// File: /workspace/github_cpp_makefile_star2_O2/ncbi[P]amr/alignment.cpp
// Function: Alignment_sp::SeqChange::setStartStopRef()
void SeqChange::setStartStopRef ()
{
  ASSERT (al);
  ASSERT (start < al->refSeq. size ());
  
  start_ref = al->refStart;
  FOR (size_t, i, start)
    if (al->refSeq [i] != '-')
      start_ref += al->al2ref_len;
      
  stop_ref = start_ref;
  FOR_START (size_t, i, start, start + len)
    if (al->refSeq [i] != '-')
      stop_ref += al->al2ref_len;
}

// Assembly:
pushq %rbx
subq $0x110, %rsp            # imm = 0x110
movq %rdi, %rbx
callq 0xc070
andl $0x0, (%rax)
movq 0x8(%rbx), %rax
testq %rax, %rax
je 0x4032a
movq 0x18(%rbx), %rcx
cmpq 0xa0(%rax), %rcx
jae 0x403fe
movq 0xb8(%rax), %rdx
movq %rdx, 0x68(%rbx)
xorl %esi, %esi
cmpq %rsi, %rcx
je 0x402f4
movq 0x98(%rax), %rdi
cmpb $0x2d, (%rdi,%rsi)
je 0x402ef
addq 0x208(%rax), %rdx
movq %rdx, 0x68(%rbx)
incq %rsi
jmp 0x402d2
movq %rdx, 0x70(%rbx)
movq 0x20(%rbx), %rsi
addq %rcx, %rsi
cmpq %rsi, %rcx
jae 0x40321
movq 0x98(%rax), %rdi
cmpb $0x2d, (%rdi,%rcx)
je 0x4031c
addq 0x208(%rax), %rdx
movq %rdx, 0x70(%rbx)
incq %rcx
jmp 0x402ff
addq $0x110, %rsp            # imm = 0x110
popq %rbx
retq
callq 0xc6d0
testl %eax, %eax
jne 0x404d2
leaq 0x21caa(%rip), %rsi     # 0x61fe8
leaq 0x70(%rsp), %rdi
leaq 0xf(%rsp), %rdx
callq 0xdbbe
leaq 0x50(%rsp), %rdi
movl $0x146, %esi            # imm = 0x146
callq 0xe2d5
leaq 0x90(%rsp), %rdi
leaq 0x70(%rsp), %rsi
leaq 0x50(%rsp), %rdx
callq 0xe26e
leaq 0x1de57(%rip), %rdx     # 0x5e1d1
leaq 0xb0(%rsp), %rdi
leaq 0x90(%rsp), %rsi
callq 0xe24f
leaq 0x221aa(%rip), %rsi     # 0x62540
leaq 0x10(%rsp), %rdi
leaq 0xe(%rsp), %rdx
callq 0xdbbe
leaq 0x1e520(%rip), %rdx     # 0x5e8cc
leaq 0x30(%rsp), %rdi
leaq 0x10(%rsp), %rsi
callq 0xe24f
leaq 0xd0(%rsp), %rdi
leaq 0xb0(%rsp), %rsi
leaq 0x30(%rsp), %rdx
callq 0xe26e
leaq 0x2260f(%rip), %rdx     # 0x629eb
leaq 0xf0(%rsp), %rdi
leaq 0xd0(%rsp), %rsi
callq 0xe24f
leaq 0xf0(%rsp), %rdi
callq 0x101d0
callq 0xc6d0
testl %eax, %eax
jne 0x404d2
leaq 0x21bd6(%rip), %rsi     # 0x61fe8
leaq 0x70(%rsp), %rdi
leaq 0xf(%rsp), %rdx
callq 0xdbbe
leaq 0x50(%rsp), %rdi
movl $0x147, %esi            # imm = 0x147
callq 0xe2d5
leaq 0x90(%rsp), %rdi
leaq 0x70(%rsp), %rsi
leaq 0x50(%rsp), %rdx
callq 0xe26e
leaq 0x1dd83(%rip), %rdx     # 0x5e1d1
leaq 0xb0(%rsp), %rdi
leaq 0x90(%rsp), %rsi
callq 0xe24f
leaq 0x220d6(%rip), %rsi     # 0x62540
leaq 0x10(%rsp), %rdi
leaq 0xe(%rsp), %rdx
callq 0xdbbe
leaq 0x1e44c(%rip), %rdx     # 0x5e8cc
leaq 0x30(%rsp), %rdi
leaq 0x10(%rsp), %rsi
callq 0xe24f
leaq 0xd0(%rsp), %rdi
leaq 0xb0(%rsp), %rsi
leaq 0x30(%rsp), %rdx
callq 0xe26e
leaq 0x220c0(%rip), %rdx     # 0x62570
leaq 0xf0(%rsp), %rdi
leaq 0xd0(%rsp), %rsi
callq 0xe24f
leaq 0xf0(%rsp), %rdi
callq 0x101d0
pushq $0x1
popq %rdi
callq 0xc6f0
jmp 0x404de
jmp 0x404f0
movq %rax, %rbx
leaq 0xf0(%rsp), %rdi
callq 0xcbe8
jmp 0x404f3
movq %rax, %rbx
leaq 0xd0(%rsp), %rdi
callq 0xcbe8
jmp 0x40507
jmp 0x40504
movq %rax, %rbx
leaq 0x30(%rsp), %rdi
callq 0xcbe8
jmp 0x40518
jmp 0x40515
movq %rax, %rbx
leaq 0x10(%rsp), %rdi
callq 0xcbe8
jmp 0x40529
jmp 0x40526
movq %rax, %rbx
leaq 0xb0(%rsp), %rdi
callq 0xcbe8
jmp 0x4053d
jmp 0x4053a
movq %rax, %rbx
leaq 0x90(%rsp), %rdi
callq 0xcbe8
jmp 0x40551
jmp 0x4054e
movq %rax, %rbx
leaq 0x50(%rsp), %rdi
callq 0xcbe8
jmp 0x40562
jmp 0x4055f
movq %rax, %rbx
leaq 0x70(%rsp), %rdi
callq 0xcbe8
jmp 0x40573
jmp 0x40570
movq %rax, %rbx
movq %rbx, %rdi
callq 0xcaa0
nop