// File: /workspace/github_cpp_makefile_star2_O1/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, 0x18(%rsp)
movq %rdx, %r14
movq %rsi, 0x20(%rsp)
movq %rdi, %r15
movq 0x8(%rdi), %r13
movq 0x68(%r13), %rbp
cmpl $0x0, 0x60(%r13)
jne 0x1a0c0
jmp 0x1a04f
cmpl $0x40, %r12d
je 0x1a0bc
cmpl $0x3e, %r12d
jne 0x1a04f
jmp 0x1a0bc
movl $0xffffffff, %r12d      # imm = 0xFFFFFFFF
jmp 0x1a0ac
cmpl $0x0, 0x10(%rbp)
je 0x1a063
movl 0x8(%rbp), %eax
movl $0xffffffff, %r12d      # imm = 0xFFFFFFFF
cmpl 0xc(%rbp), %eax
jge 0x1a0ac
movl 0x8(%rbp), %eax
cmpl 0xc(%rbp), %eax
jl 0x1a099
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 0x1a095
movl $0x1, 0x10(%rbp)
testl %eax, %eax
je 0x1a047
movq (%rbp), %rax
movslq 0x8(%rbp), %rcx
leal 0x1(%rcx), %edx
movl %edx, 0x8(%rbp)
movzbl (%rax,%rcx), %r12d
movl %r12d, 0xc(%rsp)
cmpl $-0x1, %r12d
jne 0x1a039
jmp 0x1a336
movl %r12d, 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 0x1a425
testl %eax, %eax
js 0x1a1e3
cmpl $0xa, 0xc(%rsp)
je 0x1a108
leaq 0x18(%r13), %rdx
movq %rbp, %rdi
movl $0x2, %esi
xorl %ecx, %ecx
xorl %r8d, %r8d
callq 0x1a425
cmpq $0x0, 0x40(%r13)
jne 0x1a125
movq $0x100, 0x38(%r13)      # imm = 0x100
movl $0x100, %edi            # imm = 0x100
callq 0x7430
movq %rax, 0x40(%r13)
leaq 0x48(%r13), %r12
leaq 0x30(%r13), %rbx
cmpl $0x0, 0x10(%rbp)
je 0x1a140
movl 0x8(%rbp), %ecx
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
cmpl 0xc(%rbp), %ecx
jge 0x1a188
movl 0x8(%rbp), %eax
cmpl 0xc(%rbp), %eax
jl 0x1a176
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 0x1a172
movl $0x1, 0x10(%rbp)
testl %eax, %eax
je 0x1a1dc
movq (%rbp), %rax
movslq 0x8(%rbp), %rcx
leal 0x1(%rcx), %edx
movl %edx, 0x8(%rbp)
movzbl (%rax,%rcx), %eax
movl %eax, 0xc(%rsp)
cmpl $0x2a, %eax
jg 0x1a19d
cmpl $0xa, %eax
je 0x1a12d
cmpl $-0x1, %eax
jne 0x1a1ac
jmp 0x1a1f2
cmpl $0x2b, %eax
je 0x1a1f2
cmpl $0x3e, %eax
je 0x1a1ee
cmpl $0x40, %eax
je 0x1a1ee
movq 0x30(%r13), %rcx
movq 0x40(%r13), %rdx
leaq 0x1(%rcx), %rsi
movq %rsi, 0x30(%r13)
movb %al, (%rdx,%rcx)
movq %rbp, %rdi
movl $0x2, %esi
movq %rbx, %rdx
xorl %ecx, %ecx
movl $0x1, %r8d
callq 0x1a425
jmp 0x1a12d
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
jmp 0x1a188
movl $0xffffffff, %r12d      # imm = 0xFFFFFFFF
jmp 0x1a336
movl %eax, 0x60(%r13)
movq 0x30(%r13), %rax
incq %rax
cmpq 0x38(%r13), %rax
jb 0x1a244
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, %rsi
shrq $0x10, %rsi
orq %rax, %rsi
incq %rsi
movq %rsi, 0x38(%r13)
movq 0x40(%r13), %rdi
callq 0x7590
movq %rax, 0x40(%r13)
movq 0x30(%r13), %rax
movq 0x40(%r13), %rcx
movb $0x0, (%rcx,%rax)
cmpl $0x2b, 0xc(%rsp)
jne 0x1a32b
movq 0x38(%r13), %rsi
cmpq %rsi, 0x50(%r13)
jae 0x1a27f
movq %rsi, 0x50(%r13)
movq 0x58(%r13), %rdi
callq 0x7590
movq %rax, 0x58(%r13)
jmp 0x1a27f
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
jmp 0x1a2da
cmpl $0x0, 0x10(%rbp)
je 0x1a292
movl 0x8(%rbp), %ecx
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
cmpl 0xc(%rbp), %ecx
jge 0x1a2da
movl 0x8(%rbp), %eax
cmpl 0xc(%rbp), %eax
jl 0x1a2c8
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 0x1a2c4
movl $0x1, 0x10(%rbp)
testl %eax, %eax
je 0x1a278
movq (%rbp), %rax
movslq 0x8(%rbp), %rcx
leal 0x1(%rcx), %edx
movl %edx, 0x8(%rbp)
movzbl (%rax,%rcx), %eax
movl %eax, 0xc(%rsp)
cmpl $-0x1, %eax
je 0x1a330
cmpl $0xa, %eax
jne 0x1a27f
jmp 0x1a2f3
movq (%r12), %rax
cmpq (%rbx), %rax
jae 0x1a30f
movq %rbp, %rdi
movl $0x2, %esi
movq %r12, %rdx
xorl %ecx, %ecx
movl $0x1, %r8d
callq 0x1a425
testl %eax, %eax
jns 0x1a2ea
movl $0x0, 0x60(%r13)
movq 0x30(%r13), %rax
cmpq 0x48(%r13), %rax
movl $0xfffffffe, %r12d      # imm = 0xFFFFFFFE
cmovel %eax, %r12d
jmp 0x1a336
movl (%rbx), %r12d
jmp 0x1a336
movl $0xfffffffe, %r12d      # imm = 0xFFFFFFFE
movl %r12d, 0x10(%r15)
testl %r12d, %r12d
js 0x1a410
movq 0x8(%r15), %rax
movq 0x10(%rax), %rbx
movq 0x20(%rsp), %r13
movq 0x8(%r13), %rax
movq %rax, 0x10(%rsp)
movq %rbx, %rdi
callq 0x7140
xorl %ebp, %ebp
movq %r13, %rdi
xorl %esi, %esi
movq 0x10(%rsp), %rdx
movq %rbx, %rcx
movq %rax, %r8
callq 0x7510
movq 0x8(%r15), %rax
movq 0x40(%rax), %rbx
movq 0x8(%r14), %r13
movq %rbx, %rdi
callq 0x7140
movq %r14, %rdi
xorl %esi, %esi
movq %r13, %rdx
movq %rbx, %rcx
movq %rax, %r8
callq 0x7510
movl $0x80045, %ebx          # imm = 0x80045
movq (%r14), %r13
movsbl (%r13,%rbp), %edi
callq 0x7480
cmpb $0x1, 0x14(%r15)
jne 0x1a3c9
movsbl %al, %ecx
addl $-0x61, %ecx
cmpl $0x13, %ecx
ja 0x1a3d9
btl %ecx, %ebx
jae 0x1a3d9
movb %al, (%r13,%rbp)
incq %rbp
cmpq 0x8(%r14), %rbp
jbe 0x1a3a4
jmp 0x1a3dd
movb $0x7e, %al
jmp 0x1a3c9
movq 0x8(%r15), %rax
cmpq $0x0, 0x48(%rax)
je 0x1a410
movq 0x58(%rax), %rbx
movq 0x18(%rsp), %r15
movq 0x8(%r15), %r14
movq %rbx, %rdi
callq 0x7140
movq %r15, %rdi
xorl %esi, %esi
movq %r14, %rdx
movq %rbx, %rcx
movq %rax, %r8
callq 0x7510
testl %r12d, %r12d
setns %al
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq