// File: /workspace/github_cpp_makefile_star2_O2/ncbi[P]amr/alignment.cpp
// Function: Alignment_sp::SeqChange::setSeq()
void SeqChange::setSeq ()
{ 
  ASSERT (al);
  ASSERT (al->targetSeq. size () == al->refSeq. size ());
  ASSERT (start + len <= al->targetSeq. size ());
  
  reference = al->refSeq.    substr (start, len);
  allele    = al->targetSeq. substr (start, len);
  
  replaceStr (reference, "-", "");
  replaceStr (allele,    "-", "");
  
  QC_ASSERT (reference != allele);
  ASSERT (isUpper (reference));
  ASSERT (isUpper (allele));
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x108, %rsp            # imm = 0x108
movq %rdi, %rbx
callq 0xc070
andl $0x0, (%rax)
movq 0x8(%rbx), %rsi
testq %rsi, %rsi
je 0x3fab8
movq %rax, %r14
movq 0x38(%rsi), %rax
cmpq 0xa0(%rsi), %rax
jne 0x3fb8c
movq 0x18(%rbx), %rdx
movq 0x20(%rbx), %rcx
leaq (%rcx,%rdx), %rdi
cmpq %rax, %rdi
ja 0x3fc60
addq $0x98, %rsi
leaq 0x8(%rsp), %r12
movq %r12, %rdi
callq 0xc5f0
leaq 0x28(%rbx), %r15
movq %r15, %rdi
movq %r12, %rsi
callq 0xc710
movq %r12, %rdi
callq 0xcbe8
movq 0x8(%rbx), %rsi
movq 0x18(%rbx), %rdx
addq $0x30, %rsi
movq 0x20(%rbx), %rcx
leaq 0x8(%rsp), %r12
movq %r12, %rdi
callq 0xc5f0
addq $0x48, %rbx
movq %rbx, %rdi
movq %r12, %rsi
callq 0xc710
movq %r12, %rdi
callq 0xcbe8
leaq 0x20d94(%rip), %rsi     # 0x60761
leaq 0x8(%rsp), %rdi
leaq 0x68(%rsp), %rdx
callq 0xdbbe
leaq 0x2373c(%rip), %rsi     # 0x6311f
leaq 0x28(%rsp), %rdi
leaq 0x48(%rsp), %rdx
callq 0xdbbe
leaq 0x8(%rsp), %rsi
leaq 0x28(%rsp), %rdx
movq %r15, %rdi
callq 0x113c0
leaq 0x28(%rsp), %rdi
callq 0xcbe8
leaq 0x8(%rsp), %rdi
callq 0xcbe8
leaq 0x20d42(%rip), %rsi     # 0x60761
leaq 0x8(%rsp), %rdi
leaq 0x68(%rsp), %rdx
callq 0xdbbe
leaq 0x236ea(%rip), %rsi     # 0x6311f
leaq 0x28(%rsp), %rdi
leaq 0x48(%rsp), %rdx
callq 0xdbbe
leaq 0x8(%rsp), %rsi
leaq 0x28(%rsp), %rdx
movq %rbx, %rdi
callq 0x113c0
leaq 0x28(%rsp), %rdi
callq 0xcbe8
leaq 0x8(%rsp), %rdi
callq 0xcbe8
andl $0x0, (%r14)
movq %r15, %rdi
movq %rbx, %rsi
callq 0x2a3f3
testb %al, %al
je 0x3fd34
andl $0x0, (%r14)
movq %r15, %rdi
callq 0x11c45
testb %al, %al
je 0x3fe08
andl $0x0, (%r14)
movq %rbx, %rdi
callq 0x11c45
testb %al, %al
je 0x3fedc
addq $0x108, %rsp            # imm = 0x108
popq %rbx
popq %r12
popq %r14
popq %r15
retq
callq 0xc6d0
testl %eax, %eax
jne 0x3ffb0
leaq 0x2251c(%rip), %rsi     # 0x61fe8
leaq 0xe8(%rsp), %rdi
leaq 0x7(%rsp), %rdx
callq 0xdbbe
leaq 0xc8(%rsp), %rdi
movl $0x133, %esi            # imm = 0x133
callq 0xe2d5
leaq 0x48(%rsp), %rdi
leaq 0xe8(%rsp), %rsi
leaq 0xc8(%rsp), %rdx
callq 0xe26e
leaq 0x1e6c0(%rip), %rdx     # 0x5e1d1
leaq 0x68(%rsp), %rdi
leaq 0x48(%rsp), %rsi
callq 0xe24f
leaq 0x2299e(%rip), %rsi     # 0x624c5
leaq 0x88(%rsp), %rdi
leaq 0x6(%rsp), %rdx
callq 0xdbbe
leaq 0x1ed8c(%rip), %rdx     # 0x5e8cc
leaq 0xa8(%rsp), %rdi
leaq 0x88(%rsp), %rsi
callq 0xe24f
leaq 0x28(%rsp), %rdi
leaq 0x68(%rsp), %rsi
leaq 0xa8(%rsp), %rdx
callq 0xe26e
leaq 0x22e78(%rip), %rdx     # 0x629eb
leaq 0x8(%rsp), %rdi
leaq 0x28(%rsp), %rsi
callq 0xe24f
leaq 0x8(%rsp), %rdi
callq 0x101d0
callq 0xc6d0
testl %eax, %eax
jne 0x3ffb0
leaq 0x22448(%rip), %rsi     # 0x61fe8
leaq 0xe8(%rsp), %rdi
leaq 0x7(%rsp), %rdx
callq 0xdbbe
leaq 0xc8(%rsp), %rdi
movl $0x134, %esi            # imm = 0x134
callq 0xe2d5
leaq 0x48(%rsp), %rdi
leaq 0xe8(%rsp), %rsi
leaq 0xc8(%rsp), %rdx
callq 0xe26e
leaq 0x1e5ec(%rip), %rdx     # 0x5e1d1
leaq 0x68(%rsp), %rdi
leaq 0x48(%rsp), %rsi
callq 0xe24f
leaq 0x228ca(%rip), %rsi     # 0x624c5
leaq 0x88(%rsp), %rdi
leaq 0x6(%rsp), %rdx
callq 0xdbbe
leaq 0x1ecb8(%rip), %rdx     # 0x5e8cc
leaq 0xa8(%rsp), %rdi
leaq 0x88(%rsp), %rsi
callq 0xe24f
leaq 0x28(%rsp), %rdi
leaq 0x68(%rsp), %rsi
leaq 0xa8(%rsp), %rdx
callq 0xe26e
leaq 0x228a5(%rip), %rdx     # 0x624ec
leaq 0x8(%rsp), %rdi
leaq 0x28(%rsp), %rsi
callq 0xe24f
leaq 0x8(%rsp), %rdi
callq 0x101d0
callq 0xc6d0
testl %eax, %eax
jne 0x3ffb0
leaq 0x22374(%rip), %rsi     # 0x61fe8
leaq 0xe8(%rsp), %rdi
leaq 0x7(%rsp), %rdx
callq 0xdbbe
leaq 0xc8(%rsp), %rdi
movl $0x135, %esi            # imm = 0x135
callq 0xe2d5
leaq 0x48(%rsp), %rdi
leaq 0xe8(%rsp), %rsi
leaq 0xc8(%rsp), %rdx
callq 0xe26e
leaq 0x1e518(%rip), %rdx     # 0x5e1d1
leaq 0x68(%rsp), %rdi
leaq 0x48(%rsp), %rsi
callq 0xe24f
leaq 0x227f6(%rip), %rsi     # 0x624c5
leaq 0x88(%rsp), %rdi
leaq 0x6(%rsp), %rdx
callq 0xdbbe
leaq 0x1ebe4(%rip), %rdx     # 0x5e8cc
leaq 0xa8(%rsp), %rdi
leaq 0x88(%rsp), %rsi
callq 0xe24f
leaq 0x28(%rsp), %rdi
leaq 0x68(%rsp), %rsi
leaq 0xa8(%rsp), %rdx
callq 0xe26e
leaq 0x227ff(%rip), %rdx     # 0x6251a
leaq 0x8(%rsp), %rdi
leaq 0x28(%rsp), %rsi
callq 0xe24f
leaq 0x8(%rsp), %rdi
callq 0x101d0
callq 0xc6d0
testl %eax, %eax
jne 0x3ffb0
leaq 0x222a0(%rip), %rsi     # 0x61fe8
leaq 0xe8(%rsp), %rdi
leaq 0x7(%rsp), %rdx
callq 0xdbbe
leaq 0xc8(%rsp), %rdi
movl $0x13d, %esi            # imm = 0x13D
callq 0xe2d5
leaq 0x48(%rsp), %rdi
leaq 0xe8(%rsp), %rsi
leaq 0xc8(%rsp), %rdx
callq 0xe26e
leaq 0x1e444(%rip), %rdx     # 0x5e1d1
leaq 0x68(%rsp), %rdi
leaq 0x48(%rsp), %rsi
callq 0xe24f
leaq 0x22722(%rip), %rsi     # 0x624c5
leaq 0x88(%rsp), %rdi
leaq 0x6(%rsp), %rdx
callq 0xdbbe
leaq 0x1eb10(%rip), %rdx     # 0x5e8cc
leaq 0xa8(%rsp), %rdi
leaq 0x88(%rsp), %rsi
callq 0xe24f
leaq 0x28(%rsp), %rdi
leaq 0x68(%rsp), %rsi
leaq 0xa8(%rsp), %rdx
callq 0xe26e
leaq 0x22461(%rip), %rdx     # 0x62250
leaq 0x8(%rsp), %rdi
leaq 0x28(%rsp), %rsi
callq 0xe24f
leaq 0x8(%rsp), %rdi
callq 0x101d0
callq 0xc6d0
testl %eax, %eax
jne 0x3ffb0
leaq 0x221cc(%rip), %rsi     # 0x61fe8
leaq 0xe8(%rsp), %rdi
leaq 0x7(%rsp), %rdx
callq 0xdbbe
leaq 0xc8(%rsp), %rdi
movl $0x13e, %esi            # imm = 0x13E
callq 0xe2d5
leaq 0x48(%rsp), %rdi
leaq 0xe8(%rsp), %rsi
leaq 0xc8(%rsp), %rdx
callq 0xe26e
leaq 0x1e370(%rip), %rdx     # 0x5e1d1
leaq 0x68(%rsp), %rdi
leaq 0x48(%rsp), %rsi
callq 0xe24f
leaq 0x2264e(%rip), %rsi     # 0x624c5
leaq 0x88(%rsp), %rdi
leaq 0x6(%rsp), %rdx
callq 0xdbbe
leaq 0x1ea3c(%rip), %rdx     # 0x5e8cc
leaq 0xa8(%rsp), %rdi
leaq 0x88(%rsp), %rsi
callq 0xe24f
leaq 0x28(%rsp), %rdi
leaq 0x68(%rsp), %rsi
leaq 0xa8(%rsp), %rdx
callq 0xe26e
leaq 0x22368(%rip), %rdx     # 0x6222b
leaq 0x8(%rsp), %rdi
leaq 0x28(%rsp), %rsi
callq 0xe24f
leaq 0x8(%rsp), %rdi
callq 0x101d0
callq 0xc6d0
testl %eax, %eax
jne 0x3ffb0
leaq 0x220f8(%rip), %rsi     # 0x61fe8
leaq 0xe8(%rsp), %rdi
leaq 0x7(%rsp), %rdx
callq 0xdbbe
leaq 0xc8(%rsp), %rdi
movl $0x13f, %esi            # imm = 0x13F
callq 0xe2d5
leaq 0x48(%rsp), %rdi
leaq 0xe8(%rsp), %rsi
leaq 0xc8(%rsp), %rdx
callq 0xe26e
leaq 0x1e29c(%rip), %rdx     # 0x5e1d1
leaq 0x68(%rsp), %rdi
leaq 0x48(%rsp), %rsi
callq 0xe24f
leaq 0x2257a(%rip), %rsi     # 0x624c5
leaq 0x88(%rsp), %rdi
leaq 0x6(%rsp), %rdx
callq 0xdbbe
leaq 0x1e968(%rip), %rdx     # 0x5e8cc
leaq 0xa8(%rsp), %rdi
leaq 0x88(%rsp), %rsi
callq 0xe24f
leaq 0x28(%rsp), %rdi
leaq 0x68(%rsp), %rsi
leaq 0xa8(%rsp), %rdx
callq 0xe26e
leaq 0x222a8(%rip), %rdx     # 0x6223f
leaq 0x8(%rsp), %rdi
leaq 0x28(%rsp), %rsi
callq 0xe24f
leaq 0x8(%rsp), %rdi
callq 0x101d0
pushq $0x1
popq %rdi
callq 0xc6f0
jmp 0x3ffcc
jmp 0x3ffdb
jmp 0x3ffcc
jmp 0x3ffdb
jmp 0x3ffcc
jmp 0x3ffdb
jmp 0x3ffcc
jmp 0x3ffdb
jmp 0x3ffcc
jmp 0x3ffdb
movq %rax, %rbx
leaq 0x8(%rsp), %rdi
callq 0xcbe8
jmp 0x3ffde
movq %rax, %rbx
leaq 0x28(%rsp), %rdi
callq 0xcbe8
jmp 0x3fff7
jmp 0x3fff4
jmp 0x3fff4
jmp 0x3fff4
jmp 0x3fff4
jmp 0x3fff4
movq %rax, %rbx
leaq 0xa8(%rsp), %rdi
callq 0xcbe8
jmp 0x40013
jmp 0x40010
jmp 0x40010
jmp 0x40010
jmp 0x40010
jmp 0x40010
movq %rax, %rbx
leaq 0x88(%rsp), %rdi
callq 0xcbe8
jmp 0x4002f
jmp 0x4002c
jmp 0x4002c
jmp 0x4002c
jmp 0x4002c
jmp 0x4002c
movq %rax, %rbx
leaq 0x68(%rsp), %rdi
callq 0xcbe8
jmp 0x40048
jmp 0x40045
jmp 0x40045
jmp 0x40045
jmp 0x40045
jmp 0x40045
movq %rax, %rbx
leaq 0x48(%rsp), %rdi
callq 0xcbe8
jmp 0x40061
jmp 0x4005e
jmp 0x4005e
jmp 0x4005e
jmp 0x4005e
jmp 0x4005e
movq %rax, %rbx
leaq 0xc8(%rsp), %rdi
callq 0xcbe8
jmp 0x4007d
jmp 0x4007a
jmp 0x4007a
jmp 0x4007a
jmp 0x4007a
jmp 0x4007a
movq %rax, %rbx
leaq 0xe8(%rsp), %rdi
jmp 0x400b0
jmp 0x400b7
jmp 0x400b7
jmp 0x400b7
jmp 0x400b7
jmp 0x400b7
jmp 0x400b7
jmp 0x40099
jmp 0x400a8
jmp 0x400b7
movq %rax, %rbx
leaq 0x28(%rsp), %rdi
callq 0xcbe8
jmp 0x400ab
movq %rax, %rbx
leaq 0x8(%rsp), %rdi
callq 0xcbe8
jmp 0x400ba
movq %rax, %rbx
movq %rbx, %rdi
callq 0xcaa0