LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_sortbench.c
// Function: gt_sortbench_cmp
static int gt_sortbench_cmp(const void *px, const void *py)
{
  const GtUword x = *(const GtUword*)px;
  const GtUword y = *(const GtUword*)py;
  ncmp++;
  if (val[x]==gas && val[y]==gas) {
    if (x == candidate) {
      freeze(x);
    } else {
      freeze(y);
    }
  }
  if (val[x] == gas)
    candidate = x;
  else if (val[y] == gas)
    candidate = y;
  if (val[x] < val[y])
  {
    return -1;
  }
  if (val[x] > val[y])
  {
    return 1;
  }
  return 0;
}

// Assembly:
pushq %rbx
movq (%rdi), %rdx
movq (%rsi), %rax
leaq 0x3fba89(%rip), %rcx    # 0x4c9478
incq (%rcx)
leaq 0x3fba77(%rip), %rcx    # 0x4c9470
movq (%rcx), %rcx
leaq (%rcx,%rdx,8), %rsi
leaq 0x3fba89(%rip), %rdi    # 0x4c9490
movq (%rdi), %r8
cmpq %r8, (%rsi)
jne 0xcda3b
cmpq %r8, (%rcx,%rax,8)
jne 0xcda3b
leaq (%rcx,%rax,8), %r8
leaq 0x3fba68(%rip), %r9     # 0x4c9488
leaq 0x3fba59(%rip), %r10    # 0x4c9480
movq (%r10), %r11
leaq 0x1(%r11), %rbx
cmpq (%r9), %rdx
movq %rbx, (%r10)
cmoveq %rsi, %r8
movq %r11, (%r8)
movq (%rdi), %rdi
cmpq %rdi, (%rsi)
je 0xcda4c
movq %rax, %rdx
cmpq %rdi, (%rcx,%rax,8)
jne 0xcda56
leaq 0x3fba35(%rip), %rdi    # 0x4c9488
movq %rdx, (%rdi)
movq (%rsi), %rdx
xorl %esi, %esi
cmpq (%rcx,%rax,8), %rdx
seta %sil
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
cmovael %esi, %eax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_speck.c
// Function: gt_speck_arguments_new
static void *gt_speck_arguments_new(void)
{
  SpeccheckArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->specfile = gt_str_new();
  arguments->format = gt_str_new();
  arguments->s2fi = gt_seqid2file_info_new();
  arguments->ofi = gt_output_file_info_new();
  arguments->tci = gt_typecheck_info_new();
  arguments->outfp = NULL;
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x295fef(%rip), %rdx    # 0x3649b3
movl $0x1, %edi
movl $0x38, %esi
movl $0x38, %ecx
callq 0x1093ef
movq %rax, %rbx
callq 0x1208f8
movq %rax, (%rbx)
callq 0x1208f8
movq %rax, 0x8(%rbx)
callq 0x17b020
movq %rax, 0x18(%rbx)
callq 0x10ff7c
movq %rax, 0x20(%rbx)
callq 0x18b9bc
movq %rax, 0x28(%rbx)
movq $0x0, 0x30(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_speck.c
// Function: gt_speck_arguments_delete
static void gt_speck_arguments_delete(void *tool_arguments)
{
  SpeccheckArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->specfile);
  gt_str_delete(arguments->format);
  gt_file_delete(arguments->outfp);
  gt_seqid2file_info_delete(arguments->s2fi);
  gt_output_file_info_delete(arguments->ofi);
  gt_typecheck_info_delete(arguments->tci);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xcea67
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x121b03
movq 0x8(%rbx), %rdi
callq 0x121b03
movq 0x30(%rbx), %rdi
callq 0x1040fc
movq 0x18(%rbx), %rdi
callq 0x17b067
movq 0x20(%rbx), %rdi
callq 0x110231
movq 0x28(%rbx), %rdi
callq 0x18b9e8
leaq 0x295f5a(%rip), %rsi    # 0x3649b3
movq %rbx, %rdi
movl $0x4c, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_speck.c
// Function: gt_speck_arguments_check
static int gt_speck_arguments_check(GT_UNUSED int rest_argc,
                                    void *tool_arguments,
                                    GT_UNUSED GtError *err)
{
  SpeccheckArguments *arguments = tool_arguments;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(arguments);

  if ((arguments->outfp || (!arguments->outfp && !isatty(STDOUT_FILENO)))
      && arguments->colored) {
    gt_warning("not printing to terminal, disabling colored output");
    arguments->colored = false;
  }

  return had_err = 0;
}

// Assembly:
pushq %rbx
movq %rsi, %rbx
testq %rdx, %rdx
je 0xcebd6
movq %rdx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xcec13
testq %rbx, %rbx
je 0xcec0e
cmpq $0x0, 0x30(%rbx)
je 0xcebfc
cmpb $0x1, 0x11(%rbx)
jne 0xcec0a
leaq 0x295fd3(%rip), %rdi    # 0x364bc2
xorl %eax, %eax
callq 0x125448
movb $0x0, 0x11(%rbx)
jmp 0xcec0a
movl $0x1, %edi
callq 0x17d80
testl %eax, %eax
je 0xcebe2
xorl %eax, %eax
popq %rbx
retq
callq 0x212d3
callq 0x2129a
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_speck.c
// Function: gt_speck_record_warning
static void gt_speck_record_warning(void *data, const char *format, va_list ap)
{
  char buf[BUFSIZ];
  gt_assert(data && format);
  (void) vsnprintf(buf, (BUFSIZ * sizeof (char)), format, ap);
  gt_spec_results_record_warning((GtSpecResults*) data, buf);
}

// Assembly:
pushq %r14
pushq %rbx
subq $0x2008, %rsp           # imm = 0x2008
testq %rdi, %rdi
je 0xcf1b3
movq %rdx, %rcx
movq %rsi, %rdx
testq %rsi, %rsi
je 0xcf1b3
movq %rdi, %rbx
movq %rsp, %r14
movl $0x2000, %esi           # imm = 0x2000
movq %r14, %rdi
callq 0x17480
movq %rbx, %rdi
movq %r14, %rsi
callq 0x17e329
addq $0x2008, %rsp           # imm = 0x2008
popq %rbx
popq %r14
retq
callq 0x2149b
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_splicesiteinfo.c
// Function: gt_splicesiteinfo_arguments_new
static void* gt_splicesiteinfo_arguments_new(void)
{
  SpliceSiteInfoArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->s2fi = gt_seqid2file_info_new();
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x295a90(%rip), %rdx    # 0x364c73
movl $0x1, %edi
movl $0x20, %esi
movl $0x28, %ecx
callq 0x1093ef
movq %rax, %rbx
callq 0x17b020
movq %rax, 0x8(%rbx)
callq 0x10ff7c
movq %rax, 0x10(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_splicesiteinfo.c
// Function: gt_splicesiteinfo_arguments_delete
static void gt_splicesiteinfo_arguments_delete(void *tool_arguments)
{
  SpliceSiteInfoArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_seqid2file_info_delete(arguments->s2fi);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xcf24a
pushq %rbx
movq %rdi, %rbx
movq 0x18(%rdi), %rdi
callq 0x1040fc
movq 0x10(%rbx), %rdi
callq 0x110231
movq 0x8(%rbx), %rdi
callq 0x17b067
leaq 0x295a37(%rip), %rsi    # 0x364c73
movq %rbx, %rdi
movl $0x35, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_splicesiteinfo.c
// Function: gt_splicesiteinfo_option_parser_new
static GtOptionParser* gt_splicesiteinfo_option_parser_new(void *tool_arguments)
{
  SpliceSiteInfoArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  op = gt_option_parser_new("[option ...] [GFF3_file ...]", "Show information "
                            "about splice sites given in GFF3 files.");

  /* -seqfile, -matchdesc, -usedesc and -regionmapping */
  gt_seqid2file_register_options(op, arguments->s2fi);

  /* -addintrons */
  option = gt_option_new_bool("addintrons", "add intron features between "
                              "existing exon features\n(before computing the "
                              "information to be shown)",
                              &arguments->addintrons, false);
  gt_option_parser_add_option(op, option);

  /* output file options */
  gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);

  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);

  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xcf2cb
movq %rdi, %rbx
leaq 0x2842ab(%rip), %rdi    # 0x353509
leaq 0x295a50(%rip), %rsi    # 0x364cb5
callq 0x10cc4e
movq %rax, %r14
movq 0x8(%rbx), %rsi
movq %rax, %rdi
callq 0x17b366
leaq 0x287c41(%rip), %rdi    # 0x356ec1
leaq 0x295a67(%rip), %rsi    # 0x364cee
movq %rbx, %rdx
xorl %ecx, %ecx
callq 0x10f451
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
movq 0x10(%rbx), %rdi
addq $0x18, %rbx
movq %r14, %rsi
movq %rbx, %rdx
callq 0x10ffa3
leaq 0x84be6(%rip), %rsi     # 0x153e9c
movq %r14, %rdi
xorl %edx, %edx
callq 0x10cd8d
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x214d4
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_stat.c
// Function: gt_stat_arguments_delete
static void gt_stat_arguments_delete(void *tool_arguments)
{
  StatArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xcfba8
pushq %rbx
movq %rdi, %rbx
movq 0x18(%rdi), %rdi
callq 0x1040fc
movq 0x10(%rbx), %rdi
callq 0x110231
leaq 0x295458(%rip), %rsi    # 0x364ff2
movq %rbx, %rdi
movl $0x37, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_stat.c
// Function: gt_stat_runner
static int gt_stat_runner(int argc, const char **argv, int parsed_args,
                          void *tool_arguments, GtError *err)
{
  StatArguments *arguments = tool_arguments;
  GtNodeStream *gff3_in_stream, *sort_stream, *add_introns_stream = NULL,
               *stat_stream;
  int had_err;
  gt_error_check(err);

  /* create a gff3 input stream */
  gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
                                                  argv + parsed_args);
  if (arguments->verbose)
    gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) gff3_in_stream);

  /* create add introns stream if -addintrons was used */
  if (arguments->addintrons) {
    sort_stream = gt_sort_stream_new(gff3_in_stream);
    add_introns_stream = gt_add_introns_stream_new(sort_stream);
  }

  /* create stat stream */
  stat_stream = gt_stat_stream_new(arguments->addintrons
                                   ? add_introns_stream : gff3_in_stream,
                                   arguments->gene_length_distribution,
                                   arguments->gene_score_distribution,
                                   arguments->exon_length_distribution,
                                   arguments->exon_number_distribution,
                                   arguments->intron_length_distribution,
                                   arguments->cds_length_distribution,
                                   arguments->used_sources);

  /* pull the features through the stream , compute the statistics, and free
     them afterwards */
  had_err = gt_node_stream_pull(stat_stream, err);

  /* show statistics */
  if (!had_err)
    gt_stat_stream_show_stats((GtStatStream*) stat_stream, arguments->outfp);

  /* free */
  gt_node_stream_delete(stat_stream);
  gt_node_stream_delete(gff3_in_stream);

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movq %r8, %r14
movq %rcx, %rbx
movl %edx, %r12d
movq %rsi, %r15
movl %edi, %ebp
testq %r8, %r8
je 0xcfd42
movq %r14, %rdi
callq 0x101a9a
testb %al, %al
jne 0xcfdee
subl %r12d, %ebp
movslq %r12d, %rax
leaq (%r15,%rax,8), %rsi
movl %ebp, %edi
callq 0x14d00b
movq %rax, %r15
cmpb $0x1, 0x8(%rbx)
jne 0xcfd64
movq %r15, %rdi
callq 0x14ce62
cmpb $0x1, 0x7(%rbx)
jne 0xcfd7c
movq %r15, %rdi
callq 0x17e1d7
movq %rax, %rdi
callq 0x126660
jmp 0xcfd7e
xorl %eax, %eax
cmpb $0x0, 0x7(%rbx)
movq %r15, %rdi
cmovneq %rax, %rdi
movzbl (%rbx), %esi
movzbl 0x1(%rbx), %edx
movzbl 0x3(%rbx), %ecx
movzbl 0x2(%rbx), %r8d
movzbl 0x4(%rbx), %r9d
movzbl 0x5(%rbx), %eax
movzbl 0x6(%rbx), %r10d
pushq %r10
pushq %rax
callq 0x182cae
addq $0x10, %rsp
movq %rax, %r12
movq %rax, %rdi
movq %r14, %rsi
callq 0x16adca
movl %eax, %ebp
testl %eax, %eax
jne 0xcfdd3
movq 0x18(%rbx), %rsi
movq %r12, %rdi
callq 0x182d3e
movq %r12, %rdi
callq 0x16ac6e
movq %r15, %rdi
callq 0x16ac6e
movl %ebp, %eax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
callq 0x217e4
nop
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_tagerator.c
// Function: gt_tagerator_arguments_new
static void *gt_tagerator_arguments_new(void)
{
  TageratorOptions *arguments;

  arguments = gt_malloc(sizeof (TageratorOptions));
  arguments->indexname = gt_str_new();
  arguments->tagfiles = gt_str_array_new();
  arguments->outputspec = gt_str_array_new();
  arguments->outputmode = 0;
  arguments->numberofmodedescentries = sizeof (outputmodedesctable)/
                                       sizeof (outputmodedesctable[0]);
  arguments->outputhelp
    = gt_getargmodekeywords(outputmodedesctable,
                            arguments->numberofmodedescentries,
                            "output");
  arguments->modedesc = outputmodedesctable;
  return arguments;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
leaq 0x2953dc(%rip), %rsi    # 0x36523b
movl $0x68, %edi
movl $0x30, %edx
callq 0x1092b2
movq %rax, %rbx
callq 0x1208f8
movq %rax, 0x10(%rbx)
callq 0x121b54
movq %rax, (%rbx)
callq 0x121b54
movq %rax, 0x8(%rbx)
movl $0x0, 0x54(%rbx)
movq $0xb, 0x60(%rbx)
leaq 0x3ee6bf(%rip), %r14    # 0x4be560
leaq 0x2a53cf(%rip), %rdx    # 0x375277
movl $0xb, %esi
movq %r14, %rdi
callq 0x1c0a85
movq %rax, 0x18(%rbx)
movq %r14, 0x30(%rbx)
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_tagerator.c
// Function: gt_tagerator_arguments_delete
static void gt_tagerator_arguments_delete(void *tool_arguments)
{
  TageratorOptions *arguments = tool_arguments;

  if (!arguments)
  {
    return;
  }
  gt_str_delete(arguments->indexname);
  gt_str_delete(arguments->outputhelp);
  gt_str_array_delete(arguments->tagfiles);
  gt_str_array_delete(arguments->outputspec);
  gt_option_delete(arguments->refoptionesaindex);
  gt_option_delete(arguments->refoptionpckindex);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xcff1b
pushq %rbx
movq %rdi, %rbx
movq 0x10(%rdi), %rdi
callq 0x121b03
movq 0x18(%rbx), %rdi
callq 0x121b03
movq (%rbx), %rdi
callq 0x121e8b
movq 0x8(%rbx), %rdi
callq 0x121e8b
movq 0x20(%rbx), %rdi
callq 0x10f386
movq 0x28(%rbx), %rdi
callq 0x10f386
leaq 0x29532e(%rip), %rsi    # 0x36523b
movq %rbx, %rdi
movl $0x4d, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_tallymer.c
// Function: gt_tyr_arguments_new
static void *gt_tyr_arguments_new(void)
{
  GtToolbox *tyr_toolbox = gt_toolbox_new();
  gt_toolbox_add_tool(tyr_toolbox, "mkindex", gt_tyr_mkindex());
  gt_toolbox_add_tool(tyr_toolbox, "occratio", gt_tyr_occratio());
  gt_toolbox_add_tool(tyr_toolbox, "search", gt_tyr_search());
  return tyr_toolbox;
}

// Assembly:
pushq %rbx
callq 0x12391a
movq %rax, %rbx
leaq 0x21f(%rip), %rdi       # 0xd074a
leaq 0x249(%rip), %rsi       # 0xd077b
leaq 0x27c(%rip), %rdx       # 0xd07b5
leaq 0x485(%rip), %rcx       # 0xd09c5
leaq 0x4da(%rip), %r8        # 0xd0a21
callq 0x1233ec
leaq 0x289ede(%rip), %rsi    # 0x35a431
movq %rbx, %rdi
movq %rax, %rdx
callq 0x12394f
leaq 0x6bb(%rip), %rdi       # 0xd0c20
leaq 0x6fc(%rip), %rsi       # 0xd0c68
leaq 0x754(%rip), %rdx       # 0xd0cc7
leaq 0x8f9(%rip), %rcx       # 0xd0e73
leaq 0xcce(%rip), %r8        # 0xd124f
callq 0x1233ec
leaq 0x2952cd(%rip), %rsi    # 0x36585a
movq %rbx, %rdi
movq %rax, %rdx
callq 0x12394f
leaq 0x1080(%rip), %rdi      # 0xd161f
leaq 0x10c3(%rip), %rsi      # 0xd1669
leaq 0x10fe(%rip), %rdx      # 0xd16ab
leaq 0x1219(%rip), %rcx      # 0xd17cd
leaq 0x130f(%rip), %r8       # 0xd18ca
callq 0x1233ec
leaq 0x280b53(%rip), %rsi    # 0x35111a
movq %rbx, %rdi
movq %rax, %rdx
callq 0x12394f
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_tallymer.c
// Function: gt_tyr_option_parser_new
static GtOptionParser* gt_tyr_option_parser_new(void *tool_arguments)
{
  GtToolbox *index_toolbox = tool_arguments;
  GtOptionParser *op;

  gt_assert(index_toolbox != NULL);
  op = gt_option_parser_new(
                    "[option ...] tallymer_tool [argument ...]",
                    "Call a tallymer subtool and pass argument(s) to it.");
  gt_option_parser_set_comment_func(op, gt_toolbox_show, index_toolbox);
  gt_option_parser_set_min_args(op, 1U);
  gt_option_parser_refer_to_manual(op);
  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xd0635
movq %rdi, %rbx
leaq 0x295d64(%rip), %rdi    # 0x366358
leaq 0x295d87(%rip), %rsi    # 0x366382
callq 0x10cc4e
movq %rax, %r14
leaq 0x534a4(%rip), %rsi     # 0x123aae
movq %rax, %rdi
movq %rbx, %rdx
callq 0x10cd8d
movq %r14, %rdi
movl $0x1, %esi
callq 0x10d766
movq %r14, %rdi
callq 0x10cd7d
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x2196f
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_tallymer.c
// Function: gt_tyr_mkindex_arguments_new
static void *gt_tyr_mkindex_arguments_new(void)
{
  Tyr_mkindex_options *arguments
    = gt_malloc(sizeof (Tyr_mkindex_options));
  arguments->str_storeindex = gt_str_new();
  arguments->str_inputindex = gt_str_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x295111(%rip), %rsi    # 0x365863
movl $0x48, %edi
movl $0x48, %edx
callq 0x1092b2
movq %rax, %rbx
callq 0x1208f8
movq %rax, 0x30(%rbx)
callq 0x1208f8
movq %rax, 0x38(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_tallymer.c
// Function: gt_tyr_mkindex_arguments_delete
static void gt_tyr_mkindex_arguments_delete(void *tool_arguments)
{
  Tyr_mkindex_options *arguments = tool_arguments;

  if (!arguments)
  {
    return;
  }
  gt_str_delete(arguments->str_storeindex);
  gt_str_delete(arguments->str_inputindex);
  gt_option_delete(arguments->refoptionpl);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xd07b4
pushq %rbx
movq %rdi, %rbx
movq 0x30(%rdi), %rdi
callq 0x121b03
movq 0x38(%rbx), %rdi
callq 0x121b03
movq 0x28(%rbx), %rdi
callq 0x10f386
leaq 0x2950bd(%rip), %rsi    # 0x365863
movq %rbx, %rdi
movl $0x59, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_tallymer.c
// Function: gt_tyr_occratio_arguments_new
static void *gt_tyr_occratio_arguments_new(void)
{
  Tyr_occratio_options *arguments
    = gt_malloc(sizeof (Tyr_occratio_options));
  arguments->mersizesstrings = gt_str_array_new();
  arguments->outputspec = gt_str_array_new();
  arguments->str_inputindex = gt_str_new();
  arguments->outputvector = NULL;
  arguments->outputmode = 0;
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x294c3b(%rip), %rsi    # 0x365863
movl $0x48, %edi
movl $0x142, %edx            # imm = 0x142
callq 0x1092b2
movq %rax, %rbx
callq 0x121b54
movq %rax, (%rbx)
callq 0x121b54
movq %rax, 0x8(%rbx)
callq 0x1208f8
movq %rax, 0x10(%rbx)
movq $0x0, 0x38(%rbx)
movl $0x0, 0x40(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_tallymer.c
// Function: gt_tyr_occratio_arguments_delete
static void gt_tyr_occratio_arguments_delete(void *tool_arguments)
{
  Tyr_occratio_options *arguments = tool_arguments;

  if (!arguments)
  {
    return;
  }
  gt_str_array_delete(arguments->mersizesstrings);
  gt_str_array_delete(arguments->outputspec);
  gt_str_delete(arguments->str_inputindex);
  gt_option_delete(arguments->refoptionmersizes);
  gt_free(arguments->outputvector);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xd0cc6
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x121e8b
movq 0x8(%rbx), %rdi
callq 0x121e8b
movq 0x10(%rbx), %rdi
callq 0x121b03
movq 0x18(%rbx), %rdi
callq 0x10f386
movq 0x38(%rbx), %rdi
leaq 0x294bc1(%rip), %r14    # 0x365863
movq %r14, %rsi
movl $0x157, %edx            # imm = 0x157
callq 0x109670
movq %rbx, %rdi
movq %r14, %rsi
movl $0x158, %edx            # imm = 0x158
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_tallymer.c
// Function: showitvdistribution
static void showitvdistribution(const GtArrayuint64_t *dist,
                                const GtBitsequence *outputvector)
{
  GtUword idx;

  gt_assert(outputvector != NULL);
  for (idx=0; idx < dist->nextfreeuint64_t; idx++)
  {
    if (GT_ISIBITSET(outputvector,idx) && dist->spaceuint64_t[idx] > 0)
    {
      /*@ignore@*/
      printf(""GT_WU" " Formatuint64_t "\n",
              idx,
              PRINTuint64_tcast(dist->spaceuint64_t[idx]));
      /*@end@*/
    }
  }
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
testq %rsi, %rsi
je 0xd161a
movq %rdi, %r14
cmpq $0x0, 0x10(%rdi)
je 0xd160e
movq %rsi, %rbx
leaq 0x2b9bd9(%rip), %r15    # 0x38b1ab
xorl %r12d, %r12d
movq %r12, %rax
shrq $0x6, %rax
movq (%rbx,%rax,8), %rax
movl %r12d, %ecx
shlq %cl, %rax
shrq $0x3f, %rax
je 0xd1605
movq (%r14), %rax
movq (%rax,%r12,8), %rdx
testq %rdx, %rdx
je 0xd1605
movq %r15, %rdi
movq %r12, %rsi
xorl %eax, %eax
callq 0x17070
incq %r12
cmpq 0x10(%r14), %r12
jb 0xd15d5
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
callq 0x21ac5
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_tallymer.c
// Function: gt_tyr_search_arguments_new
static void *gt_tyr_search_arguments_new(void)
{
  Tyr_search_options *arguments
    = gt_malloc(sizeof (Tyr_search_options));
  arguments->str_inputindex = gt_str_new();
  arguments->strandspec = gt_str_new();
  arguments->queryfilenames = gt_str_array_new();
  arguments->showmodespec = gt_str_array_new();
  arguments->showmode = 0;
  arguments->strand = 0;
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x29423c(%rip), %rsi    # 0x365863
movl $0x30, %edi
movl $0x326, %edx            # imm = 0x326
callq 0x1092b2
movq %rax, %rbx
callq 0x1208f8
movq %rax, (%rbx)
callq 0x1208f8
movq %rax, 0x10(%rbx)
callq 0x121b54
movq %rax, 0x8(%rbx)
callq 0x121b54
movq %rax, 0x18(%rbx)
movq $0x0, 0x20(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_tallymer.c
// Function: gt_tyr_search_arguments_delete
static void gt_tyr_search_arguments_delete(void *tool_arguments)
{
  Tyr_search_options *arguments = tool_arguments;

  if (!arguments)
  {
    return;
  }
  gt_str_delete(arguments->str_inputindex);
  gt_str_delete(arguments->strandspec);
  gt_str_array_delete(arguments->queryfilenames);
  gt_str_array_delete(arguments->showmodespec);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xd16aa
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x121b03
movq 0x10(%rbx), %rdi
callq 0x121b03
movq 0x8(%rbx), %rdi
callq 0x121e8b
movq 0x18(%rbx), %rdi
callq 0x121e8b
leaq 0x2941c7(%rip), %rsi    # 0x365863
movq %rbx, %rdi
movl $0x33c, %edx            # imm = 0x33C
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_tallymer.c
// Function: gt_tyr_search_arguments_check
static int gt_tyr_search_arguments_check(int rest_argc,
                                         void *tool_arguments,
                                         GtError *err)
{
  Optionargmodedesc showmodedesctable[] =
  {
    {"qseqnum","query sequence number",SHOWQSEQNUM},
    {"qpos","query position",SHOWQPOS},
    {"counts","number of occurrence counts",SHOWCOUNTS},
    {"sequence","mer-sequence",SHOWSEQUENCE}
  };

  Optionargmodedesc stranddesctable[] =
  {
    {"f","forward strand",STRAND_FORWARD},
    {"p","reverse strand",STRAND_REVERSE},
    {"fp","forward and reverse strand",STRAND_FORWARD | STRAND_REVERSE}
  };
  GtUword idx;
  Tyr_search_options *arguments = tool_arguments;

  if (rest_argc != 0)
  {
    gt_error_set(err,"superfluous arguments");
    return -1;
  }
  for (idx=0; idx<gt_str_array_size(arguments->showmodespec); idx++)
  {
    if (gt_optionargaddbitmask(showmodedesctable,
                         sizeof (showmodedesctable)/
                         sizeof (showmodedesctable[0]),
                         &arguments->showmode,
                         "-output",
                         gt_str_array_get(arguments->showmodespec,idx),
                         err) != 0)
    {
      return -1;
    }
  }
  if (gt_optionargaddbitmask(stranddesctable,
                          sizeof (stranddesctable)/
                          sizeof (stranddesctable[0]),
                          &arguments->strand,
                          "-output",
                          gt_str_get(arguments->strandspec),err) != 0)
  {
    return -1;
  }
  return 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0xb8, %rsp
movq %rdx, %rbx
movq %rsi, %r14
movl %edi, %eax
leaq 0x3ecf03(%rip), %rsi    # 0x4be6f0
leaq 0x50(%rsp), %rdi
movl $0xc, %ecx
rep  movsq (%rsi), %es:(%rdi)
leaq 0x3ecf4f(%rip), %rsi    # 0x4be750
movq %rsp, %rdi
movl $0x9, %ecx
rep  movsq (%rsi), %es:(%rdi)
testl %eax, %eax
je 0xd182b
leaq 0x2877aa(%rip), %rsi    # 0x358fc1
movq %rbx, %rdi
xorl %eax, %eax
callq 0x1019cf
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
jmp 0xd18b8
movq 0x18(%r14), %rdi
callq 0x121e78
testq %rax, %rax
je 0xd1886
leaq 0x24(%r14), %r15
xorl %r12d, %r12d
leaq 0x2884e8(%rip), %r13    # 0x359d2f
leaq 0x50(%rsp), %rbp
movq 0x18(%r14), %rdi
movq %r12, %rsi
callq 0x121cfa
movl $0x4, %esi
movq %rbp, %rdi
movq %r15, %rdx
movq %r13, %rcx
movq %rax, %r8
movq %rbx, %r9
callq 0x1c094c
testl %eax, %eax
jne 0xd1821
incq %r12
movq 0x18(%r14), %rdi
callq 0x121e78
cmpq %rax, %r12
jb 0xd184c
movq 0x10(%r14), %rdi
addq $0x20, %r14
callq 0x120d23
leaq 0x288495(%rip), %rcx    # 0x359d2f
movq %rsp, %rdi
movl $0x3, %esi
movq %r14, %rdx
movq %rax, %r8
movq %rbx, %r9
callq 0x1c094c
movl %eax, %ecx
xorl %eax, %eax
negl %ecx
sbbl %eax, %eax
addq $0xb8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_tallymer.c
// Function: gt_tyr_search_runner
static int gt_tyr_search_runner(GT_UNUSED int argc,
                                GT_UNUSED const char **argv,
                                GT_UNUSED int parsed_args,
                                void *tool_arguments,
                                GtError *err)
{
  Tyr_search_options *arguments = tool_arguments;

  if (gt_tyrsearch(gt_str_get(arguments->str_inputindex),
                   arguments->queryfilenames,
                   arguments->showmode,
                   arguments->strand,
                   arguments->verbose,
                   arguments->performtest,
                   err) != 0)
  {
    return -1;
  }
  return 0;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %r8, %rbx
movq %rcx, %r14
movq (%rcx), %rdi
callq 0x120d23
movq 0x8(%r14), %rsi
movl 0x24(%r14), %edx
movl 0x20(%r14), %ecx
movzbl 0x28(%r14), %r8d
movzbl 0x29(%r14), %r9d
movq %rbx, (%rsp)
movq %rax, %rdi
callq 0x20c4d0
xorl %ecx, %ecx
negl %eax
sbbl %ecx, %ecx
movl %ecx, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
nop
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_template.c
// Function: gt_template_option_parser_new
static GtOptionParser* gt_template_option_parser_new(void *tool_arguments)
{
  TemplateArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [file]", /* XXX */
                            "DESCRIBE YOUR TOOL IN ONE LINE HERE."); /* XXX */

  /* -bool */
  option = gt_option_new_bool("bool", "bool option template",
                              &arguments->bool_option_template, false);
  gt_option_parser_add_option(op, option);

  /* -str */
  option = gt_option_new_string("str", "str option template",
                                arguments->str_option_template, NULL);
  gt_option_parser_add_option(op, option);

  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xd1a01
movq %rdi, %r14
leaq 0x281d22(%rip), %rdi    # 0x3536c2
leaq 0x294bff(%rip), %rsi    # 0x3665a6
callq 0x10cc4e
movq %rax, %rbx
leaq 0x2fe078(%rip), %rdi    # 0x3cfa2e
leaq 0x294c0e(%rip), %rsi    # 0x3665cb
movq %r14, %rdx
xorl %ecx, %ecx
callq 0x10f451
movq %rbx, %rdi
movq %rax, %rsi
callq 0x10cd10
movq 0x8(%r14), %rdx
leaq 0x2a95b7(%rip), %rdi    # 0x37af94
leaq 0x294bfc(%rip), %rsi    # 0x3665e0
xorl %ecx, %ecx
callq 0x10f987
movq %rbx, %rdi
movq %rax, %rsi
callq 0x10cd10
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x21afe
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_template.c
// Function: gt_template_arguments_check
static int gt_template_arguments_check(GT_UNUSED int rest_argc,
                                       void *tool_arguments,
                                       GT_UNUSED GtError *err)
{
  TemplateArguments *arguments = tool_arguments;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(arguments);

  /* XXX: do some checking after the option have been parsed (usally this is not
     necessary and this function can be removed completely). */
  if (gt_str_length(arguments->str_option_template))
    printf("%s\n", gt_str_get(arguments->str_option_template));

  return had_err;
}

// Assembly:
pushq %rbx
movq %rsi, %rbx
testq %rdx, %rdx
je 0xd1a1b
movq %rdx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xd1a48
testq %rbx, %rbx
je 0xd1a43
movq 0x8(%rbx), %rdi
callq 0x120d4c
testq %rax, %rax
je 0xd1a3f
movq 0x8(%rbx), %rdi
callq 0x120d23
movq %rax, %rdi
callq 0x17bd0
xorl %eax, %eax
popq %rbx
retq
callq 0x21b6c
callq 0x21b35
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_template.c
// Function: gt_template_runner
static int gt_template_runner(int argc, const char **argv, int parsed_args,
                              void *tool_arguments, GT_UNUSED GtError *err)
{
  TemplateArguments *arguments = tool_arguments;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

  /* XXX */
  if (arguments->bool_option_template)
    printf("argc=%d, parsed_args=%d\n", argc, parsed_args);
  printf("argv[0]=%s\n", argv[0]);

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movq %rcx, %r15
movl %edx, %ebp
movq %rsi, %rbx
movl %edi, %r14d
testq %r8, %r8
je 0xd1a70
movq %r8, %rdi
callq 0x101a9a
testb %al, %al
jne 0xd1ab1
testq %r15, %r15
je 0xd1aac
cmpb $0x1, (%r15)
jne 0xd1a8e
leaq 0x294ba1(%rip), %rdi    # 0x366623
movl %r14d, %esi
movl %ebp, %edx
xorl %eax, %eax
callq 0x17070
movq (%rbx), %rsi
leaq 0x294ba4(%rip), %rdi    # 0x36663c
xorl %eax, %eax
callq 0x17070
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
callq 0x21bda
callq 0x21ba3
nop
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_tir.c
// Function: gt_tir_arguments_new
static void* gt_tir_arguments_new(void)
{
  GtTirArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->str_indexname = gt_str_new();
  arguments->str_overlaps = gt_str_new();
  arguments->refseq_file = gt_str_new();
  arguments->cutoffs = gt_str_new();
  arguments->hmm_files = gt_str_array_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x294b78(%rip), %rdx    # 0x366660
movl $0x1, %edi
movl $0xb0, %esi
movl $0x40, %ecx
callq 0x1093ef
movq %rax, %rbx
callq 0x1208f8
movq %rax, (%rbx)
callq 0x1208f8
movq %rax, 0x10(%rbx)
callq 0x1208f8
movq %rax, 0x18(%rbx)
callq 0x1208f8
movq %rax, 0x8(%rbx)
callq 0x121b54
movq %rax, 0xa0(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_tir.c
// Function: gt_tir_arguments_delete
static void gt_tir_arguments_delete(void *tool_arguments)
{
  GtTirArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->str_indexname);
  gt_str_delete(arguments->cutoffs);
  gt_str_delete(arguments->refseq_file);
  gt_str_delete(arguments->str_overlaps);
  gt_str_array_delete(arguments->hmm_files);
  gt_option_delete(arguments->optionoverlaps);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xd1b8c
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x121b03
movq 0x8(%rbx), %rdi
callq 0x121b03
movq 0x18(%rbx), %rdi
callq 0x121b03
movq 0x10(%rbx), %rdi
callq 0x121b03
movq 0xa0(%rbx), %rdi
callq 0x121e8b
movq 0x98(%rbx), %rdi
callq 0x10f386
leaq 0x294ae2(%rip), %rsi    # 0x366660
movq %rbx, %rdi
movl $0x53, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_tir.c
// Function: gt_tir_arguments_check
static int gt_tir_arguments_check(GT_UNUSED int rest_argc,
                                       void *tool_arguments,
                                       GT_UNUSED GtError *err)
{
  GtTirArguments *arguments = tool_arguments;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(arguments);

  if (!had_err) {
    if (gt_option_is_set(arguments->optionoverlaps)) {
      if (strcmp(gt_str_get(arguments->str_overlaps), "no") == 0) {
        arguments->best_overlaps = false;
        arguments->no_overlaps = true;
        arguments->longest_overlaps = false;
      } else if (strcmp(gt_str_get(arguments->str_overlaps), "best") == 0 ) {
        arguments->best_overlaps = true;
        arguments->no_overlaps = false;
        arguments->longest_overlaps = false;
      } else if (strcmp(gt_str_get(arguments->str_overlaps), "longest") == 0 ) {
        arguments->best_overlaps = false;
        arguments->no_overlaps = false;
        arguments->longest_overlaps = true;
      } else if (strcmp(gt_str_get(arguments->str_overlaps), "all") == 0 ) {
        arguments->best_overlaps = false;
        arguments->no_overlaps = false;
        arguments->longest_overlaps = false;
      } else {
        gt_assert(0); /* cannot happen */
      }
    } else {
      /* default is "best" */
      arguments->longest_overlaps = false;
      arguments->best_overlaps = true;  /* take best prediction
                                           if overlap occurs, default */
      arguments->no_overlaps = false; /* overlapping predictions (not)
                                         allowed*/
    }
  }

  return had_err;
}

// Assembly:
pushq %rbx
movq %rsi, %rbx
testq %rdx, %rdx
je 0xd2069
movq %rdx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xd2145
testq %rbx, %rbx
je 0xd2140
movq 0x98(%rbx), %rdi
callq 0x10fe52
testb %al, %al
je 0xd20fd
movq 0x10(%rbx), %rdi
callq 0x120d23
leaq 0x2f6949(%rip), %rsi    # 0x3c89db
movq %rax, %rdi
callq 0x17a40
testl %eax, %eax
je 0xd210f
movq 0x10(%rbx), %rdi
callq 0x120d23
leaq 0x2f691a(%rip), %rsi    # 0x3c89c8
movq %rax, %rdi
callq 0x17a40
testl %eax, %eax
je 0xd211a
movq 0x10(%rbx), %rdi
callq 0x120d23
leaq 0x2882b6(%rip), %rsi    # 0x35a380
movq %rax, %rdi
callq 0x17a40
testl %eax, %eax
je 0xd212e
movq 0x10(%rbx), %rdi
callq 0x120d23
leaq 0x2f68d0(%rip), %rsi    # 0x3c89b6
movq %rax, %rdi
callq 0x17a40
testl %eax, %eax
jne 0xd214a
movw $0x0, 0x88(%rbx)
jmp 0xd2123
movb $0x0, 0x8a(%rbx)
movw $0x1, 0x88(%rbx)
jmp 0xd212a
movw $0x100, 0x88(%rbx)      # imm = 0x100
jmp 0xd2123
movw $0x1, 0x88(%rbx)
movb $0x0, 0x8a(%rbx)
xorl %eax, %eax
popq %rbx
retq
movw $0x0, 0x88(%rbx)
movb $0x1, 0x8a(%rbx)
jmp 0xd212a
callq 0x21cba
callq 0x21c48
callq 0x21c81
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_trieins.c
// Function: gt_trieins
int gt_trieins(int argc, const char **argv, GtError *err)
{
  bool haserr = false;
  int parsed_args;
  bool onlyins = false;

  gt_error_check(err);

  switch (parse_options(&onlyins,&parsed_args, argc, argv, err)) {
    case GT_OPTION_PARSER_OK: break;
    case GT_OPTION_PARSER_ERROR: return -1;
    case GT_OPTION_PARSER_REQUESTS_EXIT: return 0;
  }
  gt_assert(parsed_args == 1);

  if (gt_test_trieins(onlyins,argv[parsed_args],err) != 0)
  {
    haserr = true;
  }
  return haserr ? -1 : 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movq %rdx, %rbx
movq %rsi, %r14
movl %edi, %ebp
movb $0x0, 0x3(%rsp)
testq %rdx, %rdx
je 0xd254e
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xd2610
testq %rbx, %rbx
je 0xd254e
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xd2615
leaq 0x2947ef(%rip), %rdi    # 0x366d44
leaq 0x2947fc(%rip), %rsi    # 0x366d58
callq 0x10cc4e
movq %rax, %r15
leaq 0x27cd61(%rip), %rsi    # 0x34f2cc
movq %rax, %rdi
callq 0x10ceab
leaq 0x2d5afc(%rip), %rdi    # 0x3a8076
leaq 0x294806(%rip), %rsi    # 0x366d87
leaq 0x3(%rsp), %rdx
xorl %ecx, %ecx
callq 0x10f451
movq %r15, %rdi
movq %rax, %rsi
callq 0x10cd10
movq %r15, %rdi
movl $0x1, %esi
movl $0x1, %edx
callq 0x10d784
leaq 0x52e17(%rip), %r8      # 0x1253c8
leaq 0x4(%rsp), %rsi
movq %r15, %rdi
movl %ebp, %edx
movq %r14, %rcx
movq %rbx, %r9
callq 0x10d796
movl %eax, %ebp
movq %r15, %rdi
callq 0x10f2d0
cmpl $0x1, %ebp
je 0xd25de
cmpl $0x2, %ebp
jne 0xd25e5
xorl %eax, %eax
jmp 0xd2605
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
jmp 0xd2605
cmpl $0x1, 0x4(%rsp)
jne 0xd261a
movzbl 0x3(%rsp), %edi
movq 0x8(%r14), %rsi
movq %rbx, %rdx
callq 0x20a258
movl %eax, %ecx
xorl %eax, %eax
negl %ecx
sbbl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
callq 0x21dd5
callq 0x21d9e
callq 0x21e0c
nop
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_uniq.c
// Function: gt_uniq_arguments_delete
static void gt_uniq_arguments_delete(void *tool_arguments)
{
  UniqArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xd26a0
pushq %rbx
movq %rdi, %rbx
movq 0x10(%rdi), %rdi
callq 0x1040fc
movq 0x8(%rbx), %rdi
callq 0x110231
leaq 0x29470d(%rip), %rsi    # 0x366d9f
movq %rbx, %rdi
movl $0x31, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_uniq.c
// Function: gt_uniq_option_parser_new
static GtOptionParser* gt_uniq_option_parser_new(void *tool_arguments)
{
  UniqArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [GFF3_file]", "Filter out repeated "
                            "feature node graphs in a sorted GFF3 file.");

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  /* output file options */
  gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);

  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
  gt_option_parser_set_max_args(op, 1);

  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xd2712
movq %rdi, %r14
leaq 0x27c9db(%rip), %rdi    # 0x34f08f
leaq 0x294712(%rip), %rsi    # 0x366dcd
callq 0x10cc4e
movq %rax, %rbx
movq %r14, %rdi
callq 0x10f473
movq %rbx, %rdi
movq %rax, %rsi
callq 0x10cd10
movq 0x8(%r14), %rdi
addq $0x10, %r14
movq %rbx, %rsi
movq %r14, %rdx
callq 0x10ffa3
leaq 0x817ac(%rip), %rsi     # 0x153e9c
movq %rbx, %rdi
xorl %edx, %edx
callq 0x10cd8d
movq %rbx, %rdi
movl $0x1, %esi
callq 0x10d775
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x21e43
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_uniq.c
// Function: gt_uniq_runner
static int gt_uniq_runner(GT_UNUSED int argc, const char **argv,
                          int parsed_args, void *tool_arguments, GtError *err)
{
  UniqArguments *arguments = tool_arguments;
  GtNodeStream *gff3_in_stream,
               *uniq_stream = NULL,
               *gff3_out_stream = NULL;
  int had_err;

  gt_error_check(err);
  gt_assert(arguments);

  /* create gff3 input stream */
  gff3_in_stream = gt_gff3_in_stream_new_sorted(argv[parsed_args]);
  if (arguments->verbose && arguments->outfp)
    gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) gff3_in_stream);

  /* create uniq stream */
  uniq_stream = gt_uniq_stream_new(gff3_in_stream);

  /* create gff3 output stream */
  gff3_out_stream = gt_gff3_out_stream_new(uniq_stream, arguments->outfp);

  /* pull the features through the stream and free them afterwards */
  had_err = gt_node_stream_pull(gff3_out_stream, err);

  /* free */
  gt_node_stream_delete(gff3_out_stream);
  gt_node_stream_delete(uniq_stream);
  gt_node_stream_delete(gff3_in_stream);

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movq %r8, %rbx
movq %rcx, %r14
movl %edx, %ebp
movq %rsi, %r15
testq %r8, %r8
je 0xd273b
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xd27b3
testq %r14, %r14
je 0xd27ae
movslq %ebp, %rax
movq (%r15,%rax,8), %rdi
callq 0x14d0a8
movq %rax, %r15
cmpb $0x1, (%r14)
jne 0xd2764
cmpq $0x0, 0x10(%r14)
je 0xd2764
movq %r15, %rdi
callq 0x14ce62
movq %r15, %rdi
callq 0x18c7d0
movq %rax, %r12
movq 0x10(%r14), %rsi
movq %rax, %rdi
callq 0x14e310
movq %rax, %r14
movq %rax, %rdi
movq %rbx, %rsi
callq 0x16adca
movl %eax, %ebx
movq %r14, %rdi
callq 0x16ac6e
movq %r12, %rdi
callq 0x16ac6e
movq %r15, %rdi
callq 0x16ac6e
movl %ebx, %eax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
callq 0x21eb1
callq 0x21e7a
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_wtree.c
// Function: gt_wtree_option_parser_new
static GtOptionParser* gt_wtree_option_parser_new(void *tool_arguments)
{
  GtToolbox *wtree_toolbox = tool_arguments;
  GtOptionParser *op;
  gt_assert(wtree_toolbox);
  op = gt_option_parser_new("[option ...] tool [argument ...]",
                            "Call an wtree manipulation tool "
                            "and pass argument(s) to it.");
  gt_option_parser_set_comment_func(op, gt_toolbox_show, wtree_toolbox);
  gt_option_parser_set_min_args(op, 1U);
  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xd2856
movq %rdi, %rbx
leaq 0x27d2d5(%rip), %rdi    # 0x34faf2
leaq 0x294635(%rip), %rsi    # 0x366e59
callq 0x10cc4e
movq %rax, %r14
leaq 0x5127b(%rip), %rsi     # 0x123aae
movq %rax, %rdi
movq %rbx, %rdx
callq 0x10cd8d
movq %r14, %rdi
movl $0x1, %esi
callq 0x10d766
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x21ee8
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_wtree.c
// Function: gt_wtree_runner
static int gt_wtree_runner(int argc, const char **argv, int parsed_args,
                              void *tool_arguments, GT_UNUSED GtError *err)
{
  GtToolbox *wtree_toolbox = tool_arguments;
  GtTool *tool = NULL;
  int had_err = 0;
  char **nargv = NULL;

  gt_error_check(err);
  gt_assert(wtree_toolbox);

  /* get wtree tools */
  tool = gt_toolbox_get_tool(wtree_toolbox, argv[parsed_args]);
  if (!tool) {
    gt_error_set(err, "wtree tool '%s' not found; option -help "
                      "lists possible tools", argv[parsed_args]);
    had_err = -1;
  }

  /* call wtree tool */
  if (!had_err) {
    gt_assert(tool);
    nargv = gt_cstr_array_prefix_first(argv + parsed_args,
                                       gt_error_get_progname(err));
    gt_error_set_progname(err, nargv[0]);
    had_err = gt_tool_run(tool, argc - parsed_args, (const char**) nargv, err);
  }

  /* free */
  gt_cstr_array_delete(nargv);

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r8, %rbx
movq %rcx, %r15
movl %edx, %r14d
movq %rsi, %r12
movl %edi, %ebp
testq %r8, %r8
je 0xd2889
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xd2920
testq %r15, %r15
je 0xd291b
movslq %r14d, %rax
leaq (%r12,%rax,8), %r13
movq (%r13), %rsi
movq %r15, %rdi
callq 0x1239f1
testq %rax, %rax
je 0xd28e5
movq %rax, %r12
movq %rbx, %rdi
callq 0x101b22
movq %r13, %rdi
movq %rax, %rsi
callq 0xe8b1a
movq %rax, %r15
movq (%rax), %rsi
movq %rbx, %rdi
callq 0x101ada
subl %r14d, %ebp
movq %r12, %rdi
movl %ebp, %esi
movq %r15, %rdx
movq %rbx, %rcx
callq 0x123470
movl %eax, %ebx
jmp 0xd2902
movq (%r13), %rdx
leaq 0x2945b5(%rip), %rsi    # 0x366ea5
xorl %r15d, %r15d
movq %rbx, %rdi
xorl %eax, %eax
callq 0x1019cf
movl $0xffffffff, %ebx       # imm = 0xFFFFFFFF
movq %r15, %rdi
callq 0xe8d46
movl %ebx, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x21f56
callq 0x21f1f
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_wtree_bench.c
// Function: gt_wtree_bench_option_parser_new
static GtOptionParser* gt_wtree_bench_option_parser_new(void *tool_arguments)
{
  GtWaveletBenchArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] encoded_sequence",
                            "Testing and benchmarking for wtree.");

  /* -safe */
  option = gt_option_new_string("safe", "safe files to disk, currently not "
                                "implemented",
                                arguments->safe, NULL);
  gt_option_parser_add_option(op, option);

  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xd29f3
movq %rdi, %rbx
leaq 0x294568(%rip), %rdi    # 0x366f1e
leaq 0x29457f(%rip), %rsi    # 0x366f3c
callq 0x10cc4e
movq %rax, %r14
movq (%rbx), %rdx
leaq 0x2fce3f(%rip), %rdi    # 0x3cf80e
leaq 0x29458a(%rip), %rsi    # 0x366f60
xorl %ecx, %ecx
callq 0x10f987
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x21f8d
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_wtree_bench.c
// Function: gt_wtree_bench_arguments_check
static int gt_wtree_bench_arguments_check(int rest_argc,
                                          void *tool_arguments,
                                          GtError *err)
{
  GtWaveletBenchArguments *arguments = tool_arguments;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(arguments);

  if (rest_argc == 0) {
    gt_error_set(err, "no encseq basename given");
    had_err = 1;
  }
  else if (rest_argc > 1) {
    gt_error_set(err, "give only one encseq basename");
    had_err = 1;
  }
  if (!had_err && gt_str_length(arguments->safe))
    printf("%s\n", gt_str_get(arguments->safe));

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movq %rdx, %r14
movq %rsi, %rbx
movl %edi, %ebp
testq %rdx, %rdx
je 0xd2a18
movq %r14, %rdi
callq 0x101a9a
testb %al, %al
jne 0xd2a83
testq %rbx, %rbx
je 0xd2a7e
testl %ebp, %ebp
je 0xd2a2f
cmpl $0x2, %ebp
jl 0xd2a4a
leaq 0x294599(%rip), %rsi    # 0x366fc6
jmp 0xd2a36
leaq 0x294577(%rip), %rsi    # 0x366fad
xorl %r15d, %r15d
movq %r14, %rdi
xorl %eax, %eax
callq 0x1019cf
movl $0x1, %ebp
jmp 0xd2a4f
xorl %ebp, %ebp
movb $0x1, %r15b
testb %r15b, %r15b
je 0xd2a71
movq (%rbx), %rdi
callq 0x120d4c
testq %rax, %rax
je 0xd2a71
movq (%rbx), %rdi
callq 0x120d23
movq %rax, %rdi
callq 0x17bd0
movl %ebp, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
callq 0x21ffb
callq 0x21fc4