// File: /workspace/github_c_makefile_star2_O0/genometools[P]genometools/src/tools/gt_paircmp.c
// Function: gt_paircmp
int gt_paircmp(int argc, const char **argv, GtError *err)
{
  int parsed_args;
  Cmppairwiseopt cmppairwise;
  GtOPrval oprval;
  GtFastaReader *reader0 = NULL,
                *reader1 = NULL;

  gt_error_check(err);

  oprval = parse_options(&parsed_args, &cmppairwise, argc, argv, err);
  if (oprval == GT_OPTION_PARSER_OK)
  {
    gt_assert(parsed_args == argc);
    showsimpleoptions(&cmppairwise);
    if (cmppairwise.showedist)
    {
      GtUword edist, len1, len2;
      GtStr *s1, *s2;

      gt_assert(gt_str_array_size(cmppairwise.strings) >= 2);
      s1 = gt_str_array_get_str(cmppairwise.strings,0);
      s2 = gt_str_array_get_str(cmppairwise.strings,1UL);
      len1 = gt_str_length(s1);
      len2 = gt_str_length(s2);
      edist = gt_computegreedyunitedist((const GtUchar *) gt_str_get(s1),
                                        len1,
                                        (const GtUchar *) gt_str_get(s2),
                                        len2);
      printf(GT_WU " " GT_WU " " GT_WU " " GT_WU "%% errors\n",
             edist, len1,len2,(200 * edist)/(len1+len2));
    }
    else if (cmppairwise.print)
    {
      const GtStr *str0 = gt_str_array_get_str(cmppairwise.strings,0),
                  *str1 = gt_str_array_get_str(cmppairwise.strings,1);

      gt_squarealign_print_edit_alignment((const GtUchar *) gt_str_get(str0),0,
                                          gt_str_length(str0),
                                          (const GtUchar *) gt_str_get(str1),0,
                                          gt_str_length(str1));
    } else
    {
      size_t idx;
      Checkfunctiontabentry checkfunction_tab[] = {
        MAKECheckfunctiontabentry(gt_checkgreedyunitedist),
        MAKECheckfunctiontabentry(gt_linearalign_check),
        MAKECheckfunctiontabentry(gt_linearalign_check_local),
        MAKECheckfunctiontabentry(gt_linearalign_affinegapcost_check),
        MAKECheckfunctiontabentry(gt_linearalign_affinegapcost_check_local),
        MAKECheckfunctiontabentry(gt_diagonalbandalign_check),
        MAKECheckfunctiontabentry(gt_diagonalbandalign_affinegapcost_check)
      };

      if (cmppairwise.fasta)
      {
        gt_assert(gt_str_array_size(cmppairwise.files) == 3);
        cmppairwise.fastasequences0 = gt_str_array_new();
        cmppairwise.fastasequences1 = gt_str_array_new();

        reader0 = gt_fasta_reader_rec_new(gt_str_array_get_str(
                                                        cmppairwise.files,1UL));
        gt_fasta_reader_run(reader0, NULL, save_fastaentry,
                            NULL, cmppairwise.fastasequences0, err);
        reader1 = gt_fasta_reader_rec_new (gt_str_array_get_str(
                                                        cmppairwise.files,2UL));
        gt_fasta_reader_run(reader1, NULL, save_fastaentry,
                            NULL, cmppairwise.fastasequences1, err);
        gt_error_check(err);
      }
      for (idx = 0; idx < sizeof checkfunction_tab/sizeof checkfunction_tab[0];
           idx++)
      {
        GtUword testcases;

        printf("run %s\n",checkfunction_tab[idx].name);
        testcases
          = applycheckfunctiontosimpleoptions(checkfunction_tab[idx].function,
                                              &cmppairwise);
        printf("# number of testcases for %s: " GT_WU "\n",
               checkfunction_tab[idx].name,testcases);
      }
      gt_fasta_reader_delete(reader0);
      gt_fasta_reader_delete(reader1);
    }
  }
  freesimpleoption(&cmppairwise);
  if (oprval == GT_OPTION_PARSER_REQUESTS_EXIT)
  {
    return 0;
  }
  if (oprval == GT_OPTION_PARSER_ERROR)
  {
    return -1;
  }
  return 0;
}

// Assembly:
subq $0x168, %rsp            # imm = 0x168
movl %edi, 0x160(%rsp)
movq %rsi, 0x158(%rsp)
movq %rdx, 0x150(%rsp)
movq $0x0, 0x100(%rsp)
movq $0x0, 0xf8(%rsp)
cmpq $0x0, 0x150(%rsp)
je 0x49ecc
movq 0x150(%rsp), %rdi
callq 0xd8a60
testb $0x1, %al
jne 0x49e94
jmp 0x49ecc
movq 0x5f2105(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x4cc16e(%rip), %rsi    # 0x516013
leaq 0x4cc313(%rip), %rdx    # 0x5161bf
leaq 0x4d9018(%rip), %rcx    # 0x522ecb
leaq 0x4d901c(%rip), %r8     # 0x522ed6
movl $0x14c, %r9d            # imm = 0x14C
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x49ece
movl 0x160(%rsp), %edx
movq 0x158(%rsp), %rcx
movq 0x150(%rsp), %r8
leaq 0x14c(%rsp), %rdi
leaq 0x110(%rsp), %rsi
callq 0x4a420
movl %eax, 0x10c(%rsp)
cmpl $0x0, 0x10c(%rsp)
jne 0x4a3be
jmp 0x49f11
movl 0x14c(%rsp), %eax
cmpl 0x160(%rsp), %eax
je 0x49f59
movq 0x5f2078(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x4cc0e1(%rip), %rsi    # 0x516013
leaq 0x4cd99f(%rip), %rdx    # 0x5178d8
leaq 0x4d8f8b(%rip), %rcx    # 0x522ecb
leaq 0x4d8f8f(%rip), %r8     # 0x522ed6
movl $0x151, %r9d            # imm = 0x151
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x49f5b
leaq 0x110(%rsp), %rdi
callq 0x4a950
testb $0x1, 0x141(%rsp)
je 0x4a0c9
jmp 0x49f78
movq 0x110(%rsp), %rdi
callq 0x11fcc0
cmpq $0x2, %rax
jae 0x49fc3
movq 0x5f200e(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x4cc077(%rip), %rsi    # 0x516013
leaq 0x4d8f4a(%rip), %rdx    # 0x522eed
leaq 0x4d8f21(%rip), %rcx    # 0x522ecb
leaq 0x4d8f25(%rip), %r8     # 0x522ed6
movl $0x158, %r9d            # imm = 0x158
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x49fc5
movq 0x110(%rsp), %rdi
xorl %eax, %eax
movl %eax, %esi
callq 0x11f960
movq %rax, 0xd8(%rsp)
movq 0x110(%rsp), %rdi
movl $0x1, %esi
callq 0x11f960
movq %rax, 0xd0(%rsp)
movq 0xd8(%rsp), %rdi
callq 0x11dfa0
movq %rax, 0xe8(%rsp)
movq 0xd0(%rsp), %rdi
callq 0x11dfa0
movq %rax, 0xe0(%rsp)
movq 0xd8(%rsp), %rdi
callq 0x11dee0
movq %rax, 0x20(%rsp)
movq 0xe8(%rsp), %rax
movq %rax, 0x28(%rsp)
movq 0xd0(%rsp), %rdi
callq 0x11dee0
movq 0x20(%rsp), %rdi
movq 0x28(%rsp), %rsi
movq %rax, %rdx
movq 0xe0(%rsp), %rcx
callq 0x2f3280
movq %rax, 0xf0(%rsp)
movq 0xf0(%rsp), %rsi
movq 0xe8(%rsp), %rax
movq %rax, 0x30(%rsp)
movq 0xe0(%rsp), %rcx
imulq $0xc8, 0xf0(%rsp), %rax
movq 0xe8(%rsp), %rdi
addq 0xe0(%rsp), %rdi
xorl %edx, %edx
divq %rdi
movq 0x30(%rsp), %rdx
movq %rax, %r8
leaq 0x4d8e5c(%rip), %rdi    # 0x522f19
movb $0x0, %al
callq 0x19070
jmp 0x4a3bc
testb $0x1, 0x142(%rsp)
je 0x4a171
movq 0x110(%rsp), %rdi
xorl %eax, %eax
movl %eax, %esi
callq 0x11f960
movq %rax, 0xc8(%rsp)
movq 0x110(%rsp), %rdi
movl $0x1, %esi
callq 0x11f960
movq %rax, 0xc0(%rsp)
movq 0xc8(%rsp), %rdi
callq 0x11dee0
movq %rax, 0x8(%rsp)
movq 0xc8(%rsp), %rdi
callq 0x11dfa0
movq %rax, 0x10(%rsp)
movq 0xc0(%rsp), %rdi
callq 0x11dee0
movq %rax, 0x18(%rsp)
movq 0xc0(%rsp), %rdi
callq 0x11dfa0
movq 0x8(%rsp), %rdi
movq 0x10(%rsp), %rdx
movq 0x18(%rsp), %rcx
movq %rax, %r9
xorl %eax, %eax
movl %eax, %r8d
movq %r8, %rsi
callq 0x1e1210
jmp 0x4a3ba
leaq 0x40(%rsp), %rdi
leaq 0x5ebf43(%rip), %rsi    # 0x6360c0
movl $0x70, %edx
callq 0x19610
testb $0x1, 0x140(%rsp)
je 0x4a2f2
jmp 0x4a197
movq 0x118(%rsp), %rdi
callq 0x11fcc0
cmpq $0x3, %rax
je 0x4a1e2
movq 0x5f1def(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x4cbe58(%rip), %rsi    # 0x516013
leaq 0x4d8e49(%rip), %rdx    # 0x52300b
leaq 0x4d8d02(%rip), %rcx    # 0x522ecb
leaq 0x4d8d06(%rip), %r8     # 0x522ed6
movl $0x17c, %r9d            # imm = 0x17C
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x4a1e4
callq 0x11f5c0
movq %rax, 0x120(%rsp)
callq 0x11f5c0
movq %rax, 0x128(%rsp)
movq 0x118(%rsp), %rdi
movl $0x1, %esi
callq 0x11f960
movq %rax, %rdi
callq 0xdc9e0
movq %rax, 0x100(%rsp)
movq 0x100(%rsp), %rdi
movq 0x120(%rsp), %r8
movq 0x150(%rsp), %r9
xorl %eax, %eax
movl %eax, %ecx
leaq 0x89d(%rip), %rdx       # 0x4aae0
movq %rcx, %rsi
callq 0xdc550
movq 0x118(%rsp), %rdi
movl $0x2, %esi
callq 0x11f960
movq %rax, %rdi
callq 0xdc9e0
movq %rax, 0xf8(%rsp)
movq 0xf8(%rsp), %rdi
movq 0x128(%rsp), %r8
movq 0x150(%rsp), %r9
xorl %eax, %eax
movl %eax, %ecx
leaq 0x850(%rip), %rdx       # 0x4aae0
movq %rcx, %rsi
callq 0xdc550
cmpq $0x0, 0x150(%rsp)
je 0x4a2ee
movq 0x150(%rsp), %rdi
callq 0xd8a60
testb $0x1, %al
jne 0x4a2b6
jmp 0x4a2ee
movq 0x5f1ce3(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x4cbd4c(%rip), %rsi    # 0x516013
leaq 0x4cbef1(%rip), %rdx    # 0x5161bf
leaq 0x4d8bf6(%rip), %rcx    # 0x522ecb
leaq 0x4d8bfa(%rip), %r8     # 0x522ed6
movl $0x188, %r9d            # imm = 0x188
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x4a2f0
jmp 0x4a2f2
movq $0x0, 0xb8(%rsp)
cmpq $0x7, 0xb8(%rsp)
jae 0x4a3a0
movq 0xb8(%rsp), %rcx
leaq 0x40(%rsp), %rax
shlq $0x4, %rcx
addq %rcx, %rax
movq 0x8(%rax), %rsi
leaq 0x4d8d09(%rip), %rdi    # 0x523035
movb $0x0, %al
callq 0x19070
movq 0xb8(%rsp), %rcx
leaq 0x40(%rsp), %rax
shlq $0x4, %rcx
addq %rcx, %rax
movq (%rax), %rdi
leaq 0x110(%rsp), %rsi
callq 0x4ab70
movq %rax, 0x38(%rsp)
movq 0xb8(%rsp), %rcx
leaq 0x40(%rsp), %rax
shlq $0x4, %rcx
addq %rcx, %rax
movq 0x8(%rax), %rsi
movq 0x38(%rsp), %rdx
leaq 0x4d8cbd(%rip), %rdi    # 0x52303d
movb $0x0, %al
callq 0x19070
movq 0xb8(%rsp), %rax
addq $0x1, %rax
movq %rax, 0xb8(%rsp)
jmp 0x4a2fe
movq 0x100(%rsp), %rdi
callq 0xdc4c0
movq 0xf8(%rsp), %rdi
callq 0xdc4c0
jmp 0x4a3bc
jmp 0x4a3be
leaq 0x110(%rsp), %rdi
callq 0x4af50
cmpl $0x2, 0x10c(%rsp)
jne 0x4a3e2
movl $0x0, 0x164(%rsp)
jmp 0x4a404
cmpl $0x1, 0x10c(%rsp)
jne 0x4a3f9
movl $0xffffffff, 0x164(%rsp) # imm = 0xFFFFFFFF
jmp 0x4a404
movl $0x0, 0x164(%rsp)
movl 0x164(%rsp), %eax
addq $0x168, %rsp            # imm = 0x168
retq
nopw %cs:(%rax,%rax)