LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_extractfeat.c
// Function: gt_extractfeat_comment_func
static int gt_extractfeat_comment_func(const char *progname,
                                       void *data, GtError *err)
{
  GtStrArray *descs = gt_trans_table_get_scheme_descriptions();
  GtUword i = 0;
  printf("\nGenetic code numbers for option '-gcode':\n\n");
  for (i = 0; i < gt_str_array_size(descs); i++) {
    printf("%s\n", gt_str_array_get(descs, i));
  }
  gt_str_array_delete(descs);
  return gt_gtdata_show_help(progname, data,err);
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
movq %rdx, %rbx
movq %rsi, %r14
movq %rdi, %r15
callq 0x123c3c
movq %rax, %r12
leaq 0x2ac46c(%rip), %rdi    # 0x3554d9
callq 0x17bd0
movq %r12, %rdi
callq 0x121e78
testq %rax, %rax
je 0xa90a5
xorl %r13d, %r13d
movq %r12, %rdi
movq %r13, %rsi
callq 0x121cfa
movq %rax, %rdi
callq 0x17bd0
incq %r13
movq %r12, %rdi
callq 0x121e78
cmpq %rax, %r13
jb 0xa9082
movq %r12, %rdi
callq 0x121e8b
movq %r15, %rdi
movq %r14, %rsi
movq %rbx, %rdx
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
jmp 0x153e9c
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_extractseq.c
// Function: gt_extractseq_arguments_new
static void* gt_extractseq_arguments_new(void)
{
  ExtractSeqArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->pattern = gt_str_new();
  arguments->fastakeyfile = gt_str_new();
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2ac411(%rip), %rdx    # 0x355505
movl $0x1, %edi
movl $0x38, %esi
movl $0x2d, %ecx
callq 0x1093ef
movq %rax, %rbx
callq 0x1208f8
movq %rax, (%rbx)
callq 0x1208f8
movq %rax, 0x8(%rbx)
callq 0x10ff7c
movq %rax, 0x28(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_extractseq.c
// Function: gt_extractseq_arguments_delete
static void gt_extractseq_arguments_delete(void *tool_arguments)
{
  ExtractSeqArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_str_delete(arguments->fastakeyfile);
  gt_str_delete(arguments->pattern);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xa916b
pushq %rbx
movq %rdi, %rbx
movq 0x30(%rdi), %rdi
callq 0x1040fc
movq 0x28(%rbx), %rdi
callq 0x110231
movq 0x8(%rbx), %rdi
callq 0x121b03
movq (%rbx), %rdi
callq 0x121b03
leaq 0x2ac3a8(%rip), %rsi    # 0x355505
movq %rbx, %rdi
movl $0x3c, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_extractseq.c
// Function: gt_extractseq_arguments_check
static int gt_extractseq_arguments_check(GT_UNUSED int argc,
                                         void *tool_arguments, GtError *err)
{
  ExtractSeqArguments *arguments = tool_arguments;
  gt_error_check(err);
  gt_assert(arguments);
  if (arguments->frompos > arguments->topos) {
    gt_error_set(err,
              "argument to option '-%s' must be <= argument to option '-%s'",
              FROMPOS_OPTION_STR, TOPOS_OPTION_STR);
    return -1;
  }
  return 0;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdx, %rbx
movq %rsi, %r14
testq %rdx, %rdx
je 0xa92ea
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xa932c
testq %r14, %r14
je 0xa9327
movq 0x10(%r14), %rcx
xorl %eax, %eax
cmpq 0x18(%r14), %rcx
jbe 0xa931f
leaq 0x2ac3e4(%rip), %rsi    # 0x3556e6
leaq 0x2d95e1(%rip), %rdx    # 0x3828ea
leaq 0x2be664(%rip), %rcx    # 0x367974
movq %rbx, %rdi
xorl %eax, %eax
callq 0x1019cf
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x1a9d2
callq 0x1a999
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_extracttarget.c
// Function: gt_extracttarget_option_parser_new
static GtOptionParser* gt_extracttarget_option_parser_new(void *tool_arguments)
{
  ExtractTargetArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *o;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] -seqfile sequence_file GFF3_file",
                         "Extract target sequences given in GFF3_file from "
                         "sequence_file.");

  /* -seqfile */
  o = gt_option_new_filename_array("seqfiles",
                                   "set the sequence file from which "
                                   "to extract the features",
                                   arguments->seqfiles);
  gt_option_is_mandatory(o);
  gt_option_parser_add_option(op, o);

  gt_option_parser_set_min_max_args(op, 1, 1);

  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xa99c5
movq %rdi, %rbx
leaq 0x2abef2(%rip), %rdi    # 0x35585f
leaq 0x2abf19(%rip), %rsi    # 0x35588d
callq 0x10cc4e
movq %rax, %r14
movq (%rbx), %rdx
leaq 0x2abfb6(%rip), %rdi    # 0x35593c
leaq 0x2abf40(%rip), %rsi    # 0x3558cd
callq 0x10f9f6
movq %rax, %rbx
movq %rax, %rdi
callq 0x10fa96
movq %r14, %rdi
movq %rbx, %rsi
callq 0x10cd10
movq %r14, %rdi
movl $0x1, %esi
movl $0x1, %edx
callq 0x10d784
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x1ac0c
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_extracttarget.c
// Function: show_target
static bool show_target(GT_UNUSED GtUword pos, void *data)
{
  TargetInfo *ti = data;
  char *seq;
  gt_assert(ti);
  seq = gt_bioseq_get_sequence(ti->bioseq, ti->seqnum);
  gt_fasta_show_entry(gt_bioseq_get_description(ti->bioseq, ti->seqnum),
                      seq,
                      gt_bioseq_get_sequence_length(ti->bioseq, ti->seqnum), 0,
                      NULL);
  gt_free(seq);
  return true;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
testq %rsi, %rsi
je 0xa9e34
movq %rsi, %rbx
movq (%rsi), %rdi
movq 0x8(%rsi), %rsi
callq 0xd7118
movq %rax, %r14
movq (%rbx), %rdi
movq 0x8(%rbx), %rsi
callq 0xd71c2
movq %rax, %r15
movq (%rbx), %rdi
movq 0x8(%rbx), %rsi
callq 0xd71ae
movq %r15, %rdi
movq %r14, %rsi
movq %rax, %rdx
xorl %ecx, %ecx
xorl %r8d, %r8d
callq 0x102ec0
leaq 0x2aba00(%rip), %rsi    # 0x35581f
movq %r14, %rdi
movl $0x5d, %edx
callq 0x109670
movb $0x1, %al
popq %rbx
popq %r14
popq %r15
retq
callq 0x1ad5e
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_fastq_sample.c
// Function: gt_fastq_sample_option_parser_new
static GtOptionParser* gt_fastq_sample_option_parser_new(void *tool_arguments)
{
  GtFastqSampleArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *optionlength;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] -length <n> <fastq_file> "
                            "[<fastq_file>...]",
                            "Print samples by random choice from given FASTQ "\
                            "files using at least n sequence-chars.\n"\
                            "Output is fastq/fasta format depending on "\
                            "whether qualities are available.");

  /* -length */
  optionlength = gt_option_new_uword("length",
                                     "minimum number of chars to be chosen",
                                     &arguments->length,
                                     GT_UNDEF_UWORD);
  gt_option_is_mandatory(optionlength);
  gt_option_parser_add_option(op, optionlength);

  gt_option_parser_set_min_args(op, 1);

  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xa9f03
movq %rdi, %rbx
leaq 0x2abb09(%rip), %rdi    # 0x3559b2
leaq 0x2abb3a(%rip), %rsi    # 0x3559ea
callq 0x10cc4e
movq %rax, %r14
leaq 0x320c9a(%rip), %rdi    # 0x3cab59
leaq 0x2abbc6(%rip), %rsi    # 0x355a8c
movq %rbx, %rdx
movq $-0x1, %rcx
callq 0x10f4c7
movq %rax, %rbx
movq %rax, %rdi
callq 0x10fa96
movq %r14, %rdi
movq %rbx, %rsi
callq 0x10cd10
movq %r14, %rdi
movl $0x1, %esi
callq 0x10d766
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x1ad95
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_fastq_sample.c
// Function: gt_fastq_sample_arguments_check
static int gt_fastq_sample_arguments_check(GT_UNUSED int rest_argc,
                                           void *tool_arguments,
                                           GtError *err)
{
  GtFastqSampleArguments *arguments = tool_arguments;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(arguments);

  if (arguments->length < 1) {
    gt_error_set(err, "length must be a positive integer");
    had_err = -1;
  }
  return had_err;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdx, %rbx
movq %rsi, %r14
testq %rdx, %rdx
je 0xa9f23
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xa9f53
testq %r14, %r14
je 0xa9f4e
xorl %eax, %eax
cmpq $0x0, (%r14)
jne 0xa9f46
leaq 0x2abb9a(%rip), %rsi    # 0x355ad1
movq %rbx, %rdi
xorl %eax, %eax
callq 0x1019cf
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x1ae03
callq 0x1adcc
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_featureindex.c
// Function: gt_featureindex_arguments_new
static void* gt_featureindex_arguments_new(void)
{
  GtFeatureindexArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->seqid = gt_str_new();
  arguments->backend = gt_str_new();
  arguments->filename = gt_str_new();
  arguments->host = gt_str_new();
  arguments->user = gt_str_new();
  arguments->database = gt_str_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2ab87a(%rip), %rdx    # 0x355b9a
movl $0x1, %edi
movl $0x58, %esi
movl $0x3d, %ecx
callq 0x1093ef
movq %rax, %rbx
callq 0x1208f8
movq %rax, 0x10(%rbx)
callq 0x1208f8
movq %rax, 0x18(%rbx)
callq 0x1208f8
movq %rax, 0x20(%rbx)
callq 0x1208f8
movq %rax, 0x28(%rbx)
callq 0x1208f8
movq %rax, 0x30(%rbx)
callq 0x1208f8
movq %rax, 0x40(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_featureindex.c
// Function: gt_featureindex_arguments_delete
static void gt_featureindex_arguments_delete(void *tool_arguments)
{
  GtFeatureindexArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->seqid);
  gt_str_delete(arguments->backend);
  gt_str_delete(arguments->filename);
  gt_str_delete(arguments->host);
  gt_str_delete(arguments->user);
  gt_str_delete(arguments->pass);
  gt_str_delete(arguments->database);
  gt_option_delete(arguments->rngopt);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xaa3d8
pushq %rbx
movq %rdi, %rbx
movq 0x10(%rdi), %rdi
callq 0x121b03
movq 0x18(%rbx), %rdi
callq 0x121b03
movq 0x20(%rbx), %rdi
callq 0x121b03
movq 0x28(%rbx), %rdi
callq 0x121b03
movq 0x30(%rbx), %rdi
callq 0x121b03
movq 0x38(%rbx), %rdi
callq 0x121b03
movq 0x40(%rbx), %rdi
callq 0x121b03
movq 0x50(%rbx), %rdi
callq 0x10f386
leaq 0x2ab7d0(%rip), %rsi    # 0x355b9a
movq %rbx, %rdi
movl $0x53, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_featureindex.c
// Function: gt_featureindex_arguments_check
static int gt_featureindex_arguments_check(GT_UNUSED int rest_argc,
                                           GT_UNUSED void *tool_arguments,
                                           GT_UNUSED GtError *err)
{
  GT_UNUSED GtFeatureindexArguments *arguments = tool_arguments;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(arguments);

  return had_err;
}

// Assembly:
pushq %rbx
movq %rsi, %rbx
testq %rdx, %rdx
je 0xaa571
movq %rdx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xaa57f
testq %rbx, %rbx
je 0xaa57a
xorl %eax, %eax
popq %rbx
retq
callq 0x1af8e
callq 0x1af55
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_fingerprint.c
// Function: gt_fingerprint_arguments_new
static void* gt_fingerprint_arguments_new(void)
{
  FingerprintArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->checklist = gt_str_new();
  arguments->extract = gt_str_new();
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2ab450(%rip), %rdx    # 0x355d9f
movl $0x1, %edi
movl $0x30, %esi
movl $0x2e, %ecx
callq 0x1093ef
movq %rax, %rbx
callq 0x1208f8
movq %rax, 0x8(%rbx)
callq 0x1208f8
movq %rax, 0x10(%rbx)
callq 0x10ff7c
movq %rax, 0x20(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_fingerprint.c
// Function: gt_fingerprint_arguments_delete
static void gt_fingerprint_arguments_delete(void *tool_arguments)
{
  FingerprintArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_str_delete(arguments->extract);
  gt_str_delete(arguments->checklist);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xaa9c8
pushq %rbx
movq %rdi, %rbx
movq 0x28(%rdi), %rdi
callq 0x1040fc
movq 0x20(%rbx), %rdi
callq 0x110231
movq 0x10(%rbx), %rdi
callq 0x121b03
movq 0x8(%rbx), %rdi
callq 0x121b03
leaq 0x2ab3e5(%rip), %rsi    # 0x355d9f
movq %rbx, %rdi
movl $0x3d, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_fingerprint.c
// Function: proc_superfluous_sequence
static void proc_superfluous_sequence(const char *string,
                                      GT_UNUSED GtUword occurrences,
                                      GT_UNUSED double probability, void *data)
{
  bool *comparisons_failed = data;
  gt_assert(string && occurrences && comparisons_failed);
  printf("%s only in sequence_file(s)\n", string);
  *comparisons_failed = true;
}

// Assembly:
pushq %rbx
testq %rdi, %rdi
je 0xab37f
testq %rsi, %rsi
je 0xab37f
movq %rdx, %rbx
testq %rdx, %rdx
je 0xab37f
movq %rdi, %rax
leaq 0x2aad88(%rip), %rdi    # 0x3560f8
movq %rax, %rsi
xorl %eax, %eax
callq 0x17070
movb $0x1, (%rbx)
popq %rbx
retq
callq 0x1b2aa
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_fingerprint.c
// Function: show_duplicate
static void show_duplicate(const char *fingerprint, GtUword occurrences,
                           GT_UNUSED double probability, void *data)
{
  FingerprintInfo *info = data;
  if (occurrences > 1) {
    printf("%s\t"GT_WU"\n", fingerprint, occurrences);
    info->duplicates += occurrences - 1;
  }
  info->num_of_sequences += occurrences;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdx, %rbx
movq %rsi, %r14
cmpq $0x2, %rsi
jb 0xab3b4
movq %rdi, %rsi
leaq 0x2aadb3(%rip), %rdi    # 0x356151
movq %r14, %rdx
xorl %eax, %eax
callq 0x17070
movq (%rbx), %rax
addq %r14, %rax
decq %rax
movq %rax, (%rbx)
addq %r14, 0x8(%rbx)
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_gdiffcalc.c
// Function: gt_gdiffcalc_arguments_new
static void* gt_gdiffcalc_arguments_new(void)
{
  GtGenomediffArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->indexname = gt_str_new();
  arguments->unitfile = gt_str_new();
  arguments->indextype = gt_str_new();
  arguments->filenames = gt_str_array_new();
  arguments->with_esa = arguments->with_pck = false;
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2aae08(%rip), %rdx    # 0x3561f8
movl $0x1, %edi
movl $0x70, %esi
movl $0x2e, %ecx
callq 0x1093ef
movq %rax, %rbx
callq 0x1208f8
movq %rax, 0x50(%rbx)
callq 0x1208f8
movq %rax, 0x60(%rbx)
callq 0x1208f8
movq %rax, 0x58(%rbx)
callq 0x121b54
movq %rax, 0x68(%rbx)
movw $0x0, 0x2(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_gdiffcalc.c
// Function: gt_gdiffcalc_arguments_delete
static void gt_gdiffcalc_arguments_delete(void *tool_arguments)
{
  GtGenomediffArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->indexname);
  gt_str_delete(arguments->unitfile);
  gt_str_delete(arguments->indextype);
  gt_str_array_delete(arguments->filenames);
  gt_option_delete(arguments->ref_unitfile);
  gt_encseq_options_delete(arguments->loadopts);
  gt_index_options_delete(arguments->idxopts);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xab493
pushq %rbx
movq %rdi, %rbx
movq 0x50(%rdi), %rdi
callq 0x121b03
movq 0x60(%rbx), %rdi
callq 0x121b03
movq 0x58(%rbx), %rdi
callq 0x121b03
movq 0x68(%rbx), %rdi
callq 0x121e8b
movq 0x48(%rbx), %rdi
callq 0x10f386
movq 0x38(%rbx), %rdi
callq 0x1017c9
movq 0x40(%rbx), %rdi
callq 0x1be8d8
leaq 0x2aad73(%rip), %rsi    # 0x3561f8
movq %rbx, %rdi
movl $0x42, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_gdiffcalc.c
// Function: gt_gdiffcalc_arguments_check
static int gt_gdiffcalc_arguments_check(GT_UNUSED int rest_argc,
                                       void *tool_arguments,
                                       GT_UNUSED GtError *err)
{
  GtGenomediffArguments *arguments = tool_arguments;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(arguments);

  gt_assert(rest_argc == 1);
  if (!had_err)
    arguments->with_units = gt_option_is_set(arguments->ref_unitfile);

  return had_err;
}

// Assembly:
pushq %rbp
pushq %rbx
pushq %rax
movq %rsi, %rbx
movl %edi, %ebp
testq %rdx, %rdx
je 0xab6be
movq %rdx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xab6e7
testq %rbx, %rbx
je 0xab6dd
cmpl $0x1, %ebp
jne 0xab6e2
movq 0x48(%rbx), %rdi
callq 0x10fe52
movb %al, 0x4(%rbx)
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %rbp
retq
callq 0x1b38c
callq 0x1b353
callq 0x1b31a
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_genomediff.c
// Function: gt_genomediff_arguments_new
static void* gt_genomediff_arguments_new(void)
{
  GtGenomediffArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->indexname = gt_str_new();
  arguments->unitfile = gt_str_new();
  arguments->indextype = gt_str_new();
  arguments->filenames = gt_str_array_new();
  arguments->with_esa = arguments->with_pck = false;
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2aa94a(%rip), %rdx    # 0x356596
movl $0x1, %edi
movl $0x70, %esi
movl $0x2c, %ecx
callq 0x1093ef
movq %rax, %rbx
callq 0x1208f8
movq %rax, 0x50(%rbx)
callq 0x1208f8
movq %rax, 0x60(%rbx)
callq 0x1208f8
movq %rax, 0x58(%rbx)
callq 0x121b54
movq %rax, 0x68(%rbx)
movw $0x0, 0x2(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_gff3.c
// Function: gt_gff3_arguments_new
static void* gt_gff3_arguments_new(void)
{
  GFF3Arguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->newsource = gt_str_new();
  arguments->offsetfile = gt_str_new();
  arguments->tci = gt_typecheck_info_new();
  arguments->xci = gt_xrfcheck_info_new();
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2aa229(%rip), %rdx    # 0x356978
movl $0x1, %edi
movl $0x50, %esi
movl $0x44, %ecx
callq 0x1093ef
movq %rax, %rbx
callq 0x1208f8
movq %rax, 0x20(%rbx)
callq 0x1208f8
movq %rax, 0x18(%rbx)
callq 0x18b9bc
movq %rax, 0x30(%rbx)
callq 0x18e650
movq %rax, 0x38(%rbx)
callq 0x10ff7c
movq %rax, 0x40(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_gff3.c
// Function: gt_gff3_arguments_delete
static void gt_gff3_arguments_delete(void *tool_arguments)
{
  GFF3Arguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_str_delete(arguments->newsource);
  gt_output_file_info_delete(arguments->ofi);
  gt_typecheck_info_delete(arguments->tci);
  gt_xrfcheck_info_delete(arguments->xci);
  gt_str_delete(arguments->offsetfile);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xac7ec
pushq %rbx
movq %rdi, %rbx
movq 0x48(%rdi), %rdi
callq 0x1040fc
movq 0x20(%rbx), %rdi
callq 0x121b03
movq 0x40(%rbx), %rdi
callq 0x110231
movq 0x30(%rbx), %rdi
callq 0x18b9e8
movq 0x38(%rbx), %rdi
callq 0x18e67c
movq 0x18(%rbx), %rdi
callq 0x121b03
leaq 0x2aa19a(%rip), %rsi    # 0x356978
movq %rbx, %rdi
movl $0x57, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_gff3_to_gtf.c
// Function: gt_gff3_to_gtf_arguments_delete
static void gt_gff3_to_gtf_arguments_delete(void *tool_arguments)
{
  GFF3ToGTFArguments *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 0xacf9a
pushq %rbx
movq %rdi, %rbx
movq 0x8(%rdi), %rdi
callq 0x1040fc
movq (%rbx), %rdi
callq 0x110231
leaq 0x2aa058(%rip), %rsi    # 0x356fe4
movq %rbx, %rdi
movl $0x2c, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_gff3_to_gtf.c
// Function: gt_gff3_to_gtf_runner
static int gt_gff3_to_gtf_runner(int argc, const char **argv, int parsed_args,
                                 void *tool_arguments, GtError *err)
{
  GFF3ToGTFArguments *arguments = tool_arguments;
  GtNodeStream *gff3_in_stream = NULL, *gtf_out_stream = NULL;
  int had_err;

  gt_error_check(err);
  gt_assert(arguments);

  /* create a gff3 input stream */
  gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
                                                  argv + parsed_args);

  /* create a gtf output stream */
  gtf_out_stream = gt_gtf_out_stream_new(gff3_in_stream, arguments->outfp);

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

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

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movq %r8, %rbx
movq %rcx, %r14
movl %edx, %r12d
movq %rsi, %r15
movl %edi, %ebp
testq %r8, %r8
je 0xacffc
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xad051
testq %r14, %r14
je 0xad04c
subl %r12d, %ebp
movslq %r12d, %rax
leaq (%r15,%rax,8), %rsi
movl %ebp, %edi
callq 0x14d00b
movq %rax, %r15
movq 0x8(%r14), %rsi
movq %rax, %rdi
callq 0x154310
movq %rax, %r14
movq %rax, %rdi
movq %rbx, %rsi
callq 0x16adca
movl %eax, %ebx
movq %r15, %rdi
callq 0x16ac6e
movq %r14, %rdi
callq 0x16ac6e
movl %ebx, %eax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
callq 0x1b950
callq 0x1b919
nop
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_gff3validator.c
// Function: gt_gff3validator_arguments_new
static void* gt_gff3validator_arguments_new(void)
{
  GFF3ValidatorArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->tci = gt_typecheck_info_new();
  arguments->xci = gt_xrfcheck_info_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2a9fbe(%rip), %rdx    # 0x357041
movl $0x1, %edi
movl $0x18, %esi
movl $0x23, %ecx
callq 0x1093ef
movq %rax, %rbx
callq 0x18b9bc
movq %rax, (%rbx)
callq 0x18e650
movq %rax, 0x8(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_gff3validator.c
// Function: gt_gff3validator_arguments_delete
static void gt_gff3validator_arguments_delete(void *tool_arguments)
{
  GFF3ValidatorArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_typecheck_info_delete(arguments->tci);
  gt_xrfcheck_info_delete(arguments->xci);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xad0df
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x18b9e8
movq 0x8(%rbx), %rdi
callq 0x18e67c
leaq 0x2a9f70(%rip), %rsi    # 0x357041
movq %rbx, %rdi
movl $0x2f, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_gff3validator.c
// Function: gt_gff3validator_option_parser_new
static GtOptionParser* gt_gff3validator_option_parser_new(void *tool_arguments)
{
  GFF3ValidatorArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [GFF3_file ...]",
                         "Strictly validate given GFF3 files.");

  /* typecheck options */
  gt_typecheck_info_register_options(arguments->tci, op);

  /* xrfcheck options */
  gt_xrfcheck_info_register_options(arguments->xci, op);

  /* -strict */
  option = gt_option_new_bool("strict", "be very strict during GFF3 parsing "
                              "(stricter than the specification requires)",
                              &arguments->strict, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xad156
movq %rdi, %r14
leaq 0x2a6416(%rip), %rdi    # 0x353509
leaq 0x2a9f87(%rip), %rsi    # 0x357081
callq 0x10cc4e
movq %rax, %rbx
movq (%r14), %rdi
movq %rax, %rsi
callq 0x18bac7
movq 0x8(%r14), %rdi
movq %rbx, %rsi
callq 0x18e6ac
addq $0x10, %r14
leaq 0x2dbd7d(%rip), %rdi    # 0x388ea1
leaq 0x2a99c4(%rip), %rsi    # 0x356aef
movq %r14, %rdx
xorl %ecx, %ecx
callq 0x10f451
movq %rax, %r14
movq %rax, %rdi
callq 0x10fbef
movq %rbx, %rdi
movq %r14, %rsi
callq 0x10cd10
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x1b987
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_gtf_to_gff3.c
// Function: gt_gtf_to_gff3_arguments_delete
static void gt_gtf_to_gff3_arguments_delete(void *tool_arguments)
{
  GTFToGFF3Arguments *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 0xad324
pushq %rbx
movq %rdi, %rbx
movq 0x10(%rdi), %rdi
callq 0x1040fc
movq 0x8(%rbx), %rdi
callq 0x110231
leaq 0x2a9dbb(%rip), %rsi    # 0x3570d1
movq %rbx, %rdi
movl $0x2f, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_gtf_to_gff3.c
// Function: gt_gtf_to_gff3_option_parser_new
static GtOptionParser* gt_gtf_to_gff3_option_parser_new(void *tool_arguments)
{
  GTFToGFF3Arguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  op = gt_option_parser_new("[GTF_file]",
                            "Parse GTF2.2 file and convert it to GFF3.");

  /* -tidy */
  option = gt_option_new_bool("tidy", "try to tidy the GTF file up during "
                              "parsing", &arguments->tidy, 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_max_args(op, 1);

  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xad395
movq %rdi, %rbx
leaq 0x2a9dd5(%rip), %rdi    # 0x35710d
leaq 0x2a9dd9(%rip), %rsi    # 0x357118
callq 0x10cc4e
movq %rax, %r14
leaq 0x2dbb19(%rip), %rdi    # 0x388e67
leaq 0x2a9ded(%rip), %rsi    # 0x357142
movq %rbx, %rdx
xorl %ecx, %ecx
callq 0x10f451
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
movq 0x8(%rbx), %rdi
addq $0x10, %rbx
movq %r14, %rsi
movq %rbx, %rdx
callq 0x10ffa3
movq %r14, %rdi
movl $0x1, %esi
callq 0x10d775
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x1ba2c
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_gtf_to_gff3.c
// Function: gt_gtf_to_gff3_runner
static int gt_gtf_to_gff3_runner(GT_UNUSED int argc, const char **argv,
                                 int parsed_args, void *tool_arguments,
                                 GtError *err)
{
  GTFToGFF3Arguments *arguments = tool_arguments;
  GtNodeStream *gtf_in_stream = NULL, *gff3_out_stream = NULL;
  int had_err;

  gt_error_check(err);
  gt_assert(arguments);

  /* create a GTF input stream */
  gtf_in_stream = gt_gtf_in_stream_new(argv[parsed_args]);
  if (arguments->tidy)
    gt_gtf_in_stream_enable_tidy_mode(gtf_in_stream);

  /* create a GFF3 output stream */
  gff3_out_stream = gt_gff3_out_stream_new(gtf_in_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(gtf_in_stream);

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movq %r8, %rbx
movq %rcx, %r14
movl %edx, %ebp
movq %rsi, %r15
testq %r8, %r8
je 0xad3bd
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xad41d
testq %r14, %r14
je 0xad418
movslq %ebp, %rax
movq (%r15,%rax,8), %rdi
callq 0x154286
movq %rax, %r15
cmpb $0x1, (%r14)
jne 0xad3df
movq %r15, %rdi
callq 0x1542f3
movq 0x10(%r14), %rsi
movq %r15, %rdi
callq 0x14e310
movq %rax, %r14
movq %rax, %rdi
movq %rbx, %rsi
callq 0x16adca
movl %eax, %ebx
movq %r14, %rdi
callq 0x16ac6e
movq %r15, %rdi
callq 0x16ac6e
movl %ebx, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
callq 0x1ba9a
callq 0x1ba63
nop
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_guessprot.c
// Function: gt_guessprot
int gt_guessprot(int argc, const char **argv, GtError *err)
{
  int i, parsed_args, retval;
  GtStrArray *filenametab;

  gt_error_check(err);

  switch (parse_options(&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;
  }

  filenametab = gt_str_array_new();
  for (i=parsed_args; i < argc; i++)
  {
    gt_str_array_add_cstr(filenametab,argv[i]);
  }
  retval = gt_files_guess_if_protein_sequences(filenametab,err);
  gt_str_array_delete(filenametab);
  if (retval < 0)
  {
    return -1;
  }
  if (retval == 1)
  {
    /*@ignore@*/
    exit(EXIT_FAILURE); /* guess it is a protein sequence */
    /*@end@*/

  } else
  {
    return 0;
  }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rdx, %rbx
movq %rsi, %r15
movl %edi, %r14d
testq %rdx, %rdx
je 0xad462
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xad523
testq %rbx, %rbx
je 0xad462
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xad528
leaq 0x2ec1cb(%rip), %rdi    # 0x399634
leaq 0x2a9d39(%rip), %rsi    # 0x3571a9
callq 0x10cc4e
movq %rax, %r13
movq %rax, %rdi
movl $0x1, %esi
callq 0x10d766
leaq 0x77f3c(%rip), %r8      # 0x1253c8
leaq 0x4(%rsp), %rsi
movq %r13, %rdi
movl %r14d, %edx
movq %r15, %rcx
movq %rbx, %r9
callq 0x10d796
movl %eax, %r12d
movq %r13, %rdi
callq 0x10f2d0
movl $0xffffffff, %ebp       # imm = 0xFFFFFFFF
cmpl $0x1, %r12d
je 0xad512
cmpl $0x2, %r12d
jne 0xad4c2
xorl %ebp, %ebp
jmp 0xad512
callq 0x121b54
movq %rax, %r12
movslq 0x4(%rsp), %rax
cmpl %eax, %r14d
jle 0xad4f2
leaq (%r15,%rax,8), %r15
subl %eax, %r14d
xorl %r13d, %r13d
movq (%r15,%r13,8), %rsi
movq %r12, %rdi
callq 0x121c30
incq %r13
cmpl %r13d, %r14d
jne 0xad4de
movq %r12, %rdi
movq %rbx, %rsi
callq 0x1047c0
movl %eax, %ebx
movq %r12, %rdi
callq 0x121e8b
testl %ebx, %ebx
js 0xad512
xorl %ebp, %ebp
cmpl $0x1, %ebx
je 0xad52d
movl %ebp, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x1bb08
callq 0x1bad1
movl $0x1, %edi
callq 0x17940
nop
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_hop.c
// Function: gt_hop_arguments_check
int gt_hop_arguments_check(GT_UNUSED int rest_argc, void *tool_arguments,
    GtError* err)
{
  GtHopArguments *args = (GtHopArguments*) tool_arguments;
  int had_err = 0;

  if (!args->aggressive &&
      !args->moderate &&
      !args->conservative &&
      !args->expert &&
      !args->state_of_truth)
  {
    gt_error_set(err, "Select correction mode: "
        "-aggressive, -moderate, -conservative or -expert");
    had_err = -1;
  }
  else if (args->aggressive || args->state_of_truth)
  {
    args->hmin = 3UL;
    args->read_hmin = 1UL;
    args->qmax = 120UL;
    args->altmax = (double) 1.00;
    args->cogmin = (double) 0.00;
    args->mapqmin = 0UL;
    args->covmin = 1UL;
    args->clenmax = ULONG_MAX;
    args->allow_multiple = true;
  }
  else if (args->moderate)
  {
    args->hmin = 3UL;
    args->read_hmin = 1UL;
    args->qmax = 120UL;
    args->altmax = (double) 0.99;
    args->cogmin = (double) 0.00;
    args->mapqmin = 10UL;
    args->covmin = 1UL;
    args->clenmax = ULONG_MAX;
    args->allow_multiple = true;
  }
  else if (args->conservative)
  {
    args->hmin = 3UL;
    args->read_hmin = 2UL;
    args->qmax = 120UL;
    args->altmax = (double) 0.80;
    args->cogmin = (double) 0.10;
    args->mapqmin = 21UL;
    args->covmin = 1UL;
    args->clenmax = ULONG_MAX;
    args->allow_multiple = false;
  }

  if (gt_str_length(args->outprefix) == 0)
  {
    gt_error_set(err, "outprefix cannot be an empty string");
    had_err = -1;
  }
  return had_err;
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
movq %rdx, %rbx
movq %rsi, %r14
movb 0x66(%rsi), %al
testb %al, %al
jne 0xad574
cmpb $0x0, 0x67(%r14)
jne 0xad569
cmpb $0x0, 0x68(%r14)
jne 0xad569
cmpb $0x0, 0x69(%r14)
jne 0xad569
cmpb $0x0, 0x6a(%r14)
je 0xad666
testb %al, %al
jne 0xad574
cmpb $0x1, 0x6a(%r14)
jne 0xad5e0
movq $0x3, 0x30(%r14)
movl $0x1, %eax
movq %rax, 0x40(%r14)
movq $0x78, 0x58(%r14)
movsd 0x2a1c93(%rip), %xmm0   # 0x34f228
movups %xmm0, 0x70(%r14)
movq $0x0, 0x50(%r14)
movq %rax, 0x48(%r14)
movq $-0x1, 0x38(%r14)
movb $0x1, 0x65(%r14)
xorl %ebp, %ebp
movq 0x28(%r14), %rdi
callq 0x120d4c
testq %rax, %rax
jne 0xad5d9
leaq 0x2a9c87(%rip), %rsi    # 0x357251
movq %rbx, %rdi
xorl %eax, %eax
callq 0x1019cf
movl $0xffffffff, %ebp       # imm = 0xFFFFFFFF
movl %ebp, %eax
popq %rbx
popq %r14
popq %rbp
retq
cmpb $0x1, 0x67(%r14)
jne 0xad617
movq $0x3, 0x30(%r14)
movl $0x1, %eax
movq %rax, 0x40(%r14)
movq $0x78, 0x58(%r14)
movsd 0x2a9be8(%rip), %xmm0   # 0x3571f0
movups %xmm0, 0x70(%r14)
movq $0xa, 0x50(%r14)
jmp 0xad5a2
xorl %ebp, %ebp
cmpb $0x1, 0x68(%r14)
jne 0xad5b5
movq $0x3, 0x30(%r14)
movq $0x2, 0x40(%r14)
movq $0x78, 0x58(%r14)
movaps 0x2a9ba1(%rip), %xmm0   # 0x3571e0
movups %xmm0, 0x70(%r14)
movq $0x15, 0x50(%r14)
movq $0x1, 0x48(%r14)
movq $-0x1, 0x38(%r14)
movb $0x0, 0x65(%r14)
jmp 0xad5b5
leaq 0x2a9b9b(%rip), %rsi    # 0x357208
movq %rbx, %rdi
xorl %eax, %eax
callq 0x1019cf
movl $0xffffffff, %ebp       # imm = 0xFFFFFFFF
jmp 0xad5b5
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_hop.c
// Function: gt_hop_arguments_new
static void* gt_hop_arguments_new(void)
{
  GtHopArguments *arguments = gt_malloc(sizeof (*arguments));
  arguments->encseqinput = gt_str_new();
  arguments->annotation = gt_str_new();
  arguments->atype = gt_str_new();
  arguments->map = gt_str_new();
  arguments->outfilename = gt_str_new();
  arguments->outprefix = gt_str_new();
  arguments->readset = gt_str_array_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2a9bc4(%rip), %rsi    # 0x357275
movl $0x88, %edi
movl $0x27, %edx
callq 0x1092b2
movq %rax, %rbx
callq 0x1208f8
movq %rax, (%rbx)
callq 0x1208f8
movq %rax, 0x8(%rbx)
callq 0x1208f8
movq %rax, 0x20(%rbx)
callq 0x1208f8
movq %rax, 0x10(%rbx)
callq 0x1208f8
movq %rax, 0x18(%rbx)
callq 0x1208f8
movq %rax, 0x28(%rbx)
callq 0x121b54
movq %rax, 0x80(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_hop.c
// Function: gt_hop_arguments_delete
static void gt_hop_arguments_delete(void *tool_arguments)
{
  GtHopArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->encseqinput);
  gt_str_delete(arguments->annotation);
  gt_str_delete(arguments->atype);
  gt_str_delete(arguments->map);
  gt_str_delete(arguments->outfilename);
  gt_str_delete(arguments->outprefix);
  gt_str_array_delete(arguments->readset);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xad768
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x121b03
movq 0x8(%rbx), %rdi
callq 0x121b03
movq 0x20(%rbx), %rdi
callq 0x121b03
movq 0x10(%rbx), %rdi
callq 0x121b03
movq 0x18(%rbx), %rdi
callq 0x121b03
movq 0x28(%rbx), %rdi
callq 0x121b03
movq 0x80(%rbx), %rdi
callq 0x121e8b
leaq 0x2a9b1b(%rip), %rsi    # 0x357275
movq %rbx, %rdi
movl $0x3d, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_id_to_md5.c
// Function: gt_id_to_md5_arguments_new
static void *gt_id_to_md5_arguments_new(void)
{
  SeqidsToMD5Arguments *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 0x2a9b4a(%rip), %rdx    # 0x35808d
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_id_to_md5.c
// Function: gt_id_to_md5_arguments_delete
static void gt_id_to_md5_arguments_delete(void *tool_arguments)
{
  SeqidsToMD5Arguments *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 0xae5aa
pushq %rbx
movq %rdi, %rbx
movq 0x18(%rdi), %rdi
callq 0x1040fc
movq 0x10(%rbx), %rdi
callq 0x110231
movq 0x8(%rbx), %rdi
callq 0x17b067
leaq 0x2a9af1(%rip), %rsi    # 0x35808d
movq %rbx, %rdi
movl $0x35, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_id_to_md5.c
// Function: gt_id_to_md5_option_parser_new
static GtOptionParser* gt_id_to_md5_option_parser_new(void *tool_arguments)
{
  SeqidsToMD5Arguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  op = gt_option_parser_new("[option ...] [GFF3_file ...]",
                            "Change sequence IDs in given GFF3 files to MD5 "
                            "fingerprints of the corresponding sequences.");

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

  /* -subtargetids */
  option = gt_option_new_bool("subtargetids", "substitute the target IDs with "
                              "MD5 sums", &arguments->substitute_target_ids,
                              true);
  gt_option_parser_add_option(op, option);

  /* -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);

  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xae646
movq %rdi, %r14
leaq 0x2a4f47(%rip), %rdi    # 0x353509
leaq 0x2a9afc(%rip), %rsi    # 0x3580c5
callq 0x10cc4e
movq %rax, %rbx
movq 0x8(%r14), %rsi
movq %rax, %rdi
callq 0x17b366
leaq 0x1(%r14), %rdx
leaq 0x2a9b39(%rip), %rdi    # 0x358121
leaq 0x2a9b3f(%rip), %rsi    # 0x35812e
movl $0x1, %ecx
callq 0x10f451
movq %rbx, %rdi
movq %rax, %rsi
callq 0x10cd10
movq %r14, %rdi
callq 0x10f473
movq %rbx, %rdi
movq %rax, %rsi
callq 0x10cd10
movq 0x10(%r14), %rdi
addq $0x18, %r14
movq %rbx, %rsi
movq %r14, %rdx
callq 0x10ffa3
leaq 0xa586b(%rip), %rsi     # 0x153e9c
movq %rbx, %rdi
xorl %edx, %edx
callq 0x10cd8d
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x1bccc
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_id_to_md5.c
// Function: gt_id_to_md5_runner
static int gt_id_to_md5_runner(GT_UNUSED int argc, const char **argv,
                                   int parsed_args, void *tool_arguments,
                                   GtError *err)
{
  GtNodeStream *gff3_in_stream, *id_to_md5_stream = NULL,
               *add_ids_stream = NULL, *gff3_out_stream = NULL;
  SeqidsToMD5Arguments *arguments = tool_arguments;
  GtRegionMapping *region_mapping;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

  /* create a gff3 input stream */
  gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
                                                  argv + parsed_args);
  if (arguments->verbose && arguments->outfp)
    gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) gff3_in_stream);
  /* add automatically generated sequence IDs later to avoid collisions */
  gt_gff3_in_stream_disable_add_ids(gff3_in_stream);

  /* create region mapping */
  region_mapping = gt_seqid2file_region_mapping_new(arguments->s2fi, err);
  if (!region_mapping)
    had_err = -1;

  if (!had_err) {
    /* create seqid to md5 stream */
    id_to_md5_stream =
      gt_id_to_md5_stream_new(gff3_in_stream, region_mapping,
                              arguments->substitute_target_ids);

    /* create add IDs stream */
    add_ids_stream = gt_add_ids_stream_new(id_to_md5_stream);

    /* create gff3 output stream */
    gff3_out_stream = gt_gff3_out_stream_new(add_ids_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(add_ids_stream);
  gt_node_stream_delete(id_to_md5_stream);
  gt_node_stream_delete(gff3_in_stream);

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r8, %r14
movq %rcx, %r15
movl %edx, %ebp
movq %rsi, %r12
movl %edi, %ebx
testq %r8, %r8
je 0xae678
movq %r14, %rdi
callq 0x101a9a
testb %al, %al
jne 0xae742
testq %r15, %r15
je 0xae73d
subl %ebp, %ebx
movslq %ebp, %rax
leaq (%r12,%rax,8), %rsi
movl %ebx, %edi
callq 0x14d00b
movq %rax, %rbx
cmpb $0x1, (%r15)
jne 0xae6a9
cmpq $0x0, 0x18(%r15)
je 0xae6a9
movq %rbx, %rdi
callq 0x14ce62
movq %rbx, %rdi
callq 0x14cf7f
movq 0x8(%r15), %rdi
movq %r14, %rsi
callq 0x17b3bd
testq %rax, %rax
je 0xae6fe
movzbl 0x1(%r15), %edx
movq %rbx, %rdi
movq %rax, %rsi
callq 0x15d8d8
movq %rax, %r12
movq %rax, %rdi
callq 0x125eb4
movq %rax, %r13
movq 0x18(%r15), %rsi
movq %rax, %rdi
callq 0x14e310
movq %rax, %r15
movq %rax, %rdi
movq %r14, %rsi
callq 0x16adca
movl %eax, %ebp
jmp 0xae70c
movl $0xffffffff, %ebp       # imm = 0xFFFFFFFF
xorl %r15d, %r15d
xorl %r13d, %r13d
xorl %r12d, %r12d
movq %r15, %rdi
callq 0x16ac6e
movq %r13, %rdi
callq 0x16ac6e
movq %r12, %rdi
callq 0x16ac6e
movq %rbx, %rdi
callq 0x16ac6e
movl %ebp, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x1bd3a
callq 0x1bd03
nop
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_idxlocali.c
// Function: gt_idxlocali_arguments_delete
static void gt_idxlocali_arguments_delete(void *tool_arguments)
{
  IdxlocaliOptions *arguments = tool_arguments;

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

// Assembly:
testq %rdi, %rdi
je 0xae7c7
pushq %rbx
movq %rdi, %rbx
movq 0x8(%rdi), %rdi
callq 0x121b03
movq (%rbx), %rdi
callq 0x121e8b
movq 0x10(%rbx), %rdi
callq 0x10f386
movq 0x18(%rbx), %rdi
callq 0x10f386
leaq 0x2a99b1(%rip), %rsi    # 0x35816a
movq %rbx, %rdi
movl $0x2c, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_idxlocali.c
// Function: gt_idxlocali_arguments_check
static int gt_idxlocali_arguments_check(GT_UNUSED int rest_argc,
                                        void *tool_arguments,
                                        GT_UNUSED GtError * err)
{
  IdxlocaliOptions *arguments = tool_arguments;

  if (gt_option_is_set(arguments->refoptionesaindex))
  {
    arguments->withesa = true;
  } else
  {
    gt_assert(gt_option_is_set(arguments->refoptionpckindex));
    arguments->withesa = false;
  }
  return 0;
}

// Assembly:
pushq %rbx
movq %rsi, %rbx
movq 0x10(%rsi), %rdi
callq 0x10fe52
movb $0x1, %cl
testb %al, %al
jne 0xaea58
movq 0x18(%rbx), %rdi
callq 0x10fe52
testb %al, %al
je 0xaea5f
xorl %ecx, %ecx
movb %cl, 0x20(%rbx)
xorl %eax, %eax
popq %rbx
retq
callq 0x1bda8
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_idxlocali.c
// Function: gt_idxlocali_runner
static int gt_idxlocali_runner(GT_UNUSED int argc,
                               GT_UNUSED const char **argv,
                               GT_UNUSED int parsed_args,
                               void *tool_arguments,
                               GtError * err)
{
  IdxlocaliOptions *arguments = tool_arguments;
  bool haserr = false;
  GtUword idx;

  gt_error_check(err);
  gt_assert(arguments != NULL);

  gt_assert(parsed_args == argc);
  printf("# indexname(%s)=%s\n", arguments->withesa ? "esa" : "pck",
         gt_str_get(arguments->indexname));
  for (idx = 0; idx < gt_str_array_size (arguments->queryfiles); idx++)
  {
    printf("# queryfile=%s\n",gt_str_array_get (arguments->queryfiles, idx));
  }
  printf("# threshold="GT_WU"\n", arguments->threshold);
  if (!haserr && gt_runidxlocali (arguments, err) != 0)
  {
    haserr = true;
  }
  return haserr ? -1 : 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movq %r8, %rbx
movq %rcx, %r14
movl %edx, %ebp
movl %edi, %r15d
testq %r8, %r8
je 0xaea8c
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xaeb49
testq %r14, %r14
je 0xaeb3f
cmpl %r15d, %ebp
jne 0xaeb44
leaq 0x2b41dd(%rip), %rax    # 0x362c82
cmpb $0x0, 0x20(%r14)
leaq 0x2a7d2d(%rip), %r15    # 0x3567de
cmovneq %rax, %r15
movq 0x8(%r14), %rdi
callq 0x120d23
leaq 0x2a984b(%rip), %rdi    # 0x358310
xorl %ebp, %ebp
movq %r15, %rsi
movq %rax, %rdx
xorl %eax, %eax
callq 0x17070
movq (%r14), %rdi
callq 0x121e78
testq %rax, %rax
je 0xaeb13
leaq 0x2a4362(%rip), %r15    # 0x352e4a
xorl %r12d, %r12d
movq (%r14), %rdi
movq %r12, %rsi
callq 0x121cfa
movq %r15, %rdi
movq %rax, %rsi
xorl %eax, %eax
callq 0x17070
incq %r12
movq (%r14), %rdi
callq 0x121e78
cmpq %rax, %r12
jb 0xaeaeb
movq 0x28(%r14), %rsi
leaq 0x2a9806(%rip), %rdi    # 0x358324
xorl %eax, %eax
callq 0x17070
movq %r14, %rdi
movq %rbx, %rsi
callq 0x1bc959
negl %eax
sbbl %ebp, %ebp
movl %ebp, %eax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
callq 0x1be53
callq 0x1be1a
callq 0x1bde1
nop
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_inlineseq_add.c
// Function: gt_inlineseq_add_arguments_new
static void *gt_inlineseq_add_arguments_new(void)
{
  InlineseqAddArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->s2fi = gt_seqid2file_info_new();
  arguments->ofi = gt_output_file_info_new();
  arguments->outfp = NULL;
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2a97ba(%rip), %rdx    # 0x358335
movl $0x1, %edi
movl $0x18, %esi
movl $0x24, %ecx
callq 0x1093ef
movq %rax, %rbx
callq 0x17b020
movq %rax, (%rbx)
callq 0x10ff7c
movq %rax, 0x8(%rbx)
movq $0x0, 0x10(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_inlineseq_add.c
// Function: gt_inlineseq_add_arguments_delete
static void gt_inlineseq_add_arguments_delete(void *tool_arguments)
{
  InlineseqAddArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_seqid2file_info_delete(arguments->s2fi);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xaebe8
pushq %rbx
movq %rdi, %rbx
movq 0x10(%rdi), %rdi
callq 0x1040fc
movq (%rbx), %rdi
callq 0x17b067
movq 0x8(%rbx), %rdi
callq 0x110231
leaq 0x2a975b(%rip), %rsi    # 0x358335
movq %rbx, %rdi
movl $0x32, %edx
popq %rbx
jmp 0x109670
retq