// File: /workspace/github_c_makefile_star2_O1/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:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x78, %rsp
movq %rdx, %rbx
movq %rsi, 0x60(%rsp)
movl %edi, 0x38(%rsp)
testq %rdx, %rdx
je 0xb4efc
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xb58aa
testq %rbx, %rbx
je 0xb4efc
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xb58af
callq 0x121b54
movq %rax, %r14
callq 0x121b54
leaq 0x31(%rsp), %r15
movq %rax, -0x31(%r15)
callq 0x121b54
movq %rax, -0x29(%r15)
callq 0x1208f8
movq %rax, -0x9(%r15)
movq %rbx, 0x70(%rsp)
leaq 0x32(%rsp), %rbx
movb $0x0, (%rbx)
movw $0x0, -0x2(%rbx)
xorps %xmm0, %xmm0
movups %xmm0, -0x22(%rbx)
movq $0x0, -0x12(%rbx)
leaq 0x29d65b(%rip), %rdi    # 0x3525a8
leaq 0x2a60c4(%rip), %rsi    # 0x35b018
callq 0x10cc4e
movq %rax, %rbp
leaq 0x29a369(%rip), %rsi    # 0x34f2cc
movq %rax, %rdi
callq 0x10ceab
movq -0x32(%rbx), %rdx
leaq 0x33596f(%rip), %rdi    # 0x3ea8e5
leaq 0x2a3e44(%rip), %rsi    # 0x358dc1
callq 0x10f9b8
movq %rax, %r13
movq %rbp, %rdi
movq %rax, %rsi
callq 0x10cd10
movq -0x2a(%rbx), %rdx
leaq 0x2bf01a(%rip), %rdi    # 0x373fb5
leaq 0x2a3e36(%rip), %rsi    # 0x358dd8
callq 0x10f9f6
movq %rax, %r12
movq %rbp, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x2b6950(%rip), %rdi    # 0x36b90c
leaq 0x2a6079(%rip), %rsi    # 0x35b03c
movq %r14, 0x40(%rsp)
movq %r14, %rdx
callq 0x10f9b8
movq %rax, %r14
movq %rbp, %rdi
movq %rax, %rsi
callq 0x10cd10
movq -0xa(%rbx), %rdx
leaq 0x3191ba(%rip), %rdi    # 0x3ce1a3
leaq 0x2a606a(%rip), %rsi    # 0x35b05a
xorl %ecx, %ecx
callq 0x10f987
movq %rax, %r15
movq %rbp, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x2c5b73(%rip), %rdi    # 0x37ab7f
leaq 0x2a6050(%rip), %rsi    # 0x35b063
leaq 0x31(%rsp), %rdx
xorl %ecx, %ecx
callq 0x10f451
movq %rax, 0x58(%rsp)
movq %rbp, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x2e9c4f(%rip), %rdi    # 0x39ec85
leaq 0x2a6040(%rip), %rsi    # 0x35b07d
movq %rbx, %rdx
xorl %ecx, %ecx
callq 0x10f451
movq %rax, %rbx
movq %rbp, %rdi
movq %rax, %rsi
callq 0x10cd10
movq %r13, %rdi
movq %r12, %rsi
callq 0x10fd9f
movq %r13, %rdi
movq %r14, %rsi
callq 0x10fd9f
movq %r13, %rdi
movq %r15, %rsi
callq 0x10fd9f
movq %r12, %rdi
movq %r14, %rsi
callq 0x10fd9f
movq %r12, 0x50(%rsp)
movq %r12, %rdi
movq %r15, %rsi
callq 0x10fd9f
movq %r14, %rdi
movq %r15, %rsi
callq 0x10fd9f
movq 0x58(%rsp), %rdi
movq 0x70(%rsp), %r12
movq %r13, %rsi
callq 0x10fbff
movq %rbx, %rdi
movq %r13, %rsi
callq 0x10fbff
leaq 0x70308(%rip), %r8      # 0x1253c8
leaq 0x4c(%rsp), %rsi
movq %rbp, %rdi
movl 0x38(%rsp), %edx
movq 0x60(%rsp), %rcx
movq %r12, %r9
callq 0x10d796
movl %eax, %ebx
testl %eax, %eax
jne 0xb525b
movq %r15, %rbx
movq 0x50(%rsp), %r15
movq %r13, %rdi
callq 0x10fe52
testb %al, %al
je 0xb5125
movq (%rsp), %rdi
callq 0x121e78
cmpq $0x2, %rax
je 0xb5259
leaq 0x2a3ec6(%rip), %rsi    # 0x358fd7
movq %r12, %rdi
xorl %eax, %eax
callq 0x1019cf
movl $0x1, %ebx
jmp 0xb525b
movq %r15, %rdi
callq 0x10fe52
testb %al, %al
je 0xb5195
movq 0x8(%rsp), %rdi
callq 0x121e78
cmpq $0x2, %rax
je 0xb5259
movq 0x8(%rsp), %rdi
callq 0x121e78
cmpq $0x3, %rax
jne 0xb5179
movq 0x8(%rsp), %rdi
xorl %esi, %esi
callq 0x121cfa
leaq 0x2cdcc6(%rip), %rsi    # 0x382e2e
movq %rax, %rdi
callq 0x17a40
testl %eax, %eax
jne 0xb5179
movb $0x1, 0x30(%rsp)
cmpb $0x0, 0x30(%rsp)
movl $0x0, %ebx
jne 0xb525b
leaq 0x2a5f03(%rip), %rsi    # 0x35b093
jmp 0xb5111
movq %r14, %rdi
callq 0x10fe52
testb %al, %al
je 0xb5249
movq 0x40(%rsp), %r14
movq %r14, %rdi
callq 0x121e78
cmpq $0x2, %rax
jne 0xb585f
leaq 0x2a5ccb(%rip), %rsi    # 0x35ae8e
movl $0x10, %edi
movl $0xc3, %edx
callq 0x1092b2
movq %rax, 0x20(%rsp)
xorl %ebx, %ebx
movq %r14, %rdi
xorl %esi, %esi
callq 0x121d35
movq %rax, %rdi
callq 0x120e79
movq 0x20(%rsp), %rcx
movq %rax, (%rcx)
movl $0x1, %esi
movq %r14, %rdi
callq 0x121cfa
leaq 0x2d042d(%rip), %rsi    # 0x385634
leaq 0x68(%rsp), %rdx
movq %rax, %rdi
xorl %eax, %eax
callq 0x177f0
cmpl $0x1, %eax
jne 0xb5223
cmpq $0x0, 0x68(%rsp)
jg 0xb5239
leaq 0x2a5ed0(%rip), %rsi    # 0x35b0fa
movq %r12, %rdi
xorl %eax, %eax
callq 0x1019cf
movl $0x1, %ebx
movq 0x68(%rsp), %rax
movq 0x20(%rsp), %rcx
movq %rax, 0x8(%rcx)
jmp 0xb525b
movq %rbx, %rdi
callq 0x10fe52
testb %al, %al
je 0xb586b
xorl %ebx, %ebx
movq %rbp, %rdi
callq 0x10f2d0
testl %ebx, %ebx
movq %rbx, %r14
jne 0xb528e
xorl %r14d, %r14d
movl 0x38(%rsp), %eax
cmpl %eax, 0x4c(%rsp)
je 0xb528e
leaq 0x2a5edc(%rip), %rsi    # 0x35b15a
movq %r12, %rdi
xorl %eax, %eax
callq 0x1019cf
movl $0x1, %r14d
movq 0x40(%rsp), %rdi
callq 0x121e8b
testl %r14d, %r14d
jne 0xb57e5
movl 0x38(%rsp), %eax
cmpl %eax, 0x4c(%rsp)
jne 0xb58b4
movq (%rsp), %rdi
callq 0x121e78
testq %rax, %rax
je 0xb52f0
cmpb $0x0, 0x31(%rsp)
jne 0xb5388
movq (%rsp), %rdi
xorl %esi, %esi
callq 0x121cfa
movq %rax, %rbx
movq (%rsp), %rdi
movl $0x1, %esi
callq 0x121cfa
leaq 0x2a5e8e(%rip), %rdi    # 0x35b179
jmp 0xb537b
movq 0x8(%rsp), %rdi
callq 0x121e78
testq %rax, %rax
je 0xb5330
movq 0x8(%rsp), %rdi
cmpb $0x1, 0x30(%rsp)
jne 0xb535b
movl $0x1, %esi
callq 0x121cfa
movq %rax, %rbx
movq 0x8(%rsp), %rdi
movl $0x2, %esi
callq 0x121cfa
leaq 0x2a5e64(%rip), %rdi    # 0x35b192
jmp 0xb537b
movq 0x20(%rsp), %rax
testq %rax, %rax
je 0xb5877
movq (%rax), %rdi
callq 0x120d23
movq 0x20(%rsp), %rcx
movq 0x8(%rcx), %rdx
leaq 0x2a5e70(%rip), %rdi    # 0x35b1c6
movq %rax, %rsi
jmp 0xb5381
xorl %esi, %esi
callq 0x121cfa
movq %rax, %rbx
movq 0x8(%rsp), %rdi
movl $0x1, %esi
callq 0x121cfa
leaq 0x2a5e34(%rip), %rdi    # 0x35b1af
movq %rbx, %rsi
movq %rax, %rdx
xorl %eax, %eax
callq 0x17070
cmpb $0x1, 0x31(%rsp)
jne 0xb5434
movq %r14, %r13
movq (%rsp), %rdi
callq 0x121e78
cmpq $0x1, %rax
jbe 0xb58b9
movq (%rsp), %rdi
xorl %esi, %esi
callq 0x121d35
movq %rax, %r15
movq (%rsp), %rdi
movl $0x1, %esi
callq 0x121d35
movq %rax, %r12
movq %r15, %rdi
callq 0x120d4c
movq %rax, %r14
movq %r12, %rdi
callq 0x120d4c
movq %rax, %rbx
movq %r15, %rdi
callq 0x120d23
movq %rax, %r15
movq %r12, %rdi
callq 0x120d23
movq %r15, %rdi
movq %r14, %rsi
movq %rax, %rdx
movq %rbx, %rcx
callq 0x20a6c2
movq %rax, %rsi
imulq $0xc8, %rax, %rax
leaq (%rbx,%r14), %rcx
xorl %edx, %edx
divq %rcx
leaq 0x2a5ab5(%rip), %rdi    # 0x35aed1
movq %r14, %rdx
movq %rbx, %rcx
movq %rax, %r8
xorl %eax, %eax
callq 0x17070
movq %r13, %r14
jmp 0xb57e5
movq %r14, 0x60(%rsp)
cmpb $0x1, 0x32(%rsp)
jne 0xb54a3
movq (%rsp), %rdi
xorl %esi, %esi
callq 0x121d35
movq %rax, %rbx
movq (%rsp), %rdi
movl $0x1, %esi
callq 0x121d35
movq %rax, %r14
movq %rbx, %rdi
callq 0x120d23
movq %rax, %r15
movq %rbx, %rdi
callq 0x120d4c
movq %rax, %rbx
movq %r14, %rdi
callq 0x120d23
movq %rax, %r12
movq %r14, %rdi
callq 0x120d4c
movq %r15, %rdi
xorl %esi, %esi
movq %rbx, %rdx
movq %r12, %rcx
xorl %r8d, %r8d
movq %rax, %r9
callq 0x1820b7
jmp 0xb57e0
cmpb $0x1, 0x30(%rsp)
jne 0xb555f
movq 0x8(%rsp), %rdi
callq 0x121e78
cmpq $0x3, %rax
jne 0xb58c3
callq 0x121b54
movq %rax, 0x10(%rsp)
callq 0x121b54
movq %rax, 0x18(%rsp)
movq 0x8(%rsp), %rdi
movl $0x1, %esi
callq 0x121d35
movq %rax, %rdi
callq 0x103703
movq %rax, %r14
movq 0x10(%rsp), %r8
leaq 0x3cc(%rip), %rbx       # 0xb58c8
movq %rax, %rdi
xorl %esi, %esi
movq %rbx, %rdx
xorl %ecx, %ecx
movq %r12, %r9
callq 0x1032b8
movq 0x8(%rsp), %rdi
movl $0x2, %esi
callq 0x121d35
movq %rax, %rdi
callq 0x103703
movq %rax, %r15
movq 0x18(%rsp), %r8
movq %rax, %rdi
xorl %esi, %esi
movq %rbx, %rdx
xorl %ecx, %ecx
movq %r12, %r9
callq 0x1032b8
testq %r12, %r12
movq %r14, 0x58(%rsp)
movq %r15, 0x50(%rsp)
je 0xb5571
movq %r12, %rdi
callq 0x101a9a
testb %al, %al
je 0xb5571
callq 0x1d3b5
movq $0x0, 0x50(%rsp)
movq $0x0, 0x58(%rsp)
xorl %r14d, %r14d
movq %r14, %rax
shlq $0x4, %rax
leaq 0x408e2e(%rip), %rcx    # 0x4be3b0
movq (%rax,%rcx), %r15
movq 0x8(%rax,%rcx), %r12
leaq 0x2a5a5b(%rip), %rdi    # 0x35afed
movq %r12, %rsi
xorl %eax, %eax
callq 0x17070
movq (%rsp), %rdi
callq 0x121e78
testq %rax, %rax
je 0xb563e
movq %r12, 0x40(%rsp)
movq %r14, 0x38(%rsp)
movb $0x1, %r13b
movq (%rsp), %rdi
xorl %esi, %esi
callq 0x121cfa
movq %rax, %r14
movq (%rsp), %rdi
xorl %esi, %esi
callq 0x121cfa
movq %rax, %rdi
callq 0x172f0
movq %rax, %rbx
movq (%rsp), %rdi
movl $0x1, %esi
callq 0x121cfa
movq %rax, %r12
movq (%rsp), %rdi
movl $0x1, %esi
callq 0x121cfa
movq %rax, %rdi
callq 0x172f0
movzbl %r13b, %ebp
movl %ebp, %edi
andl $0x1, %edi
movq %r14, %rsi
movq %rbx, %rdx
movq %r12, %rcx
movq %rax, %r8
callq *%r15
movl $0x0, %r13d
testb $0x1, %bpl
jne 0xb55bb
movl $0x2, %edx
movq 0x38(%rsp), %r14
movq 0x40(%rsp), %r12
jmp 0xb57ae
movq 0x8(%rsp), %rdi
callq 0x121e78
testq %rax, %rax
je 0xb5728
cmpb $0x1, 0x30(%rsp)
jne 0xb5750
movq 0x10(%rsp), %rdi
callq 0x121e78
movl $0x2, %edx
testq %rax, %rax
je 0xb57ae
movq %r12, 0x40(%rsp)
movq %r14, 0x38(%rsp)
xorl %r14d, %r14d
movq 0x18(%rsp), %rdi
callq 0x121e78
testq %rax, %rax
je 0xb5706
xorl %r13d, %r13d
movq 0x10(%rsp), %rdi
movq %r14, %rsi
callq 0x121cfa
movq %rax, %rbx
movq 0x10(%rsp), %rdi
movq %r14, %rsi
callq 0x121cfa
movq %rax, %rdi
callq 0x172f0
movq %rax, %rbp
movq 0x18(%rsp), %rdi
movq %r13, %rsi
callq 0x121cfa
movq %rax, %r12
movq 0x18(%rsp), %rdi
movq %r13, %rsi
callq 0x121cfa
movq %rax, %rdi
callq 0x172f0
movl $0x1, %edi
movq %rbx, %rsi
movq %rbp, %rdx
movq %r12, %rcx
movq %rax, %r8
callq *%r15
incq %r13
movq 0x18(%rsp), %rdi
callq 0x121e78
cmpq %rax, %r13
jb 0xb5693
incq %r14
movq 0x10(%rsp), %rdi
callq 0x121e78
cmpq %rax, %r14
jb 0xb5681
movq 0x38(%rsp), %r14
movq 0x40(%rsp), %r12
jmp 0xb577c
movq 0x20(%rsp), %rax
testq %rax, %rax
je 0xb5783
movq (%rax), %rdi
callq 0x120d23
movq 0x20(%rsp), %rcx
movq 0x8(%rcx), %rdx
movq %r15, %rdi
movq %rax, %rsi
callq 0x20a526
jmp 0xb57ab
movq 0x8(%rsp), %rdi
xorl %esi, %esi
callq 0x121cfa
movq %rax, %rbx
movq 0x8(%rsp), %rdi
movl $0x1, %esi
callq 0x121cfa
movq %r15, %rdi
movq %rbx, %rsi
movq %rax, %rdx
callq 0x20a3a4
movl $0x2, %edx
jmp 0xb57ae
movq 0x28(%rsp), %rdi
callq 0x120d4c
testq %rax, %rax
je 0xb58be
movq 0x28(%rsp), %rdi
callq 0x120d23
movq %r15, %rdi
movq %rax, %rsi
callq 0x20a467
movq %rax, %rdx
leaq 0x2a5840(%rip), %rdi    # 0x35aff5
movq %r12, %rsi
xorl %eax, %eax
callq 0x17070
incq %r14
cmpq $0x7, %r14
jne 0xb5574
movq 0x58(%rsp), %rdi
callq 0x10327d
movq 0x50(%rsp), %rdi
callq 0x10327d
movq 0x60(%rsp), %r14
movq (%rsp), %rdi
callq 0x121e8b
movq 0x8(%rsp), %rdi
callq 0x121e8b
movq 0x28(%rsp), %rdi
callq 0x121b03
movq 0x20(%rsp), %rax
testq %rax, %rax
je 0xb582a
movq (%rax), %rdi
callq 0x121b03
movq 0x20(%rsp), %rdi
leaq 0x2a566e(%rip), %rsi    # 0x35ae8e
movl $0xee, %edx
callq 0x109670
cmpb $0x1, 0x30(%rsp)
jne 0xb5845
movq 0x10(%rsp), %rdi
callq 0x121e8b
movq 0x18(%rsp), %rdi
callq 0x121e8b
xorl %eax, %eax
cmpl $0x1, %r14d
sete %al
negl %eax
addq $0x78, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
leaq 0x2a5894(%rip), %rsi    # 0x35b0fa
jmp 0xb5111
leaq 0x2a58b8(%rip), %rsi    # 0x35b12a
jmp 0xb5111
movq 0x28(%rsp), %rdi
callq 0x120d4c
testq %rax, %rax
je 0xb5388
movq 0x28(%rsp), %rdi
callq 0x120d23
leaq 0x2a5940(%rip), %rdi    # 0x35b1db
movq %rax, %rsi
xorl %eax, %eax
callq 0x17070
jmp 0xb5388
callq 0x1d30a
callq 0x1d2d3
callq 0x1d343
callq 0x1d427
callq 0x1d3ee
callq 0x1d37c