shrq $0x8, %rdx
orq %rcx, %rdx
movq %rdx, %rsi
shrq $0x10, %rsi
orq %rdx, %rsi
incq %rsi
movq %rsi, 0x38(%r13)
movq %rax, %rdi
callq 0x7590
movq %rax, 0x40(%r13)
movq 0x30(%r13), %rcx
movb $0x0, (%rax,%rcx)
cmpl $0x2b, 0xc(%rsp)
jne 0x1a0a7
movq %r12, 0x10(%rsp)
movq 0x38(%r13), %rsi
cmpq %rsi, 0x50(%r13)
jae 0x19ff6
movq %rsi, 0x50(%r13)
movq 0x58(%r13), %rdi
callq 0x7590
movq %rax, 0x58(%r13)
leaq 0x48(%r13), %r12
movl 0x8(%rbp), %ecx
movl 0xc(%rbp), %eax
movl $0xfffffffe, %r14d      # imm = 0xFFFFFFFE
cmpl $0x0, 0x10(%rbp)
je 0x1a014
cmpl %eax, %ecx
jge 0x19f4d
cmpl %eax, %ecx
jl 0x1a04a
movl $0x0, 0x8(%rbp)
movq (%rbp), %rsi
movq 0x18(%rbp), %rdi
movl $0x4000, %edx           # imm = 0x4000
callq 0x7660
movl %eax, 0xc(%rbp)
cmpl $0x3fff, %eax           # imm = 0x3FFF
jg 0x1a04a
movl $0x1, 0x10(%rbp)
testl %eax, %eax
je 0x19f4d
movq (%rbp), %rdx
movslq 0x8(%rbp), %rsi
leal 0x1(%rsi), %ecx
movl %ecx, 0x8(%rbp)
movzbl (%rdx,%rsi), %edx
movl %edx, 0xc(%rsp)
cmpl $0xa, %edx
jne 0x1a006
jmp 0x1a06c
cmpq %rcx, %rdx
jae 0x1a08f
movq %rbp, %rdi
movl $0x2, %esi
movq %r12, %rdx
xorl %ecx, %ecx
movl $0x1, %r8d
callq 0x1a18f
movq (%rbx), %rcx
movq (%r12), %rdx
testl %eax, %eax
jns 0x1a067
movl $0x0, 0x60(%r13)
cmpq %rdx, %rcx
movq 0x10(%rsp), %r12
jne 0x19f4d
jmp 0x1a0aa
movq (%rbx), %rcx
movq 0x18(%rsp), %rbp
movl %ecx, 0x10(%rbp)
testl %ecx, %ecx
js 0x19f56
movq %r12, 0x10(%rsp)
movq 0x8(%rbp), %rax
movq 0x10(%rax), %rbx
movq 0x20(%rsp), %r13
movq 0x8(%r13), %r12
movq %rbx, %rdi
callq 0x7140
xorl %r14d, %r14d
movq %r13, %rdi
xorl %esi, %esi
movq %r12, %rdx
movq %rbx, %rcx
movq %rax, %r8
callq 0x7510
movq 0x8(%rbp), %rax
movq 0x40(%rax), %rbx
movq 0x8(%r15), %r12
movq %rbx, %rdi
callq 0x7140
movq %r15, %rdi
xorl %esi, %esi
movq %r12, %rdx
movq %rbx, %rcx
movq %rax, %r8
callq 0x7510
movl $0x80045, %ebx          # imm = 0x80045
movq (%r15), %r12
movsbl (%r12,%r14), %edi
callq 0x7480
cmpb $0x1, 0x14(%rbp)
jne 0x1a13d
movsbl %al, %ecx
addl $-0x61, %ecx
cmpl $0x13, %ecx
ja 0x1a14c
btl %ecx, %ebx
jae 0x1a14c
movb %al, (%r12,%r14)
incq %r14
cmpq 0x8(%r15), %r14
jbe 0x1a11a
jmp 0x1a150
movb $0x7e, %al
jmp 0x1a13d
movq 0x8(%rbp), %rax
movb $0x1, %bl
cmpq $0x0, 0x48(%rax)
je 0x19f58
movq 0x58(%rax), %r14
movq 0x10(%rsp), %r12
movq 0x8(%r12), %r15
movq %r14, %rdi
callq 0x7140
movq %r12, %rdi
xorl %esi, %esi
movq %r15, %rdx
movq %r14, %rcx
movq %rax, %r8
callq 0x7510
jmp 0x19f58