// File: /workspace/github_cpp_makefile_star2_O3/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), %rax
testq %rax, %rax
je 0x5da44
movq 0x18(%rbx), %rcx
cmpq 0xa0(%rax), %rcx
jae 0x5dae3
movq 0xb8(%rax), %rdx
movq %rdx, 0x68(%rbx)
testq %rcx, %rcx
je 0x5d9ff
movq 0x98(%rax), %rsi
xorl %edi, %edi
cmpb $0x2d, (%rsi,%rdi)
je 0x5d9f7
addq 0x208(%rax), %rdx
movq %rdx, 0x68(%rbx)
incq %rdi
cmpq %rdi, %rcx
jne 0x5d9e6
movq %rdx, 0x70(%rbx)
movq 0x20(%rbx), %rsi
leaq (%rsi,%rcx), %rdi
cmpq %rdi, %rcx
jae 0x5da32
addq 0x98(%rax), %rcx
xorl %edi, %edi
cmpb $0x2d, (%rcx,%rdi)
je 0x5da2a
addq 0x208(%rax), %rdx
movq %rdx, 0x70(%rbx)
incq %rdi
cmpq %rdi, %rsi
jne 0x5da19
addq $0x108, %rsp            # imm = 0x108
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0xb6b0
testl %eax, %eax
jne 0x5db82
leaq 0x98(%rsp), %r14
movq %r14, -0x10(%r14)
leaq 0x395b4(%rip), %rsi     # 0x97018
leaq 0x395c3(%rip), %rdx     # 0x9702e
leaq 0x88(%rsp), %rdi
callq 0xdc76
leaq 0xa8(%rsp), %rdi
movl $0x146, %esi            # imm = 0x146
callq 0xe1b2
leaq 0xc8(%rsp), %rdi
leaq 0x88(%rsp), %rsi
leaq 0xa8(%rsp), %rdx
callq 0xe10a
leaq 0x35723(%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 0x5db8c
movups (%rcx), %xmm0
movups %xmm0, (%r15)
jmp 0x5db99
callq 0xb6b0
testl %eax, %eax
jne 0x5db82
leaq 0x98(%rsp), %r14
movq %r14, -0x10(%r14)
leaq 0x39515(%rip), %rsi     # 0x97018
leaq 0x39524(%rip), %rdx     # 0x9702e
leaq 0x88(%rsp), %rdi
callq 0xdc76
leaq 0xa8(%rsp), %rdi
movl $0x147, %esi            # imm = 0x147
callq 0xe1b2
leaq 0xc8(%rsp), %rdi
leaq 0x88(%rsp), %rsi
leaq 0xa8(%rsp), %rdx
callq 0xe10a
leaq 0x35684(%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 0x5dc0d
movups (%rcx), %xmm0
movups %xmm0, (%r15)
jmp 0x5dc1a
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 0x399ae(%rip), %rsi     # 0x97570
leaq 0x399d6(%rip), %rdx     # 0x9759f
leaq 0x68(%rsp), %rdi
callq 0xdc76
leaq 0x35cd7(%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 0x5dc87
movups (%rcx), %xmm0
movups %xmm0, (%r13)
jmp 0x5dc94
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 0x3992d(%rip), %rsi     # 0x97570
leaq 0x39955(%rip), %rdx     # 0x9759f
leaq 0x68(%rsp), %rdi
callq 0xdc76
leaq 0x35c56(%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 0x5dcf7
movups (%rcx), %xmm0
movups %xmm0, (%r13)
jmp 0x5dd04
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 0xe10a
leaq 0x39d52(%rip), %rsi     # 0x97a1b
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 0x5dd67
movups (%rcx), %xmm0
movups %xmm0, (%rbp)
jmp 0x5dd74
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 0xe10a
leaq 0x39867(%rip), %rsi     # 0x975a0
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 0x5dd95
movups (%rcx), %xmm0
movups %xmm0, (%rbp)
jmp 0x5dda2
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 0x1155a
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 0x1155a
jmp 0x5ddc7
jmp 0x5dde3
movq %rax, %rbx
movq 0x48(%rsp), %rdi
cmpq %rbp, %rdi
je 0x5dde6
movq 0x58(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5dde6
movq %rax, %rbx
leaq 0xf8(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x5de0e
movq 0xf8(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5de0e
jmp 0x5de0b
movq %rax, %rbx
movq 0x28(%rsp), %rdi
cmpq %r13, %rdi
je 0x5de2c
movq 0x38(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5de2c
jmp 0x5de29
movq %rax, %rbx
movq 0x68(%rsp), %rdi
cmpq %r12, %rdi
je 0x5de4a
movq 0x78(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5de4a
jmp 0x5de47
movq %rax, %rbx
movq 0x8(%rsp), %rdi
cmpq %r15, %rdi
je 0x5de68
movq 0x18(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5de68
jmp 0x5de65
movq %rax, %rbx
leaq 0xd8(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x5de90
movq 0xd8(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5de90
jmp 0x5de8d
movq %rax, %rbx
leaq 0xb8(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x5deb8
movq 0xb8(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5deb8
jmp 0x5deb5
movq %rax, %rbx
movq 0x88(%rsp), %rdi
cmpq %r14, %rdi
je 0x5dedc
movq 0x98(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5dedc
jmp 0x5ded9
movq %rax, %rbx
movq %rbx, %rdi
callq 0xba60