// File: /workspace/github_cpp_makefile_star2_O1/BenLangmead[P]bowtie/./hit.h
// Function: HitSink::HitSink(OutFileBuf&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, bool, bool, EList<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, 128>*, unsigned long, unsigned long, bool)
explicit HitSink(
		OutFileBuf& out,
		const std::string& dumpAl,
		const std::string& dumpUnal,
		const std::string& dumpMax,
		bool onePairFile,
		bool sampleMax,
		EList<string>* refnames,
		size_t nthreads,
		size_t perThreadBufSize,
		bool reorder) :
		out_(out),
		_refnames(refnames),
		mutex_(),
		dumpAlBase_(dumpAl),
		dumpUnalBase_(dumpUnal),
		dumpMaxBase_(dumpMax),
		onePairFile_(onePairFile),
		sampleMax_(sampleMax),
		quiet_(false),
		nthreads_((nthreads > 0) ? nthreads : 1),
		ptBufs_(),
		ptCounts_(nthreads_),
		perThreadBufSize_(perThreadBufSize),
		ptNumAligned_(NULL),
		reorder_(reorder),
		next_batch_to_flush_(0)
	{
		size_t nelt = 5 * nthreads_;
		ptNumAligned_ = new uint64_t[nelt];
		std::memset(reinterpret_cast<void*>(const_cast<uint64_t*>(ptNumAligned_)), 0, sizeof(uint64_t) * nelt);
		ptNumReported_ = ptNumAligned_ + nthreads_;
		ptNumReportedPaired_ = ptNumReported_ + nthreads_;
		ptNumUnaligned_ = ptNumReportedPaired_ + nthreads_;
		ptNumMaxed_ = ptNumUnaligned_ + nthreads_;
		ptBufs_.resize(nthreads_);
		ptCounts_.resize(nthreads_);
		ptCounts_.fillZero();
		initDumps();

		if (reorder_) {
			reorderInfo_.resize(nthreads_);
			for (size_t i = 0; i < nthreads_; i++) {
				reorderInfo_[i].batchId = 0;
				reorderInfo_[i].waiting = false;
				reorderInfo_[i].flushed = true;
			}
		}
	}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x38, %rsp
movl %r9d, %r15d
movq %r8, %r12
movq %rcx, %r14
movq %rdx, %rbp
movq %rdi, %rbx
movb 0x90(%rsp), %al
movq 0x88(%rsp), %rcx
movq 0x80(%rsp), %rdx
movq 0x78(%rsp), %rdi
leaq 0x496b2(%rip), %r8      # 0x69900
movq %r8, (%rbx)
movq %rsi, 0x8(%rbx)
movq %rdi, 0x10(%rbx)
xorl %esi, %esi
cmpq $0x1, %rdx
adcq %rsi, %rdx
movb $0x0, 0x18(%rbx)
movq %rdx, 0x20(%rbx)
leaq 0x28(%rbx), %rdi
movq %rdi, 0x18(%rsp)
movabsq $-0x100000000, %rdi     # imm = 0xFFFFFFFF00000000
movq %rdi, 0x28(%rbx)
movq %rsi, 0x30(%rbx)
movl $0x80, %r13d
movq %r13, 0x38(%rbx)
movq %rsi, 0x40(%rbx)
movq %rdi, 0x48(%rbx)
movq %rsi, 0x50(%rbx)
movq %rdx, 0x58(%rbx)
movq %rsi, 0x60(%rbx)
movq %rcx, 0x68(%rbx)
movq %rsi, 0x70(%rbx)
movb %al, 0x78(%rbx)
movq %rdi, 0x80(%rbx)
movq %rsi, 0x88(%rbx)
movq %r13, 0x90(%rbx)
leaq 0xc8(%rbx), %rdi
xorps %xmm0, %xmm0
movups %xmm0, 0xb8(%rbx)
movups %xmm0, 0xa8(%rbx)
movups %xmm0, 0x98(%rbx)
movq %rdi, 0x30(%rsp)
callq 0x205d4
leaq 0x108(%rbx), %rdi
leaq 0x118(%rbx), %rax
movq %rax, 0x10(%rsp)
movq %rax, 0x108(%rbx)
movq (%rbp), %rsi
movq 0x8(%rbp), %rdx
addq %rsi, %rdx
movq %rdi, 0x28(%rsp)
callq 0x20aae
leaq 0x128(%rbx), %rbp
leaq 0x138(%rbx), %rax
movq %rax, 0x8(%rsp)
movq %rax, 0x128(%rbx)
movq (%r14), %rsi
movq 0x8(%r14), %rdx
addq %rsi, %rdx
movq %rbp, %rdi
callq 0x20aae
movq %rbp, 0x20(%rsp)
leaq 0x148(%rbx), %r14
leaq 0x158(%rbx), %rax
movq %rax, (%rsp)
movq %rax, 0x148(%rbx)
movq (%r12), %rsi
movq 0x8(%r12), %rdx
addq %rsi, %rdx
movq %r14, %rdi
callq 0x20aae
movb 0x70(%rsp), %al
movb %r15b, 0x168(%rbx)
movb %al, 0x169(%rbx)
movq $0x0, 0x1c8(%rbx)
movb $0x0, 0x1f0(%rbx)
movl $0x0, 0x1b8(%rbx)
movw $0x0, 0x1bc(%rbx)
movq 0x20(%rbx), %r15
leaq (%r15,%r15,4), %rax
shrq $0x3d, %rax
leaq (,%r15,8), %rcx
leaq (%rcx,%rcx,4), %r12
xorl %edi, %edi
negq %rax
sbbq %rdi, %rdi
orq %r12, %rdi
callq 0x9030
movq %rax, %rbp
movq %rax, 0x1c8(%rbx)
movq %rax, %rdi
xorl %esi, %esi
movq %r12, %rdx
callq 0x9250
leaq (,%r15,8), %rax
addq %rbp, %rax
movq %rax, 0x1d0(%rbx)
leaq (%rax,%r15,8), %rax
movq %rax, 0x1d8(%rbx)
leaq (%rax,%r15,8), %rax
movq %rax, 0x1e0(%rbx)
leaq (%rax,%r15,8), %rax
movq %rax, 0x1e8(%rbx)
movq 0x18(%rsp), %rdi
movq %r15, %rsi
callq 0x20648
leaq 0x48(%rbx), %rdi
movq 0x20(%rbx), %rsi
callq 0x206ae
movq 0x50(%rbx), %rdi
movq 0x60(%rbx), %rdx
shlq $0x3, %rdx
xorl %esi, %esi
callq 0x9250
xorps %xmm0, %xmm0
movups %xmm0, 0x170(%rbx)
movups %xmm0, 0x180(%rbx)
movups %xmm0, 0x190(%rbx)
movups %xmm0, 0x1a0(%rbx)
movq $0x0, 0x1b0(%rbx)
cmpq $0x0, 0x110(%rbx)
setne 0x1be(%rbx)
cmpq $0x0, 0x130(%rbx)
setne 0x1bf(%rbx)
cmpq $0x0, 0x150(%rbx)
setne 0x1c0(%rbx)
cmpb $0x1, 0x78(%rbx)
jne 0x204f9
addq %rbx, %r13
movq 0x20(%rbx), %rsi
movq %r13, %rdi
callq 0x2072e
cmpq $0x0, 0x20(%rbx)
je 0x204f9
xorl %eax, %eax
xorl %ecx, %ecx
movq 0x88(%rbx), %rdx
movq $0x0, (%rdx,%rax)
movq 0x88(%rbx), %rdx
movb $0x0, 0x9(%rdx,%rax)
movq 0x88(%rbx), %rdx
movb $0x1, 0x8(%rdx,%rax)
incq %rcx
addq $0x10, %rax
cmpq 0x20(%rbx), %rcx
jb 0x204c5
addq $0x38, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %r13
jmp 0x20537
movq %rax, %r13
jmp 0x20556
movq %rax, %r13
jmp 0x20575
movq %rax, %r13
jmp 0x2057f
movq %rax, %r13
movq (%r14), %rdi
cmpq (%rsp), %rdi
je 0x20537
movq (%rsp), %rax
movq (%rax), %rsi
incq %rsi
callq 0x94c0
movq 0x20(%rsp), %rax
movq (%rax), %rdi
cmpq 0x8(%rsp), %rdi
je 0x20556
movq 0x8(%rsp), %rax
movq (%rax), %rsi
incq %rsi
callq 0x94c0
movq 0x28(%rsp), %rax
movq (%rax), %rdi
cmpq 0x10(%rsp), %rdi
je 0x20575
movq 0x10(%rsp), %rax
movq (%rax), %rsi
incq %rsi
callq 0x94c0
movq 0x30(%rsp), %rdi
callq 0x207ae
leaq 0x50(%rbx), %r14
addq $0x88, %rbx
movq (%rbx), %rdi
testq %rdi, %rdi
je 0x205a5
callq 0x95e0
xorps %xmm0, %xmm0
movups %xmm0, (%rbx)
movq $0x0, 0x10(%rbx)
movq (%r14), %rdi
testq %rdi, %rdi
je 0x205c1
callq 0x95e0
xorps %xmm0, %xmm0
movups %xmm0, (%r14)
movq $0x0, 0x10(%r14)
movq 0x18(%rsp), %rdi
callq 0x20cfe
movq %r13, %rdi
callq 0x9930
nop