// File: BenLangmead[P]bowtie/./ref_aligner.h
// Function: RefAligner::find(unsigned int, unsigned long, BitPairReference const*, SDnaStringExpandable<25, 2> const&, SStringExpandable<char, 25, 2, 0> const&, unsigned int, unsigned int, EList<Range, 128>&, EList<unsigned int, 128>&, std::set<std::pair<unsigned long, unsigned long>, std::less<std::pair<unsigned long, unsigned long>>, std::allocator<std::pair<unsigned long, unsigned long>>>*, unsigned int, bool)
virtual void find(uint32_t numToFind,
	                  const size_t tidx,
	                  const BitPairReference *refs,
	                  const BTDnaString& qry,
	                  const BTString& quals,
	                  TIndexOffU begin,
	                  TIndexOffU end,
	                  TRangeVec& ranges,
	                  EList<TIndexOffU>& results,
	                  TSetPairs* pairs = NULL,
	                  TIndexOffU aoff = OFF_MASK,
	                  bool seedOnLeft = false)
		{
			assert_gt(numToFind, 0);
			assert_gt(end, begin);
			TIndexOffU spread = end - begin;
			TIndexOffU spreadPlus = spread + 12;
			// Make sure the buffer is large enough to accommodate the spread
			if(spreadPlus > this->refbufSz_) {
				this->newBuf(spreadPlus);
			}
			// Read in the relevant stretch of the reference string
			int offset = refs->getStretch(this->refbuf_, tidx, begin, spread);
			uint8_t *buf = ((uint8_t*)this->refbuf_) + offset;
			// Look for alignments
			ASSERT_ONLY(uint32_t irsz = (uint32_t)ranges.size());
			anchor64Find(numToFind, tidx, buf, qry, quals, begin,
				     end, ranges, results, pairs, aoff, seedOnLeft);
#ifndef NDEBUG
			for(size_t i = irsz; i < results.size(); i++) {
				assert_eq(ranges[i].numMms, ranges[i].mms.size());
				assert_eq(ranges[i].numMms, ranges[i].refcs.size());
			}
#endif
		}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x88, %rsp
movb 0x40(%rbp), %al
movl 0x38(%rbp), %r10d
movq 0x30(%rbp), %r10
movq 0x28(%rbp), %r10
movq 0x20(%rbp), %r10
movl 0x18(%rbp), %r10d
movl 0x10(%rbp), %r10d
movq %rdi, -0x30(%rbp)
movl %esi, -0x34(%rbp)
movq %rdx, -0x40(%rbp)
movq %rcx, -0x48(%rbp)
movq %r8, -0x50(%rbp)
movq %r9, -0x58(%rbp)
andb $0x1, %al
movb %al, -0x59(%rbp)
movq -0x30(%rbp), %rcx
movq %rcx, -0x78(%rbp)
movl 0x18(%rbp), %eax
subl 0x10(%rbp), %eax
movl %eax, -0x60(%rbp)
movl -0x60(%rbp), %eax
addl $0xc, %eax
movl %eax, -0x64(%rbp)
movl -0x64(%rbp), %eax
cmpl 0x20(%rcx), %eax
jbe 0x58679
movq -0x78(%rbp), %rdi
movl -0x64(%rbp), %esi
callq 0x59650
movq -0x78(%rbp), %rax
movq -0x48(%rbp), %rdi
movq 0x18(%rax), %rsi
movq -0x40(%rbp), %rdx
movl 0x10(%rbp), %eax
movl %eax, %ecx
movl -0x60(%rbp), %eax
movl %eax, %r8d
callq 0x597d0
movq -0x78(%rbp), %rdi
movl %eax, -0x68(%rbp)
movq 0x18(%rdi), %rax
movslq -0x68(%rbp), %rcx
addq %rcx, %rax
movq %rax, -0x70(%rbp)
movl -0x34(%rbp), %esi
movq -0x40(%rbp), %rdx
movq -0x70(%rbp), %rcx
movq -0x50(%rbp), %r8
movq -0x58(%rbp), %r9
movl 0x10(%rbp), %r13d
movl 0x18(%rbp), %r12d
movq 0x20(%rbp), %r15
movq 0x28(%rbp), %r14
movq 0x30(%rbp), %rbx
movl 0x38(%rbp), %r11d
movb -0x59(%rbp), %r10b
movq (%rdi), %rax
andb $0x1, %r10b
movl %r13d, (%rsp)
movl %r12d, 0x8(%rsp)
movq %r15, 0x10(%rsp)
movq %r14, 0x18(%rsp)
movq %rbx, 0x20(%rsp)
movl %r11d, 0x28(%rsp)
movzbl %r10b, %r10d
movl %r10d, 0x30(%rsp)
callq *0x18(%rax)
addq $0x88, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq