// File: tedsharpe[P]ORFCall/ORFCall.cc
// Function: (anonymous namespace)::ORFCaller::processFastqs(char**, char**)
void ORFCaller::processFastqs( char** beg, char** end )
{
    std::vector<Sequence> seqs;
    std::vector<Quals> quals;
    size_t fileId = 0;
    while ( beg != end )
    {
        char const* fileName = *beg++;
        std::cerr << "Reading " << fileName << "..." << std::endl;
        FastqReader fqr(fileName);
        size_t readId = 0;
        while ( fqr.getChunk(seqs,quals) )
        {
            auto qItr = quals.begin();
            for ( Sequence const& sq : seqs )
            {
                processRead(sq,*qItr,fileName,readId++);
                ++qItr;
            }
        }
        std::cerr << readId << " reads in file " << fileId << ".\n";
        fileId += 1;
    }
}

// Assembly:
subq $0xf8, %rsp
movq %rdi, 0xf0(%rsp)
movq %rsi, 0xe8(%rsp)
movq %rdx, 0xe0(%rsp)
movq 0xf0(%rsp), %rax
movq %rax, 0x40(%rsp)
leaq 0xc8(%rsp), %rdi
callq 0x1c120
leaq 0xb0(%rsp), %rdi
callq 0x1c120
movq $0x0, 0xa8(%rsp)
movq 0xe8(%rsp), %rax
cmpq 0xe0(%rsp), %rax
je 0x61ef
movq 0xe8(%rsp), %rax
movq %rax, %rcx
addq $0x8, %rcx
movq %rcx, 0xe8(%rsp)
movq (%rax), %rax
movq %rax, 0xa0(%rsp)
movq 0x2701f(%rip), %rdi     # 0x2cff0
leaq 0x1baa1(%rip), %rsi     # 0x21a79
callq 0x4290
movq %rax, 0x38(%rsp)
jmp 0x5fe4
movq 0x38(%rsp), %rdi
movq 0xa0(%rsp), %rsi
callq 0x4290
movq %rax, 0x30(%rsp)
jmp 0x5ffd
movq 0x30(%rsp), %rdi
leaq 0x1ba79(%rip), %rsi     # 0x21a82
callq 0x4290
movq %rax, 0x28(%rsp)
jmp 0x6015
movq 0x28(%rsp), %rdi
movq 0x26f87(%rip), %rsi     # 0x2cfa8
callq 0x42b0
jmp 0x6028
movq 0xa0(%rsp), %rsi
leaq 0x78(%rsp), %rdi
callq 0xc9a0
jmp 0x603c
movq $0x0, 0x70(%rsp)
leaq 0x78(%rsp), %rdi
leaq 0xc8(%rsp), %rsi
leaq 0xb0(%rsp), %rdx
movl $0x186a0, %ecx          # imm = 0x186A0
callq 0xca30
movb %al, 0x27(%rsp)
jmp 0x606a
movb 0x27(%rsp), %al
testb $0x1, %al
jne 0x6077
jmp 0x6172
leaq 0xb0(%rsp), %rdi
callq 0x1c130
movq %rax, 0x68(%rsp)
leaq 0xc8(%rsp), %rax
movq %rax, 0x60(%rsp)
movq 0x60(%rsp), %rdi
callq 0x1c130
movq %rax, 0x58(%rsp)
movq 0x60(%rsp), %rdi
callq 0x1c160
movq %rax, 0x50(%rsp)
leaq 0x58(%rsp), %rdi
leaq 0x50(%rsp), %rsi
callq 0x1c190
testb $0x1, %al
jne 0x60cc
jmp 0x616d
leaq 0x58(%rsp), %rdi
callq 0x1c1d0
movq %rax, 0x48(%rsp)
movq 0x48(%rsp), %rax
movq %rax, 0x18(%rsp)
leaq 0x68(%rsp), %rdi
callq 0x1c1d0
movq 0x40(%rsp), %rdi
movq 0x18(%rsp), %rsi
movq %rax, %rdx
movq 0xa0(%rsp), %rcx
movq 0x70(%rsp), %r8
movq %r8, %rax
incq %rax
movq %rax, 0x70(%rsp)
callq 0xd480
jmp 0x611b
leaq 0x68(%rsp), %rdi
callq 0x1c1e0
leaq 0x58(%rsp), %rdi
callq 0x1c1e0
jmp 0x60b4
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x98(%rsp)
movl %eax, 0x94(%rsp)
jmp 0x6211
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x98(%rsp)
movl %eax, 0x94(%rsp)
leaq 0x78(%rsp), %rdi
callq 0xd520
jmp 0x6211
jmp 0x6045
movq 0x70(%rsp), %rsi
movq 0x26e72(%rip), %rdi     # 0x2cff0
callq 0x4070
movq %rax, 0x10(%rsp)
jmp 0x618a
movq 0x10(%rsp), %rdi
leaq 0x1b8f0(%rip), %rsi     # 0x21a86
callq 0x4290
movq %rax, 0x8(%rsp)
jmp 0x61a2
movq 0x8(%rsp), %rdi
movq 0xa8(%rsp), %rsi
callq 0x4070
movq %rax, (%rsp)
jmp 0x61ba
movq (%rsp), %rdi
leaq 0x1b82f(%rip), %rsi     # 0x219f4
callq 0x4290
jmp 0x61cc
movq 0xa8(%rsp), %rax
addq $0x1, %rax
movq %rax, 0xa8(%rsp)
leaq 0x78(%rsp), %rdi
callq 0xd520
jmp 0x5f92
leaq 0xb0(%rsp), %rdi
callq 0x1c200
leaq 0xc8(%rsp), %rdi
callq 0x1c200
addq $0xf8, %rsp
retq
leaq 0xb0(%rsp), %rdi
callq 0x1c200
leaq 0xc8(%rsp), %rdi
callq 0x1c200
movq 0x98(%rsp), %rdi
callq 0x4510
nopl (%rax,%rax)