// File: BenLangmead[P]bowtie/./aligner.h
// Function: PairedBWAlignerV2<EbwtRangeSource>::setQuery(PatternSourcePerThread*)
virtual void setQuery(PatternSourcePerThread* patsrc) {
		Aligner::setQuery(patsrc); // set fields & random seed
		assert(!patsrc->bufb().empty());
		// Give all of the drivers pointers to the relevant read info
		patsrc_ = patsrc;
		pool_->reset(&patsrc->bufa().name, (uint32_t)patsrc->rdid());
		if(patsrc->bufa().length() < 4 || patsrc->bufb().length() < 4) {
			if(!quiet_) {
				cerr << "Warning: Skipping pair " << patsrc->bufa().name
				     << " because a mate is less than 4 characters long" << endl;
			}
			this->done = true;
			sinkPt_->finishRead(*patsrc_, true, true);
			return;
		}
		driver_->setQuery(patsrc, NULL);
		qlen1_ = patsrc_->bufa().length();
		qlen2_ = patsrc_->bufb().length();
		if(btCnt_ != NULL) (*btCnt_) = maxBts_;
		mixedAttempts_ = 0;
		// Neither orientation is done
		this->done = false;
		// No ranges are being chased yet
		chase_ = false;
		donePe_ = doneSe1_ = doneSe2_ = false;
		pairs_fw_.clear();
		pairs_rc_.clear();
	}

// Assembly:
pushq %rbp
movq %rsp, %rbp
subq $0x30, %rsp
movq %rdi, -0x8(%rbp)
movq %rsi, -0x10(%rbp)
movq -0x8(%rbp), %rdi
movq %rdi, -0x28(%rbp)
movq -0x10(%rbp), %rsi
callq 0x4be20
movq -0x28(%rbp), %rax
movq -0x10(%rbp), %rcx
movq %rcx, 0x58(%rax)
movq 0xd8(%rax), %rax
movq %rax, -0x20(%rbp)
movq -0x10(%rbp), %rdi
callq 0x37f00
addq $0x150, %rax            # imm = 0x150
movq %rax, -0x18(%rbp)
movq -0x10(%rbp), %rdi
callq 0x499a0
movq -0x20(%rbp), %rdi
movq -0x18(%rbp), %rsi
movl %eax, %edx
callq 0x4f930
movq -0x10(%rbp), %rdi
callq 0x37f00
movq %rax, %rdi
callq 0x499c0
cmpq $0x4, %rax
jb 0x63a25
movq -0x10(%rbp), %rdi
callq 0x38890
movq %rax, %rdi
callq 0x499c0
cmpq $0x4, %rax
jae 0x63aa8
movq -0x28(%rbp), %rax
testb $0x1, 0xe1(%rax)
jne 0x63a83
movq 0x445b7(%rip), %rdi     # 0xa7ff0
leaq 0x29657(%rip), %rsi     # 0x8d097
callq 0xa5d0
movq %rax, -0x30(%rbp)
movq -0x10(%rbp), %rdi
callq 0x37f00
movq -0x30(%rbp), %rdi
movq %rax, %rsi
addq $0x150, %rsi            # imm = 0x150
callq 0x2c0d0
movq %rax, %rdi
leaq 0x29640(%rip), %rsi     # 0x8d0af
callq 0xa5d0
movq %rax, %rdi
movq 0x444ea(%rip), %rsi     # 0xa7f68
callq 0xa640
movq -0x28(%rbp), %rax
movb $0x1, 0x8(%rax)
movq 0x80(%rax), %rdi
movq 0x58(%rax), %rsi
movq (%rdi), %rax
movl $0x1, %ecx
movl %ecx, %edx
callq *0x10(%rax)
jmp 0x63b56
movq -0x28(%rbp), %rax
movq 0xd0(%rax), %rdi
movq -0x10(%rbp), %rsi
movq (%rdi), %rax
xorl %ecx, %ecx
movl %ecx, %edx
callq *0x10(%rax)
movq -0x28(%rbp), %rax
movq 0x58(%rax), %rdi
callq 0x37f00
movq %rax, %rdi
callq 0x499c0
movq %rax, %rcx
movq -0x28(%rbp), %rax
movl %ecx, 0x60(%rax)
movq 0x58(%rax), %rdi
callq 0x38890
movq %rax, %rdi
callq 0x499c0
movq %rax, %rcx
movq -0x28(%rbp), %rax
movl %ecx, 0x64(%rax)
cmpq $0x0, 0xe8(%rax)
je 0x63b18
movq -0x28(%rbp), %rax
movl 0xe4(%rax), %ecx
movq 0xe8(%rax), %rax
movl %ecx, (%rax)
movq -0x28(%rbp), %rdi
movl $0x0, 0xbc(%rdi)
movb $0x0, 0x8(%rdi)
movb $0x0, 0x68(%rdi)
movb $0x0, 0x6b(%rdi)
movb $0x0, 0x6a(%rdi)
movb $0x0, 0x69(%rdi)
addq $0xf0, %rdi
callq 0x631a0
movq -0x28(%rbp), %rdi
addq $0x120, %rdi            # imm = 0x120
callq 0x631a0
addq $0x30, %rsp
popq %rbp
retq
nopl (%rax)