// File: /workspace/github_cpp_makefile_star2_O1/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 %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x108, %rsp            # imm = 0x108
movq %rdi, %rbx
callq 0xb070
movl $0x0, (%rax)
movq 0x8(%rbx), %rcx
testq %rcx, %rcx
je 0x5db0a
movl $0x0, (%rax)
movq 0x18(%rbx), %rax
cmpq 0xa0(%rcx), %rax
jae 0x5dba9
movq 0xb8(%rcx), %rdx
movq %rdx, 0x68(%rbx)
testq %rax, %rax
je 0x5dabd
movq 0x68(%rbx), %rdx
movq 0x98(%rcx), %rsi
xorl %edi, %edi
cmpb $0x2d, (%rsi,%rdi)
je 0x5dab5
addq 0x208(%rcx), %rdx
movq %rdx, 0x68(%rbx)
incq %rdi
cmpq %rdi, %rax
jne 0x5daa4
movq 0x20(%rbx), %rdx
movq 0x68(%rbx), %rsi
movq %rsi, 0x70(%rbx)
leaq (%rdx,%rax), %rsi
cmpq %rsi, %rax
jae 0x5daf8
movq 0x70(%rbx), %rsi
addq 0x98(%rcx), %rax
xorl %edi, %edi
cmpb $0x2d, (%rax,%rdi)
je 0x5daf0
addq 0x208(%rcx), %rsi
movq %rsi, 0x70(%rbx)
incq %rdi
cmpq %rdi, %rdx
jne 0x5dadf
addq $0x108, %rsp            # imm = 0x108
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0xb6b0
testl %eax, %eax
jne 0x5dc48
leaq 0x98(%rsp), %r14
movq %r14, -0x10(%r14)
leaq 0x394fe(%rip), %rsi     # 0x97028
leaq 0x3950d(%rip), %rdx     # 0x9703e
leaq 0x88(%rsp), %rdi
callq 0xdc76
leaq 0xa8(%rsp), %rdi
movl $0x146, %esi            # imm = 0x146
callq 0xe1a8
leaq 0xc8(%rsp), %rdi
leaq 0x88(%rsp), %rsi
leaq 0xa8(%rsp), %rdx
callq 0xe100
leaq 0x3565d(%rip), %rsi     # 0x931d1
leaq 0xc8(%rsp), %rdi
callq 0xbb10
leaq 0x18(%rsp), %r15
movq %r15, -0x10(%r15)
movq (%rax), %rdx
movq %rax, %rcx
addq $0x10, %rcx
cmpq %rcx, %rdx
jne 0x5dc52
movups (%rcx), %xmm0
movups %xmm0, (%r15)
jmp 0x5dc5f
callq 0xb6b0
testl %eax, %eax
jne 0x5dc48
leaq 0x98(%rsp), %r14
movq %r14, -0x10(%r14)
leaq 0x3945f(%rip), %rsi     # 0x97028
leaq 0x3946e(%rip), %rdx     # 0x9703e
leaq 0x88(%rsp), %rdi
callq 0xdc76
leaq 0xa8(%rsp), %rdi
movl $0x147, %esi            # imm = 0x147
callq 0xe1a8
leaq 0xc8(%rsp), %rdi
leaq 0x88(%rsp), %rsi
leaq 0xa8(%rsp), %rdx
callq 0xe100
leaq 0x355be(%rip), %rsi     # 0x931d1
leaq 0xc8(%rsp), %rdi
callq 0xbb10
leaq 0x18(%rsp), %r15
movq %r15, -0x10(%r15)
movq (%rax), %rdx
movq %rax, %rcx
addq $0x10, %rcx
cmpq %rcx, %rdx
jne 0x5dcd3
movups (%rcx), %xmm0
movups %xmm0, (%r15)
jmp 0x5dce0
movl $0x1, %edi
callq 0xb6d0
movq %rdx, 0x8(%rsp)
movq (%rcx), %rdx
movq %rdx, 0x18(%rsp)
movq 0x8(%rax), %rdx
movq %rdx, 0x10(%rsp)
movq %rcx, (%rax)
movq $0x0, 0x8(%rax)
movb $0x0, 0x10(%rax)
leaq 0x78(%rsp), %r12
movq %r12, -0x10(%r12)
leaq 0x398f8(%rip), %rsi     # 0x97580
leaq 0x39920(%rip), %rdx     # 0x975af
leaq 0x68(%rsp), %rdi
callq 0xdc76
leaq 0x35c11(%rip), %rsi     # 0x938b1
leaq 0x68(%rsp), %rdi
callq 0xbb10
leaq 0x38(%rsp), %r13
movq %r13, -0x10(%r13)
movq (%rax), %rdx
movq %rax, %rcx
addq $0x10, %rcx
cmpq %rcx, %rdx
jne 0x5dd4d
movups (%rcx), %xmm0
movups %xmm0, (%r13)
jmp 0x5dd5a
movq %rdx, 0x8(%rsp)
movq (%rcx), %rdx
movq %rdx, 0x18(%rsp)
movq 0x8(%rax), %rdx
movq %rdx, 0x10(%rsp)
movq %rcx, (%rax)
movq $0x0, 0x8(%rax)
movb $0x0, 0x10(%rax)
leaq 0x78(%rsp), %r12
movq %r12, -0x10(%r12)
leaq 0x39877(%rip), %rsi     # 0x97580
leaq 0x3989f(%rip), %rdx     # 0x975af
leaq 0x68(%rsp), %rdi
callq 0xdc76
leaq 0x35b90(%rip), %rsi     # 0x938b1
leaq 0x68(%rsp), %rdi
callq 0xbb10
leaq 0x38(%rsp), %r13
movq %r13, -0x10(%r13)
movq (%rax), %rdx
movq %rax, %rcx
addq $0x10, %rcx
cmpq %rcx, %rdx
jne 0x5ddbd
movups (%rcx), %xmm0
movups %xmm0, (%r13)
jmp 0x5ddca
movq %rdx, 0x28(%rsp)
movq (%rcx), %rdx
movq %rdx, 0x38(%rsp)
movq 0x8(%rax), %rsi
leaq 0x28(%rsp), %rdx
movq %rsi, 0x8(%rdx)
movq %rcx, (%rax)
movq $0x0, 0x8(%rax)
movb $0x0, 0x10(%rax)
leaq 0xe8(%rsp), %rdi
leaq 0x8(%rsp), %rsi
callq 0xe100
leaq 0x39c9c(%rip), %rsi     # 0x97a2b
leaq 0xe8(%rsp), %rdi
callq 0xbb10
leaq 0x58(%rsp), %rbp
movq %rbp, -0x10(%rbp)
movq (%rax), %rdx
movq %rax, %rcx
addq $0x10, %rcx
cmpq %rcx, %rdx
jne 0x5de2d
movups (%rcx), %xmm0
movups %xmm0, (%rbp)
jmp 0x5de3a
movq %rdx, 0x28(%rsp)
movq (%rcx), %rdx
movq %rdx, 0x38(%rsp)
movq 0x8(%rax), %rsi
leaq 0x28(%rsp), %rdx
movq %rsi, 0x8(%rdx)
movq %rcx, (%rax)
movq $0x0, 0x8(%rax)
movb $0x0, 0x10(%rax)
leaq 0xe8(%rsp), %rdi
leaq 0x8(%rsp), %rsi
callq 0xe100
leaq 0x397b1(%rip), %rsi     # 0x975b0
leaq 0xe8(%rsp), %rdi
callq 0xbb10
leaq 0x58(%rsp), %rbp
movq %rbp, -0x10(%rbp)
movq (%rax), %rdx
movq %rax, %rcx
addq $0x10, %rcx
cmpq %rcx, %rdx
jne 0x5de5b
movups (%rcx), %xmm0
movups %xmm0, (%rbp)
jmp 0x5de68
movq %rdx, 0x48(%rsp)
movq (%rcx), %rdx
movq %rdx, 0x58(%rsp)
movq 0x8(%rax), %rdx
leaq 0x48(%rsp), %rdi
movq %rdx, 0x8(%rdi)
movq %rcx, (%rax)
movq $0x0, 0x8(%rax)
movb $0x0, 0x10(%rax)
callq 0x1151b
movq %rdx, 0x48(%rsp)
movq (%rcx), %rdx
movq %rdx, 0x58(%rsp)
movq 0x8(%rax), %rdx
leaq 0x48(%rsp), %rdi
movq %rdx, 0x8(%rdi)
movq %rcx, (%rax)
movq $0x0, 0x8(%rax)
movb $0x0, 0x10(%rax)
callq 0x1151b
jmp 0x5de8d
jmp 0x5dea9
movq %rax, %rbx
movq 0x48(%rsp), %rdi
cmpq %rbp, %rdi
je 0x5deac
movq 0x58(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5deac
movq %rax, %rbx
leaq 0xf8(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x5ded4
movq 0xf8(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5ded4
jmp 0x5ded1
movq %rax, %rbx
movq 0x28(%rsp), %rdi
cmpq %r13, %rdi
je 0x5def2
movq 0x38(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5def2
jmp 0x5deef
movq %rax, %rbx
movq 0x68(%rsp), %rdi
cmpq %r12, %rdi
je 0x5df10
movq 0x78(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5df10
jmp 0x5df0d
movq %rax, %rbx
movq 0x8(%rsp), %rdi
cmpq %r15, %rdi
je 0x5df2e
movq 0x18(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5df2e
jmp 0x5df2b
movq %rax, %rbx
leaq 0xd8(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x5df56
movq 0xd8(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5df56
jmp 0x5df53
movq %rax, %rbx
leaq 0xb8(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x5df7e
movq 0xb8(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5df7e
jmp 0x5df7b
movq %rax, %rbx
movq 0x88(%rsp), %rdi
cmpq %r14, %rdi
je 0x5dfa2
movq 0x98(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5dfa2
jmp 0x5df9f
movq %rax, %rbx
movq %rbx, %rdi
callq 0xba60