// File: /workspace/github_cpp_makefile_star2_O3/ncbi[P]amr/alignment.cpp
// Function: Alignment_sp::SeqChange::setStartTarget()
void SeqChange::setStartTarget ()
{
  ASSERT (al);
  ASSERT (start < al->targetSeq. size ());
  
  start_target = al->targetStart;
  if (al->targetStrand)
  {
    FOR (size_t, i, start)
      if (al->targetSeq [i] != '-')
        start_target += al->al2target_len;
  }
  else
  {
    FOR_REV_END (size_t, i, start + len, al->targetSeq. size ())
      if (al->targetSeq [i] != '-')
        start_target += al->al2target_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 0x5df8a
movq 0x18(%rbx), %rcx
movq 0x38(%rax), %rsi
cmpq %rsi, %rcx
jae 0x5e029
movq 0x50(%rax), %rdx
movq %rdx, 0x78(%rbx)
cmpb $0x0, 0x68(%rax)
je 0x5df51
testq %rcx, %rcx
je 0x5df78
movq 0x30(%rax), %rsi
xorl %edi, %edi
cmpb $0x2d, (%rsi,%rdi)
je 0x5df47
addq 0x210(%rax), %rdx
movq %rdx, 0x78(%rbx)
incq %rdi
cmpq %rdi, %rcx
jne 0x5df36
jmp 0x5df78
addq 0x20(%rbx), %rcx
cmpq %rcx, %rsi
jbe 0x5df78
movq 0x30(%rax), %rdi
cmpb $0x2d, -0x1(%rdi,%rsi)
je 0x5df70
addq 0x210(%rax), %rdx
movq %rdx, 0x78(%rbx)
decq %rsi
cmpq %rcx, %rsi
ja 0x5df5e
addq $0x108, %rsp            # imm = 0x108
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0xb6b0
testl %eax, %eax
jne 0x5e0c8
leaq 0x98(%rsp), %r14
movq %r14, -0x10(%r14)
leaq 0x3906e(%rip), %rsi     # 0x97018
leaq 0x3907d(%rip), %rdx     # 0x9702e
leaq 0x88(%rsp), %rdi
callq 0xdc76
leaq 0xa8(%rsp), %rdi
movl $0x158, %esi            # imm = 0x158
callq 0xe1b2
leaq 0xc8(%rsp), %rdi
leaq 0x88(%rsp), %rsi
leaq 0xa8(%rsp), %rdx
callq 0xe10a
leaq 0x351dd(%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 0x5e0d2
movups (%rcx), %xmm0
movups %xmm0, (%r15)
jmp 0x5e0df
callq 0xb6b0
testl %eax, %eax
jne 0x5e0c8
leaq 0x98(%rsp), %r14
movq %r14, -0x10(%r14)
leaq 0x38fcf(%rip), %rsi     # 0x97018
leaq 0x38fde(%rip), %rdx     # 0x9702e
leaq 0x88(%rsp), %rdi
callq 0xdc76
leaq 0xa8(%rsp), %rdi
movl $0x159, %esi            # imm = 0x159
callq 0xe1b2
leaq 0xc8(%rsp), %rdi
leaq 0x88(%rsp), %rsi
leaq 0xa8(%rsp), %rdx
callq 0xe10a
leaq 0x3513e(%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 0x5e153
movups (%rcx), %xmm0
movups %xmm0, (%r15)
jmp 0x5e160
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 0x394b4(%rip), %rsi     # 0x975bc
leaq 0x394db(%rip), %rdx     # 0x975ea
leaq 0x68(%rsp), %rdi
callq 0xdc76
leaq 0x35791(%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 0x5e1cd
movups (%rcx), %xmm0
movups %xmm0, (%r13)
jmp 0x5e1da
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 0x39433(%rip), %rsi     # 0x975bc
leaq 0x3945a(%rip), %rdx     # 0x975ea
leaq 0x68(%rsp), %rdi
callq 0xdc76
leaq 0x35710(%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 0x5e23d
movups (%rcx), %xmm0
movups %xmm0, (%r13)
jmp 0x5e24a
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 0x3980c(%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 0x5e2ad
movups (%rcx), %xmm0
movups %xmm0, (%rbp)
jmp 0x5e2ba
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 0x3936c(%rip), %rsi     # 0x975eb
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 0x5e2db
movups (%rcx), %xmm0
movups %xmm0, (%rbp)
jmp 0x5e2e8
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 0x5e30d
jmp 0x5e329
movq %rax, %rbx
movq 0x48(%rsp), %rdi
cmpq %rbp, %rdi
je 0x5e32c
movq 0x58(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5e32c
movq %rax, %rbx
leaq 0xf8(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x5e354
movq 0xf8(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5e354
jmp 0x5e351
movq %rax, %rbx
movq 0x28(%rsp), %rdi
cmpq %r13, %rdi
je 0x5e372
movq 0x38(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5e372
jmp 0x5e36f
movq %rax, %rbx
movq 0x68(%rsp), %rdi
cmpq %r12, %rdi
je 0x5e390
movq 0x78(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5e390
jmp 0x5e38d
movq %rax, %rbx
movq 0x8(%rsp), %rdi
cmpq %r15, %rdi
je 0x5e3ae
movq 0x18(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5e3ae
jmp 0x5e3ab
movq %rax, %rbx
leaq 0xd8(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x5e3d6
movq 0xd8(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5e3d6
jmp 0x5e3d3
movq %rax, %rbx
leaq 0xb8(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x5e3fe
movq 0xb8(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5e3fe
jmp 0x5e3fb
movq %rax, %rbx
movq 0x88(%rsp), %rdi
cmpq %r14, %rdi
je 0x5e422
movq 0x98(%rsp), %rsi
incq %rsi
callq 0xb5a0
jmp 0x5e422
jmp 0x5e41f
movq %rax, %rbx
movq %rbx, %rdi
callq 0xba60