// File: /workspace/github_cpp_makefile_star2_O1/tedsharpe[P]ORFCall/ORFCall.cc
// Function: (anonymous namespace)::FastqReader::getChunk(std::vector<std::vector<unsigned char, std::allocator<unsigned char>>, std::allocator<std::vector<unsigned char, std::allocator<unsigned char>>>>&, std::vector<std::vector<unsigned char, std::allocator<unsigned char>>, std::allocator<std::vector<unsigned char, std::allocator<unsigned char>>>>&, unsigned int)
bool FastqReader::getChunk( std::vector<Sequence>& seqs,
                            std::vector<Quals>& quals,
                            unsigned chunkSize )
{
    if ( mIS.eof() )
        return false;

    seqs.clear(); seqs.reserve(chunkSize);
    quals.clear(); quals.reserve(chunkSize);

    std::string seqheader;
    std::string sSeq;
    std::string qualheader;
    std::string sQual;
    Sequence sq;
    Quals qs;
    while ( ++mLineNo && std::getline(mIS,seqheader) )
    {
        if ( seqheader.empty() )
            FatalErr("Read empty header at line " << mLineNo);
        if ( ++mLineNo && !std::getline(mIS,sSeq) )
            FatalErr("Early EOF at line " << mLineNo);
        if ( !sSeq.empty() && sSeq.back() == '\r' )
            sSeq.resize(sSeq.size()-1);
        if ( sSeq.empty() )
            FatalErr("Empty sequence at line " << mLineNo);
        if ( ++mLineNo && !std::getline(mIS,qualheader) )
            FatalErr("Early EOF at line " << mLineNo);
        if ( qualheader.empty() || qualheader[0] != '+' )
            FatalErr("Quals header doesn't begin with '+' at line " << mLineNo);
        if ( ++mLineNo && !std::getline(mIS,sQual) )
            FatalErr("Early EOF at line " << mLineNo);
        if ( !sQual.empty() && sQual.back() == '\r' )
            sQual.resize(sQual.size()-1);
        if ( sSeq.size() != sQual.size() )
            FatalErr("Calls and quals of unequal length at line " << mLineNo);

        sq.clear(); sq.reserve(sSeq.size());
        qs.clear(); qs.reserve(sSeq.size());
        auto qItr(sQual.begin());
        for ( char chr : sSeq )
        {
            switch (chr)
            {
            case 'a': case 'A': sq.push_back(0); break;
            case 'c': case 'C': sq.push_back(1); break;
            case 'g': case 'G': sq.push_back(2); break;
            case 't': case 'T':
            case 'u': case 'U': sq.push_back(3); break;
            default: sq.push_back(4); break;
            }
            qs.push_back(*qItr-FASTQ_QUAL_OFFSET);
            ++qItr;
        }
        seqs.push_back(sq);
        quals.push_back(qs);
        if ( seqs.size() == chunkSize )
            return true;
    }
    if ( !mIS.eof() )
        FatalErr("Failed to read to EOF (read to line " << mLineNo << ").");
    return !seqs.empty();
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0xd8, %rsp
movq 0x8(%rdi), %rax
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
testb $0x2, 0x20(%rax,%rcx)
jne 0x7cfd
movq %rdx, %r12
movq %rsi, %r14
movq %rdi, %rbx
movq %rsi, %rdi
callq 0xb37e
movl $0x186a0, %esi          # imm = 0x186A0
movq %r14, %rdi
callq 0xb3c0
movq %r12, %rdi
callq 0xb37e
movl $0x186a0, %esi          # imm = 0x186A0
movq %r12, %rdi
callq 0xb3c0
leaq 0xb8(%rsp), %rcx
movq %rcx, -0x10(%rcx)
xorl %eax, %eax
movq %rax, -0x8(%rcx)
movb %al, (%rcx)
leaq 0x40(%rsp), %rcx
movq %rcx, -0x10(%rcx)
movq %rax, -0x8(%rcx)
movb %al, (%rcx)
leaq 0x80(%rsp), %rcx
movq %rcx, -0x10(%rcx)
movq %rax, -0x8(%rcx)
movb %al, (%rcx)
leaq 0x60(%rsp), %rcx
movq %rcx, -0x10(%rcx)
movq %rax, -0x8(%rcx)
movb %al, (%rcx)
leaq 0x10(%rsp), %rcx
movq %rax, 0x10(%rcx)
vxorps %xmm0, %xmm0, %xmm0
vmovaps %xmm0, (%rcx)
leaq 0x90(%rsp), %rcx
movq %rax, 0x10(%rcx)
vmovaps %xmm0, (%rcx)
leaq 0xf(%rsp), %rbp
movq %r14, 0xc8(%rsp)
movq %r12, 0xd0(%rsp)
incl 0x10(%rbx)
je 0x7d04
movq 0x8(%rbx), %r15
movq (%r15), %rax
movq -0x18(%rax), %rdi
addq %r15, %rdi
movl $0xa, %esi
callq 0x31d0
movsbl %al, %edx
movq %r15, %rdi
leaq 0xa8(%rsp), %rsi
callq 0x33d0
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
testb $0x5, 0x20(%rax,%rcx)
jne 0x7d04
cmpq $0x0, 0xb0(%rsp)
je 0x7e22
incl 0x10(%rbx)
je 0x7a00
movq 0x8(%rbx), %r15
movq (%r15), %rax
movq -0x18(%rax), %rdi
addq %r15, %rdi
movl $0xa, %esi
callq 0x31d0
movsbl %al, %edx
movq %r15, %rdi
leaq 0x30(%rsp), %rsi
callq 0x33d0
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
testb $0x5, 0x20(%rax,%rcx)
jne 0x7e8a
movq 0x38(%rsp), %rsi
testq %rsi, %rsi
je 0x7a25
movq 0x30(%rsp), %rax
cmpb $0xd, -0x1(%rax,%rsi)
jne 0x7a25
decq %rsi
leaq 0x30(%rsp), %rdi
xorl %edx, %edx
callq 0x3090
cmpq $0x0, 0x38(%rsp)
je 0x7e56
incl 0x10(%rbx)
je 0x7a70
movq 0x8(%rbx), %r15
movq (%r15), %rax
movq -0x18(%rax), %rdi
addq %r15, %rdi
movl $0xa, %esi
callq 0x31d0
movsbl %al, %edx
movq %r15, %rdi
leaq 0x70(%rsp), %rsi
callq 0x33d0
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
testb $0x5, 0x20(%rax,%rcx)
jne 0x7ebb
cmpq $0x0, 0x78(%rsp)
je 0x7dba
movq 0x70(%rsp), %rax
cmpb $0x2b, (%rax)
jne 0x7dba
incl 0x10(%rbx)
je 0x7ac9
movq 0x8(%rbx), %r15
movq (%r15), %rax
movq -0x18(%rax), %rdi
addq %r15, %rdi
movl $0xa, %esi
callq 0x31d0
movsbl %al, %edx
movq %r15, %rdi
leaq 0x50(%rsp), %rsi
callq 0x33d0
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
testb $0x5, 0x20(%rax,%rcx)
jne 0x7eec
movq 0x58(%rsp), %rsi
testq %rsi, %rsi
je 0x7aee
movq 0x50(%rsp), %rax
cmpb $0xd, -0x1(%rax,%rsi)
jne 0x7aee
decq %rsi
leaq 0x50(%rsp), %rdi
xorl %edx, %edx
callq 0x3090
movq 0x38(%rsp), %rsi
cmpq 0x58(%rsp), %rsi
jne 0x7dee
movq 0x10(%rsp), %rax
cmpq %rax, 0x18(%rsp)
je 0x7b0f
movq %rax, 0x18(%rsp)
leaq 0x10(%rsp), %rdi
callq 0xa10e
movq 0x90(%rsp), %rax
cmpq %rax, 0x98(%rsp)
je 0x7b33
movq %rax, 0x98(%rsp)
movq 0x38(%rsp), %rsi
leaq 0x90(%rsp), %rdi
callq 0xa10e
movq 0x38(%rsp), %r15
testq %r15, %r15
je 0x7cb9
movq 0x30(%rsp), %r14
movq 0x50(%rsp), %r12
xorl %r13d, %r13d
movzbl (%r14,%r13), %eax
cmpl $0x60, %eax
jg 0x7b83
cmpl $0x53, %eax
jg 0x7bb5
cmpl $0x41, %eax
je 0x7bd8
cmpl $0x43, %eax
je 0x7bf2
cmpl $0x47, %eax
je 0x7b9b
jmp 0x7c1b
cmpl $0x73, %eax
jg 0x7bba
cmpl $0x61, %eax
je 0x7bd8
cmpl $0x63, %eax
je 0x7bf2
cmpl $0x67, %eax
jne 0x7c1b
movb $0x2, 0xf(%rsp)
movq 0x18(%rsp), %rsi
cmpq 0x20(%rsp), %rsi
je 0x7c89
movb $0x2, (%rsi)
jmp 0x7c2f
addl $-0x54, %eax
jmp 0x7bbd
addl $-0x74, %eax
cmpl $0x2, %eax
jae 0x7c1b
movb $0x3, 0xf(%rsp)
movq 0x18(%rsp), %rsi
cmpq 0x20(%rsp), %rsi
je 0x7c0c
movb $0x3, (%rsi)
jmp 0x7c2f
movb $0x0, 0xf(%rsp)
movq 0x18(%rsp), %rsi
cmpq 0x20(%rsp), %rsi
je 0x7c7a
movb $0x0, (%rsi)
jmp 0x7c2f
movb $0x1, 0xf(%rsp)
movq 0x18(%rsp), %rsi
cmpq 0x20(%rsp), %rsi
je 0x7c98
movb $0x1, (%rsi)
jmp 0x7c2f
leaq 0x10(%rsp), %rdi
movq %rbp, %rdx
callq 0xa226
jmp 0x7c34
movb $0x4, 0xf(%rsp)
movq 0x18(%rsp), %rsi
cmpq 0x20(%rsp), %rsi
je 0x7ca7
movb $0x4, (%rsi)
incq 0x18(%rsp)
movb (%r12,%r13), %al
addb $-0x21, %al
movb %al, 0xf(%rsp)
movq 0x98(%rsp), %rsi
cmpq 0xa0(%rsp), %rsi
je 0x7c5c
movb %al, (%rsi)
incq 0x98(%rsp)
jmp 0x7c6c
leaq 0x90(%rsp), %rdi
movq %rbp, %rdx
callq 0xa226
incq %r13
cmpq %r13, %r15
jne 0x7b60
jmp 0x7cb9
leaq 0x10(%rsp), %rdi
movq %rbp, %rdx
callq 0xa226
jmp 0x7c34
leaq 0x10(%rsp), %rdi
movq %rbp, %rdx
callq 0xa226
jmp 0x7c34
leaq 0x10(%rsp), %rdi
movq %rbp, %rdx
callq 0xa226
jmp 0x7c34
leaq 0x10(%rsp), %rdi
movq %rbp, %rdx
callq 0xa226
jmp 0x7c34
movq 0xc8(%rsp), %r14
movq %r14, %rdi
leaq 0x10(%rsp), %rsi
callq 0xb494
movq 0xd0(%rsp), %r12
movq %r12, %rdi
leaq 0x90(%rsp), %rsi
callq 0xb494
movq 0x8(%r14), %rax
subq (%r14), %rax
cmpq $0x249f00, %rax         # imm = 0x249F00
jne 0x796c
movb $0x1, %bl
jmp 0x7d2c
xorl %ebx, %ebx
jmp 0x7da6
movq 0x8(%rbx), %rax
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
testb $0x2, 0x20(%rax,%rcx)
je 0x7f25
movq 0xc8(%rsp), %rcx
movq (%rcx), %rax
cmpq 0x8(%rcx), %rax
setne %bl
leaq 0xb8(%rsp), %r14
leaq 0x40(%rsp), %r15
leaq 0x80(%rsp), %r12
leaq 0x60(%rsp), %r13
movq 0x90(%rsp), %rdi
testq %rdi, %rdi
je 0x7d58
callq 0x31c0
movq 0x10(%rsp), %rdi
testq %rdi, %rdi
je 0x7d67
callq 0x31c0
movq 0x50(%rsp), %rdi
cmpq %r13, %rdi
je 0x7d76
callq 0x31c0
movq 0x70(%rsp), %rdi
cmpq %r12, %rdi
je 0x7d85
callq 0x31c0
movq 0x30(%rsp), %rdi
cmpq %r15, %rdi
je 0x7d94
callq 0x31c0
movq 0xa8(%rsp), %rdi
cmpq %r14, %rdi
je 0x7da6
callq 0x31c0
movl %ebx, %eax
addq $0xd8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x922f(%rip), %rdi      # 0x10ff0
leaq 0x4f4b(%rip), %rsi      # 0xcd13
movl $0x2c, %edx
callq 0x3210
movl 0x10(%rbx), %esi
movq 0x9214(%rip), %rdi      # 0x10ff0
callq 0x3130
movq %rax, %rdi
callq 0x30f0
jmp 0x7f1b
movq 0x91fb(%rip), %rdi      # 0x10ff0
leaq 0x4f44(%rip), %rsi      # 0xcd40
movl $0x2a, %edx
callq 0x3210
movl 0x10(%rbx), %esi
movq 0x91e0(%rip), %rdi      # 0x10ff0
callq 0x3130
movq %rax, %rdi
callq 0x30f0
jmp 0x7f1b
movq 0x91c7(%rip), %rdi      # 0x10ff0
leaq 0x4e9d(%rip), %rsi      # 0xcccd
movl $0x1a, %edx
callq 0x3210
movl 0x10(%rbx), %esi
movq 0x91ac(%rip), %rdi      # 0x10ff0
callq 0x3130
movq %rax, %rdi
callq 0x30f0
jmp 0x7f1b
movq 0x9193(%rip), %rdi      # 0x10ff0
leaq 0x4e97(%rip), %rsi      # 0xccfb
movl $0x17, %edx
callq 0x3210
movl 0x10(%rbx), %esi
movq 0x9178(%rip), %rdi      # 0x10ff0
callq 0x3130
movq %rax, %rdi
callq 0x30f0
jmp 0x7f1b
movq 0x915f(%rip), %rdi      # 0x10ff0
leaq 0x4e50(%rip), %rsi      # 0xcce8
movl $0x12, %edx
callq 0x3210
movl 0x10(%rbx), %esi
movq 0x9144(%rip), %rdi      # 0x10ff0
callq 0x3130
movq %rax, %rdi
callq 0x30f0
jmp 0x7f1b
movq 0x912e(%rip), %rdi      # 0x10ff0
leaq 0x4e1f(%rip), %rsi      # 0xcce8
movl $0x12, %edx
callq 0x3210
movl 0x10(%rbx), %esi
movq 0x9113(%rip), %rdi      # 0x10ff0
callq 0x3130
movq %rax, %rdi
callq 0x30f0
jmp 0x7f1b
movq 0x90fd(%rip), %rdi      # 0x10ff0
leaq 0x4dee(%rip), %rsi      # 0xcce8
movl $0x12, %edx
callq 0x3210
movl 0x10(%rbx), %esi
movq 0x90e2(%rip), %rdi      # 0x10ff0
callq 0x3130
movq %rax, %rdi
callq 0x30f0
movl $0x1, %edi
callq 0x3220
movq 0x90c4(%rip), %rdi      # 0x10ff0
leaq 0x4e38(%rip), %rsi      # 0xcd6b
movl $0x24, %edx
callq 0x3210
movl 0x10(%rbx), %esi
movq 0x90a9(%rip), %rdi      # 0x10ff0
callq 0x3130
movq %rax, %rbx
leaq 0x4e3a(%rip), %rsi      # 0xcd90
movl $0x2, %edx
movq %rax, %rdi
callq 0x3210
movq %rbx, %rdi
callq 0x30f0
jmp 0x7f1b
jmp 0x7f7d
jmp 0x7f7d
jmp 0x7f7d
jmp 0x7f7d
jmp 0x7f7d
jmp 0x7f7d
jmp 0x7f7d
jmp 0x7f7d
movq %rax, %rbx
leaq 0xb8(%rsp), %r14
leaq 0x40(%rsp), %r15
leaq 0x80(%rsp), %r12
leaq 0x60(%rsp), %r13
movq 0x90(%rsp), %rdi
testq %rdi, %rdi
je 0x7fac
callq 0x31c0
movq 0x10(%rsp), %rdi
testq %rdi, %rdi
je 0x7fbb
callq 0x31c0
movq 0x50(%rsp), %rdi
cmpq %r13, %rdi
je 0x7fca
callq 0x31c0
movq 0x70(%rsp), %rdi
cmpq %r12, %rdi
je 0x7fd9
callq 0x31c0
movq 0x30(%rsp), %rdi
cmpq %r15, %rdi
je 0x7fe8
callq 0x31c0
movq 0xa8(%rsp), %rdi
cmpq %r14, %rdi
je 0x7ffa
callq 0x31c0
movq %rbx, %rdi
callq 0x33a0