LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_linspace_align.c
// Function: gt_sequence_table_delete
static void gt_sequence_table_delete(GtSequenceTable *sequence_table)
{
  GtUword i;
  if (sequence_table != NULL)
  {
    for (i = 0; i < sequence_table->size ; i++)
    {
      gt_str_delete(sequence_table->seqarray[i]);
    }
    gt_free(sequence_table->seqarray);
    gt_free(sequence_table);
  }
}

// Assembly:
testq %rdi, %rdi
je 0xaeced
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
cmpq $0x0, 0x8(%rdi)
je 0xaecbf
xorl %r14d, %r14d
movq (%rbx), %rax
movq (%rax,%r14,8), %rdi
callq 0x11bdbf
incq %r14
cmpq 0x8(%rbx), %r14
jb 0xaecaa
movq (%rbx), %rdi
leaq 0x2a0d97(%rip), %r14    # 0x34fa60
movq %r14, %rsi
movl $0x80, %edx
callq 0x1045eb
movq %rbx, %rdi
movq %r14, %rsi
movl $0x81, %edx
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_linspace_align.c
// Function: gt_sequence_table_new
static GtSequenceTable* gt_sequence_table_new()
{
  GtSequenceTable *sequence_table;

  sequence_table = gt_malloc(sizeof(*sequence_table));
  sequence_table->seqarray = gt_malloc(sizeof(*sequence_table->seqarray));
  sequence_table->size = 0;
  sequence_table->maxsize = 1;
  return sequence_table;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
leaq 0x2a0d67(%rip), %rbx    # 0x34fa60
movl $0x18, %edi
movq %rbx, %rsi
movl $0x70, %edx
callq 0x104226
movq %rax, %r14
movl $0x8, %edi
movq %rbx, %rsi
movl $0x71, %edx
callq 0x104226
movq %rax, (%r14)
movq $0x0, 0x8(%r14)
movq $0x1, 0x10(%r14)
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_linspace_align.c
// Function: save_fastasequence
static int save_fastasequence(const char *seqpart, GT_UNUSED GtUword length,
                              void *data, GT_UNUSED GtError* err)
{
  GtSequenceTable *fasta_seqs = (GtSequenceTable*) data;

  if (fasta_seqs->maxsize == fasta_seqs->size)
  {
    fasta_seqs->maxsize += 10;
    fasta_seqs->seqarray = gt_realloc(fasta_seqs->seqarray,
                                      fasta_seqs->maxsize*
                                      sizeof (*fasta_seqs->seqarray));
  }
  fasta_seqs->seqarray[fasta_seqs->size++] = gt_str_new_cstr(seqpart);
  return 0;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdx, %rbx
movq %rdi, %r14
movq 0x10(%rdx), %rax
cmpq 0x8(%rdx), %rax
jne 0xaed79
leaq 0xa(%rax), %rcx
movq %rcx, 0x10(%rbx)
movq (%rbx), %rdi
leaq 0x50(,%rax,8), %rsi
leaq 0x2a0cf4(%rip), %rdx    # 0x34fa60
movl $0x1cf, %ecx            # imm = 0x1CF
callq 0x104461
movq %rax, (%rbx)
movq %r14, %rdi
callq 0x11acc9
movq (%rbx), %rcx
movq 0x8(%rbx), %rdx
leaq 0x1(%rdx), %rsi
movq %rsi, 0x8(%rbx)
movq %rax, (%rcx,%rdx,8)
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_linspace_align.c
// Function: gt_linspace_print_sequence
static void gt_linspace_print_sequence(const GtUchar *characters,
                                       GtUchar wildcardshow,
                                       const GtUchar *seq, GtUword len,
                                       FILE *fp)
{
  const GtUword linewidth = 80;
  GtUword idx;

  fprintf(fp, "######\n");
  for (idx = 0; idx < len; idx++)
  {
    GtUchar cc;
    if (characters == NULL)
    {
      cc = seq[idx];
    } else
    {
      if (GT_ISSPECIAL(seq[idx]))
      {
        cc = wildcardshow;
      } else
      {
        cc = characters[seq[idx]];
      }
    }
    fputc(cc,fp);
    if ((idx + 1) % linewidth == 0)
    {
      fputc('\n',fp);
    }
  }
  if (idx % linewidth != 0)
  {
    fputc('\n',fp);
  }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %r8, %rbx
movq %rcx, %r14
movq %rdx, 0x10(%rsp)
movl %esi, 0xc(%rsp)
movq %rdi, %r12
leaq 0x3326c9(%rip), %rdi    # 0x3e15dd
movl $0x1, %r13d
movl $0x7, %esi
movl $0x1, %edx
movq %r8, %rcx
callq 0x17fa0
testq %r14, %r14
je 0xaefdb
xorl %ebp, %ebp
movq %r13, %rax
movabsq $-0x3333333333333333, %rcx # imm = 0xCCCCCCCCCCCCCCCD
mulq %rcx
movq 0x10(%rsp), %rax
movb (%rax,%rbp), %cl
testq %r12, %r12
je 0xaef66
movl 0xc(%rsp), %eax
cmpb $-0x3, %cl
ja 0xaef68
movzbl %cl, %eax
movb (%r12,%rax), %al
jmp 0xaef68
movl %ecx, %eax
shrq $0x6, %rdx
leaq (%rdx,%rdx,4), %r15
shlq $0x4, %r15
decq %r15
movzbl %al, %edi
movq %rbx, %rsi
callq 0x17980
cmpq %rbp, %r15
jne 0xaef94
movl $0xa, %edi
movq %rbx, %rsi
callq 0x17980
incq %rbp
incq %r13
cmpq %rbp, %r14
jne 0xaef37
movabsq $-0x3333333333333333, %rax # imm = 0xCCCCCCCCCCCCCCCD
imulq %rax, %r14
rorq $0x4, %r14
movabsq $0x333333333333334, %rax # imm = 0x333333333333334
cmpq %rax, %r14
jb 0xaefdb
movl $0xa, %edi
movq %rbx, %rsi
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x17980
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_loccheck.c
// Function: gt_loccheck_runner
static int gt_loccheck_runner(int argc, const char **argv, int parsed_args,
                              GT_UNUSED void *tool_arguments, GtError *err)
{
  GtNodeStream *gff3_in_stream = NULL, *checker_stream = NULL;
  int had_err = 0;
  gt_error_check(err);

  gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
                                                  argv + parsed_args);

  checker_stream = gt_visitor_stream_new(gff3_in_stream,
                                         gt_check_boundaries_visitor_new());
  gt_assert(checker_stream);

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

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

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movq %r8, %rbx
movl %edx, %r15d
movq %rsi, %r14
movl %edi, %ebp
testq %r8, %r8
je 0xaf03b
movq %rbx, %rdi
callq 0xfcc32
testb %al, %al
jne 0xaf096
subl %r15d, %ebp
movslq %r15d, %rax
leaq (%r14,%rax,8), %rsi
movl %ebp, %edi
callq 0x145cdf
movq %rax, %r14
callq 0x128c45
movq %r14, %rdi
movq %rax, %rsi
callq 0x1841d5
testq %rax, %rax
je 0xaf091
movq %rax, %r15
movq %rax, %rdi
movq %rbx, %rsi
callq 0x162f5d
movl %eax, %ebx
movq %r14, %rdi
callq 0x162dee
movq %r15, %rdi
callq 0x162dee
movl %ebx, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
callq 0x1c426
callq 0x1c3ef
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_magicmatch.c
// Function: gt_magicmatch_option_parser_new
static GtOptionParser* gt_magicmatch_option_parser_new(void *tool_arguments)
{
  MagicMatchArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *o;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] -f sequence_file [...] -t",
                         "Compute MD5 fingerprints for each sequence given in "
                         "sequence_file(s).");

  /* -f */
  o = gt_option_new_filename_array("f", "fasta file names (at least one file "
                                   "is required)", arguments->seqfiles);
  gt_option_is_mandatory(o);
  gt_option_parser_add_option(op, o);

  /* -t */
  o = gt_option_new_bool("t", "translate the sequences of the files",
                         &arguments->translate, false);
  gt_option_is_mandatory(o);
  gt_option_parser_add_option(op, o);

  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
  gt_option_parser_set_min_max_args(op, 0, 0);

  return op;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0xaf1bd
movq %rdi, %r14
leaq 0x2a1348(%rip), %rdi    # 0x350472
leaq 0x2a1368(%rip), %rsi    # 0x350499
callq 0x107bfe
movq %rax, %rbx
movq (%r14), %rdx
leaq 0x2ae081(%rip), %rdi    # 0x35d1c4
leaq 0x2a1395(%rip), %rsi    # 0x3504df
callq 0x10a7df
movq %rax, %r15
movq %rax, %rdi
callq 0x10a87b
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
addq $0x8, %r14
leaq 0x31590b(%rip), %rdi    # 0x3c4a7b
leaq 0x2a1399(%rip), %rsi    # 0x350510
movq %r14, %rdx
xorl %ecx, %ecx
callq 0x10a235
movq %rax, %r14
movq %rax, %rdi
callq 0x10a87b
movq %rbx, %rdi
movq %r14, %rsi
callq 0x107cc0
leaq 0x9d726(%rip), %rsi     # 0x14c8c4
movq %rbx, %rdi
xorl %edx, %edx
callq 0x107d3d
movq %rbx, %rdi
xorl %esi, %esi
xorl %edx, %edx
callq 0x10874b
movq %rbx, %rax
popq %rbx
popq %r14
popq %r15
retq
callq 0x1c45d
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_magicmatch.c
// Function: gt_magicmatch_runner
static int gt_magicmatch_runner(GT_UNUSED int argc, GT_UNUSED const char **argv,
                                GT_UNUSED int parsed_args, void *tool_arguments,
                                GtError *err)
{
  MagicMatchArguments *arguments = tool_arguments;
  GtBioseq *bioseq;
  GtUword i;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

  if (arguments->translate) {
    for (i = 0; !had_err && i < gt_str_array_size(arguments->seqfiles); i++) {
      if (!(bioseq = gt_bioseq_new(gt_str_array_get(arguments->seqfiles, i),
                                   err))) {
        had_err = -1;
      }
      if (!had_err)
        translate_sequence_file(bioseq);
      gt_bioseq_delete(bioseq);
    }
  }

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r8, %rbx
movq %rcx, %r14
testq %r8, %r8
je 0xaf1e8
movq %rbx, %rdi
callq 0xfcc32
testb %al, %al
jne 0xaf2c9
testq %r14, %r14
je 0xaf2c4
xorl %eax, %eax
cmpb $0x1, 0x8(%r14)
jne 0xaf2b5
leaq 0x2d4dfc(%rip), %r12    # 0x384001
xorl %r13d, %r13d
movq %r14, (%rsp)
movq (%r14), %rdi
callq 0x11c131
cmpq %rax, %r13
jae 0xaf2a4
movq (%r14), %rdi
movq %r13, %rsi
callq 0x11bfb3
movq %rax, %rdi
movq %rbx, %rsi
callq 0xd4388
movq %rax, %rbp
testq %rax, %rax
je 0xaf2a8
movq %rbx, %r14
movq %rbp, %rdi
callq 0xd4fc8
testq %rax, %rax
je 0xaf287
xorl %r15d, %r15d
movq %rbp, %rdi
movq %r15, %rsi
callq 0xd4f66
movq %rax, %rbx
movq %rbp, %rdi
movq %r15, %rsi
callq 0xd4bb7
movq %r12, %rdi
movq %rbx, %rsi
movq %rax, %rdx
xorl %eax, %eax
callq 0x17070
incq %r15
movq %rbp, %rdi
callq 0xd4fc8
cmpq %rax, %r15
jb 0xaf24e
movq %rbp, %rdi
callq 0xd491d
incq %r13
testq %rbp, %rbp
movq %r14, %rbx
movq (%rsp), %r14
jne 0xaf20c
jmp 0xaf2b0
xorl %eax, %eax
jmp 0xaf2b5
movq %rbp, %rdi
callq 0xd491d
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x1c4cb
callq 0x1c494
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_matchtool.c
// Function: gt_matchtool_arguments_new
static void* gt_matchtool_arguments_new(void)
{
  GtMatchtoolArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->type = gt_str_new();
  arguments->matchfile = gt_str_new();
  arguments->query = gt_str_new();
  arguments->db = gt_str_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2a124a(%rip), %rdx    # 0x35054a
movl $0x1, %edi
movl $0x30, %esi
movl $0x2e, %ecx
callq 0x10436a
movq %rax, %rbx
callq 0x11ac6c
movq %rax, (%rbx)
callq 0x11ac6c
movq %rax, 0x8(%rbx)
callq 0x11ac6c
movq %rax, 0x10(%rbx)
callq 0x11ac6c
movq %rax, 0x18(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_matchtool.c
// Function: gt_matchtool_arguments_delete
static void gt_matchtool_arguments_delete(void *tool_arguments)
{
  GtMatchtoolArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->type);
  gt_str_delete(arguments->matchfile);
  gt_str_delete(arguments->query);
  gt_str_delete(arguments->db);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xaf380
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x11bdbf
movq 0x8(%rbx), %rdi
callq 0x11bdbf
movq 0x10(%rbx), %rdi
callq 0x11bdbf
movq 0x18(%rbx), %rdi
callq 0x11bdbf
leaq 0x2a11d8(%rip), %rsi    # 0x35054a
movq %rbx, %rdi
movl $0x3e, %edx
popq %rbx
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_matstat.c
// Function: gt_matstat_arguments_delete
static void gt_matstat_arguments_delete(void *tool_arguments)
{
  Gfmsubcallinfo *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_array_delete(arguments->queryfilenames);
  gt_str_array_delete(arguments->flagsoutputoption);
  gt_str_delete(arguments->indexname);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xaffa3
pushq %rbx
movq %rdi, %rbx
movq 0x30(%rdi), %rdi
callq 0x11c144
movq 0x38(%rbx), %rdi
callq 0x11c144
movq 0x28(%rbx), %rdi
callq 0x11bdbf
leaq 0x2a0a98(%rip), %rsi    # 0x350a2d
movq %rbx, %rdi
movl $0x5d, %edx
popq %rbx
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_matstat.c
// Function: gt_matstat_arguments_new_generic
static void* gt_matstat_arguments_new_generic(bool doms)
{
  Gfmsubcallinfo *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->minlength.defined = false;
  arguments->maxlength.defined = false;
  arguments->showmode = 0;
  arguments->indexname = gt_str_new();
  arguments->queryfilenames = gt_str_array_new();
  arguments->flagsoutputoption = gt_str_array_new();
  arguments->doms = doms;
  return arguments;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movl %edi, %ebx
leaq 0x2a03e2(%rip), %rdx    # 0x350a2d
movl $0x1, %edi
movl $0x88, %esi
movl $0x41, %ecx
callq 0x10436a
movq %rax, %r14
xorl %eax, %eax
movb %al, (%r14)
movb %al, 0x10(%r14)
movl $0x0, 0x20(%r14)
callq 0x11ac6c
movq %rax, 0x28(%r14)
callq 0x11be10
movq %rax, 0x30(%r14)
callq 0x11be10
movq %rax, 0x38(%r14)
movb %bl, 0x44(%r14)
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_md5_to_id.c
// Function: gt_md5_to_id_arguments_new
static void *gt_md5_to_id_arguments_new(void)
{
  MD5ToSeqidsArguments *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 0x2a066b(%rip), %rdx    # 0x350d36
movl $0x1, %edi
movl $0x20, %esi
movl $0x26, %ecx
callq 0x10436a
movq %rax, %rbx
callq 0x172c40
movq %rax, 0x8(%rbx)
callq 0x10ad60
movq %rax, 0x10(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_md5_to_id.c
// Function: gt_md5_to_id_arguments_delete
static void gt_md5_to_id_arguments_delete(void *tool_arguments)
{
  MD5ToSeqidsArguments *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 0xb0732
pushq %rbx
movq %rdi, %rbx
movq 0x18(%rdi), %rdi
callq 0xff22c
movq 0x10(%rbx), %rdi
callq 0x10b00c
movq 0x8(%rbx), %rdi
callq 0x172c87
leaq 0x2a0612(%rip), %rsi    # 0x350d36
movq %rbx, %rdi
movl $0x33, %edx
popq %rbx
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_md5_to_id.c
// Function: gt_md5_to_id_option_parser_new
static GtOptionParser* gt_md5_to_id_option_parser_new(void *tool_arguments)
{
  MD5ToSeqidsArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  op = gt_option_parser_new("[option ...] [GFF3_file ...]",
                            "Change MD5 fingerprints used as sequence IDs in "
                            "given GFF3 files to ``regular'' ones.");

  /* -seqfile, -matchdesc, -usedesc and -regionmapping */
  gt_seqid2file_register_options_ext(op, arguments->s2fi, false, true);

  /* -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);

  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xb0799
movq %rdi, %rbx
leaq 0x299db3(%rip), %rdi    # 0x34a4f9
leaq 0x2a0621(%rip), %rsi    # 0x350d6e
callq 0x107bfe
movq %rax, %r14
movq 0x8(%rbx), %rsi
movq %rax, %rdi
xorl %edx, %edx
movl $0x1, %ecx
callq 0x172cc9
movq %rbx, %rdi
callq 0x10a257
movq %r14, %rdi
movq %rax, %rsi
callq 0x107cc0
movq 0x10(%rbx), %rdi
addq $0x18, %rbx
movq %r14, %rsi
movq %rbx, %rdx
callq 0x10ad87
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x1c771
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_md5_to_id.c
// Function: gt_md5_to_id_runner
static int gt_md5_to_id_runner(GT_UNUSED int argc, const char **argv,
                                   int parsed_args, void *tool_arguments,
                                   GtError *err)
{
  GtNodeStream *gff3_in_stream, *md5_to_id_stream = NULL,
               *gff3_out_stream = NULL;
  MD5ToSeqidsArguments *arguments = tool_arguments;
  GtRegionMapping *region_mapping = NULL;
  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);

  /* create region mapping */
  if (gt_seqid2file_option_used(arguments->s2fi)) {
    region_mapping = gt_seqid2file_region_mapping_new(arguments->s2fi, err);
    if (!region_mapping)
      had_err = -1;
  }

  if (!had_err) {
    /* create seqid to md5 stream */
    md5_to_id_stream = gt_md5_to_id_stream_new(gff3_in_stream, region_mapping);

    /* create gff3 output stream */
    gff3_out_stream = gt_gff3_out_stream_new(md5_to_id_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(md5_to_id_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, %r15
movl %edx, %r12d
movq %rsi, %r14
movl %edi, %ebp
testq %r8, %r8
je 0xb07c9
movq %rbx, %rdi
callq 0xfcc32
testb %al, %al
jne 0xb087a
testq %r15, %r15
je 0xb0875
subl %r12d, %ebp
movslq %r12d, %rax
leaq (%r14,%rax,8), %rsi
movl %ebp, %edi
callq 0x145cdf
movq %rax, %r14
cmpb $0x1, (%r15)
jne 0xb07fb
cmpq $0x0, 0x18(%r15)
je 0xb07fb
movq %r14, %rdi
callq 0x145b36
movq 0x8(%r15), %rdi
callq 0x172f92
testb %al, %al
je 0xb0829
movq 0x8(%r15), %rdi
movq %rbx, %rsi
callq 0x172fdd
movq %rax, %rsi
testq %rax, %rax
jne 0xb082b
movl $0xffffffff, %ebx       # imm = 0xFFFFFFFF
xorl %r15d, %r15d
xorl %r12d, %r12d
jmp 0xb0852
xorl %esi, %esi
movq %r14, %rdi
callq 0x160704
movq %rax, %r12
movq 0x18(%r15), %rsi
movq %rax, %rdi
callq 0x146fc0
movq %rax, %r15
movq %rax, %rdi
movq %rbx, %rsi
callq 0x162f5d
movl %eax, %ebx
movq %r15, %rdi
callq 0x162dee
movq %r12, %rdi
callq 0x162dee
movq %r14, %rdi
callq 0x162dee
movl %ebx, %eax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
callq 0x1c7df
callq 0x1c7a8
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_merge.c
// Function: gt_merge_arguments_delete
static void gt_merge_arguments_delete(void *tool_arguments)
{
  MergeArguments *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 0xb08fe
pushq %rbx
movq %rdi, %rbx
movq 0x8(%rdi), %rdi
callq 0xff22c
movq (%rbx), %rdi
callq 0x10b00c
leaq 0x2a04e8(%rip), %rsi    # 0x350dd8
movq %rbx, %rdi
movl $0x30, %edx
popq %rbx
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_merge.c
// Function: gt_merge_option_parser_new
static GtOptionParser* gt_merge_option_parser_new(void *tool_arguments)
{
  MergeArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);
  op = gt_option_parser_new("[option ...] [GFF3_file ...]",
                         "Merge sorted GFF3 files in sorted fashion.");

  /* -retainids */
  option = gt_option_new_bool("retainids",
                              "when available, use the original IDs provided "
                              "in the source file\n"
                              "(memory consumption is proportional to the "
                              "input file size(s))", &arguments->retainids,
                              false);
  gt_option_parser_add_option(op, option);

  /* -tidy */
  option = gt_option_new_bool("tidy", "try to tidy the GFF3 files up "
                              "during parsing", &arguments->tidy, false);
  gt_option_parser_add_option(op, option);

  gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xb0986
movq %rdi, %rbx
leaq 0x299be7(%rip), %rdi    # 0x34a4f9
leaq 0x2a04ef(%rip), %rsi    # 0x350e08
callq 0x107bfe
movq %rax, %r14
leaq 0x10(%rbx), %rdx
leaq 0x32facf(%rip), %rdi    # 0x3e03fb
leaq 0x29d207(%rip), %rsi    # 0x34db3a
xorl %ecx, %ecx
callq 0x10a235
movq %r14, %rdi
movq %rax, %rsi
callq 0x107cc0
leaq 0x11(%rbx), %rdx
leaq 0x2cf16b(%rip), %rdi    # 0x37fabb
leaq 0x29d1b6(%rip), %rsi    # 0x34db0d
xorl %ecx, %ecx
callq 0x10a235
movq %r14, %rdi
movq %rax, %rsi
callq 0x107cc0
movq (%rbx), %rdi
addq $0x8, %rbx
movq %r14, %rsi
movq %rbx, %rdx
callq 0x10ad87
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x1c816
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_mergeesa.c
// Function: gt_mergeesa
int gt_mergeesa(int argc, const char **argv, GtError *err)
{
  GtStr *storeindex;
  GtStrArray *indexnametab;
  bool haserr = false;
  int parsed_args;

  gt_error_check(err);

  storeindex = gt_str_new();
  indexnametab = gt_str_array_new();
  switch (parse_options(storeindex, indexnametab, &parsed_args, argc, argv,
                        err)) {
    case GT_OPTION_PARSER_OK: break;
    case GT_OPTION_PARSER_ERROR:
         haserr = true; break;
    case GT_OPTION_PARSER_REQUESTS_EXIT: return 0;
  }
  if (!haserr)
  {
    GtUword i;
    GtLogger *logger;

    printf("# storeindex=%s\n",gt_str_get(storeindex));
    for (i=0; i<gt_str_array_size(indexnametab); i++)
    {
      printf("# input=%s\n",gt_str_array_get(indexnametab,i));
    }
    logger = gt_logger_new(false, GT_LOGGER_DEFLT_PREFIX, stdout);
    if (gt_performtheindexmerging(storeindex,
                              indexnametab,
                              logger,
                              err) != 0)
    {
      haserr = true;
    }
    gt_logger_delete(logger);
  }
  gt_str_delete(storeindex);
  gt_str_array_delete(indexnametab);
  return haserr ? -1 : 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rdx, %rbx
movq %rsi, %r12
movl %edi, %ebp
testq %rdx, %rdx
je 0xb0b39
movq %rbx, %rdi
callq 0xfcc32
testb %al, %al
jne 0xb0c31
callq 0x11ac6c
movq %rax, %r14
callq 0x11be10
movq %rax, %r15
leaq 0x4(%rsp), %rdx
movq %r14, %rdi
movq %rax, %rsi
movl %ebp, %ecx
movq %r12, %r8
movq %rbx, %r9
jmp 0xb0b5c
callq 0x11ac6c
movq %rax, %r14
callq 0x11be10
movq %rax, %r15
leaq 0x4(%rsp), %rdx
movq %r14, %rdi
movq %rax, %rsi
movl %ebp, %ecx
movq %r12, %r8
xorl %r9d, %r9d
callq 0xb0c36
cmpl $0x1, %eax
je 0xb0c0b
xorl %ebp, %ebp
cmpl $0x2, %eax
je 0xb0c20
movq %r14, %rdi
callq 0x11b0a1
leaq 0x2a02f0(%rip), %rdi    # 0x350e74
xorl %ebp, %ebp
movq %rax, %rsi
xorl %eax, %eax
callq 0x17070
movq %r15, %rdi
callq 0x11c131
testq %rax, %rax
je 0xb0bcf
leaq 0x2a02e1(%rip), %r12    # 0x350e85
xorl %r13d, %r13d
movq %r15, %rdi
movq %r13, %rsi
callq 0x11bfb3
movq %r12, %rdi
movq %rax, %rsi
xorl %eax, %eax
callq 0x17070
incq %r13
movq %r15, %rdi
callq 0x11c131
cmpq %rax, %r13
jb 0xb0ba7
movq 0x408302(%rip), %rax    # 0x4b8ed8
movq (%rax), %rdx
leaq 0x295cf4(%rip), %rsi    # 0x3468d4
xorl %edi, %edi
callq 0x103e40
movq %rax, %r12
movq %r14, %rdi
movq %r15, %rsi
movq %rax, %rdx
movq %rbx, %rcx
callq 0x200648
movl %eax, %ebx
movq %r12, %rdi
callq 0x1040e0
negl %ebx
sbbl %ebp, %ebp
jmp 0xb0c10
movl $0xffffffff, %ebp       # imm = 0xFFFFFFFF
movq %r14, %rdi
callq 0x11bdbf
movq %r15, %rdi
callq 0x11c144
movl %ebp, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x1c8f2
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_mergeesa.c
// Function: parse_options
static GtOPrval parse_options(GtStr *indexname,GtStrArray *indexnametab,
                              int *parsed_args, int argc,
                              const char **argv, GtError *err)
{
  GtOptionParser *op;
  GtOPrval oprval;
  GtOption *option;

  gt_error_check(err);
  op = gt_option_parser_new("storeindex <mkvindex1> <mkvindex2> ...",
                         "Merge indexes into one index.");
  gt_option_parser_set_mail_address(op,"<kurtz@zbh.uni-hamburg.de>");
  option = gt_option_new_filename_array("ii",
                                    "specify input index files (mandatory)",
                                    indexnametab);
  gt_option_is_mandatory(option);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string("indexname",
                             "specify index to be created",
                             indexname, NULL);

  gt_option_is_mandatory(option);
  gt_option_parser_add_option(op, option);

  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);
  gt_option_parser_delete(op);
  return oprval;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r9, %rbx
movq %r8, (%rsp)
movl %ecx, %ebp
movq %rdx, %r15
movq %rsi, %r14
movq %rdi, %r13
testq %r9, %r9
je 0xb0c68
movq %rbx, %rdi
callq 0xfcc32
testb %al, %al
jne 0xb0d1d
leaq 0x2a0222(%rip), %rdi    # 0x350e91
leaq 0x2a0242(%rip), %rsi    # 0x350eb8
callq 0x107bfe
movq %rax, %r12
leaq 0x295647(%rip), %rsi    # 0x3462cc
movq %rax, %rdi
callq 0x107e5c
leaq 0x3027df(%rip), %rdi    # 0x3b3473
leaq 0x2a023b(%rip), %rsi    # 0x350ed6
movq %r14, %rdx
callq 0x10a7df
movq %rax, %r14
movq %rax, %rdi
callq 0x10a87b
movq %r12, %rdi
movq %r14, %rsi
callq 0x107cc0
leaq 0x2b4e6d(%rip), %rdi    # 0x365b2d
leaq 0x2a0235(%rip), %rsi    # 0x350efc
movq %r13, %rdx
xorl %ecx, %ecx
callq 0x10a770
movq %rax, %r14
movq %rax, %rdi
callq 0x10a87b
movq %r12, %rdi
movq %r14, %rsi
callq 0x107cc0
leaq 0x6e91e(%rip), %r8      # 0x11f60c
movq %r12, %rdi
movq %r15, %rsi
movl %ebp, %edx
movq (%rsp), %rcx
movq %rbx, %r9
callq 0x10875d
movl %eax, %ebx
movq %r12, %rdi
callq 0x10a0b4
movl %ebx, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x1c929
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_mergefeat.c
// Function: gt_mergefeat_arguments_delete
static void gt_mergefeat_arguments_delete(void *tool_arguments)
{
  InterFeatArguments *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 0xb0da2
pushq %rbx
movq %rdi, %rbx
movq 0x8(%rdi), %rdi
callq 0xff22c
movq (%rbx), %rdi
callq 0x10b00c
leaq 0x2a0184(%rip), %rsi    # 0x350f18
movq %rbx, %rdi
movl $0x2b, %edx
popq %rbx
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_mergefeat.c
// Function: gt_mergefeat_option_parser_new
static GtOptionParser* gt_mergefeat_option_parser_new(void *tool_arguments)
{
  InterFeatArguments *arguments = tool_arguments;
  GtOptionParser *op;

  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [GFF3_file ...]", "Merge adjacent "
                            "features without children of the same type in "
                            "given GFF3 file(s).");

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

  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xb0de2
movq %rdi, %rbx
leaq 0x299743(%rip), %rdi    # 0x34a4f9
leaq 0x2a0193(%rip), %rsi    # 0x350f50
callq 0x107bfe
movq %rax, %r14
movq (%rbx), %rdi
addq $0x8, %rbx
movq %rax, %rsi
movq %rbx, %rdx
callq 0x10ad87
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x1c960
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_mergefeat.c
// Function: gt_mergefeat_runner
static int gt_mergefeat_runner(int argc, const char **argv, int parsed_args,
                          void *tool_arguments, GtError *err)
{
  InterFeatArguments *arguments = tool_arguments;
  GtNodeStream *gff3_in_stream,
               *merge_feature_stream,
               *gff3_out_stream;
  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 merge feature stream */
  merge_feature_stream = gt_merge_feature_stream_new(gff3_in_stream);

  /* create gff3 output stream */
  gff3_out_stream = gt_gff3_out_stream_new(merge_feature_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(merge_feature_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, %r12d
movq %rsi, %r15
movl %edi, %ebp
testq %r8, %r8
je 0xb0e0e
movq %rbx, %rdi
callq 0xfcc32
testb %al, %al
jne 0xb0e76
testq %r14, %r14
je 0xb0e71
subl %r12d, %ebp
movslq %r12d, %rax
leaq (%r15,%rax,8), %rsi
movl %ebp, %edi
callq 0x145cdf
movq %rax, %r15
movq %rax, %rdi
callq 0x16115c
movq %rax, %r12
movq 0x8(%r14), %rsi
movq %rax, %rdi
callq 0x146fc0
movq %rax, %r14
movq %rax, %rdi
movq %rbx, %rsi
callq 0x162f5d
movl %eax, %ebx
movq %r14, %rdi
callq 0x162dee
movq %r12, %rdi
callq 0x162dee
movq %r15, %rdi
callq 0x162dee
movl %ebx, %eax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
callq 0x1c9ce
callq 0x1c997
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_mkfeatureindex.c
// Function: gt_mkfeatureindex_arguments_new
static void* gt_mkfeatureindex_arguments_new(void)
{
  GtMkfeatureindexArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->backend = gt_str_new();
  arguments->filename = gt_str_new();
  arguments->host = gt_str_new();
  arguments->user = gt_str_new();
  arguments->pass = gt_str_new();
  arguments->database = gt_str_new();
  arguments->input = gt_str_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2a00f1(%rip), %rdx    # 0x350fd1
movl $0x1, %edi
movl $0x40, %esi
movl $0x38, %ecx
callq 0x10436a
movq %rax, %rbx
callq 0x11ac6c
movq %rax, (%rbx)
callq 0x11ac6c
movq %rax, 0x8(%rbx)
callq 0x11ac6c
movq %rax, 0x10(%rbx)
callq 0x11ac6c
movq %rax, 0x18(%rbx)
callq 0x11ac6c
movq %rax, 0x20(%rbx)
callq 0x11ac6c
movq %rax, 0x28(%rbx)
callq 0x11ac6c
movq %rax, 0x30(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_mkfeatureindex.c
// Function: gt_mkfeatureindex_arguments_delete
static void gt_mkfeatureindex_arguments_delete(void *tool_arguments)
{
  GtMkfeatureindexArguments *arguments = tool_arguments;
  if (!arguments) return;
  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_str_delete(arguments->input);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xb0f96
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x11bdbf
movq 0x8(%rbx), %rdi
callq 0x11bdbf
movq 0x10(%rbx), %rdi
callq 0x11bdbf
movq 0x18(%rbx), %rdi
callq 0x11bdbf
movq 0x20(%rbx), %rdi
callq 0x11bdbf
movq 0x28(%rbx), %rdi
callq 0x11bdbf
movq 0x30(%rbx), %rdi
callq 0x11bdbf
leaq 0x2a0049(%rip), %rsi    # 0x350fd1
movq %rbx, %rdi
movl $0x4e, %edx
popq %rbx
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_mkfeatureindex.c
// Function: gt_mkfeatureindex_arguments_check
static int gt_mkfeatureindex_arguments_check(GT_UNUSED int rest_argc,
                                       void *tool_arguments,
                                       GT_UNUSED GtError *err)
{
  GT_UNUSED GtMkfeatureindexArguments *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 0xb10aa
movq %rdx, %rdi
callq 0xfcc32
testb %al, %al
jne 0xb10b8
testq %rbx, %rbx
je 0xb10b3
xorl %eax, %eax
popq %rbx
retq
callq 0x1caac
callq 0x1ca73
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_mmapandread.c
// Function: gt_mmapandread_runner
static int gt_mmapandread_runner(int argc, const char **argv, int parsed_args,
                                 GT_UNUSED void *tool_arguments,
                                 GT_UNUSED GtError *err)
{
  int i, fd;
  void *map;
  struct stat sb;
  GtUint64 j;
  unsigned int byte = 0;
  gt_error_check(err);

  /* iterate over all files */
  for (i = parsed_args; i < argc; i++) {
    /* open file */
    fd = gt_xopen(argv[i], O_RDONLY, 0);

    /* get file statistics */
    gt_xfstat(fd, &sb);

    if (sb.st_size == 0)
      printf("file \"%s\" is empty\n", argv[i]);
    else if (!(sb.st_mode & S_IFREG))
      printf("\"%s\" is not a regular file\n", argv[i]);
    else {
      /* map file */
#ifndef _WIN32
      map = gt_xmmap(0, sb.st_size, PROT_READ, MAP_PRIVATE, fd, 0);
#else
      /* XXX */
      fprintf(stderr, "mmapandread not implemented\n");
      exit(EXIT_FAILURE);
#endif

      /* read file */
      printf("reading file \"%s\"\n", argv[i]);
      j = 0;
      gt_progressbar_start(&j, (GtUint64) sb.st_size);
      for (; j < (GtUint64) sb.st_size; j++)
        byte |= (unsigned int) ((char*) map)[j];
      gt_progressbar_stop();

      /* unmap file */
#ifndef _WIN32
      gt_xmunmap(map, sb.st_size);
#else
      /* XXX */
#endif
    }

    /* close file */
    gt_xclose(fd);
  }

  if (!byte)
    printf("all read files contained only null characters\n");

  return 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0xa8, %rsp
movl %edx, %r14d
movq %rsi, %rbx
movl %edi, %ebp
testq %r8, %r8
je 0xb13d4
movq %r8, %rdi
callq 0xfcc32
testb %al, %al
jne 0xb1507
cmpl %ebp, %r14d
jge 0xb14e7
movslq %r14d, %r15
leaq 0x18(%rsp), %r12
xorl %r14d, %r14d
movl %ebp, 0x14(%rsp)
movq (%rbx,%r15,8), %rdi
xorl %esi, %esi
xorl %edx, %edx
callq 0x11fb85
movl %eax, %r13d
movl %eax, %edi
movq %r12, %rsi
callq 0x11fb1b
movq 0x48(%rsp), %rsi
testq %rsi, %rsi
je 0xb1424
testb $-0x80, 0x31(%rsp)
jne 0xb143b
movq (%rbx,%r15,8), %rsi
leaq 0x29fda4(%rip), %rdi    # 0x3511c6
jmp 0xb142f
movq (%rbx,%r15,8), %rsi
leaq 0x29fd83(%rip), %rdi    # 0x3511b2
xorl %eax, %eax
callq 0x17070
jmp 0xb14ce
movq %r12, %rbp
xorl %edi, %edi
movl $0x1, %edx
movl $0x2, %ecx
movl %r13d, %r8d
xorl %r9d, %r9d
callq 0x11fbcd
movq %rax, %r12
movq (%rbx,%r15,8), %rsi
leaq 0x29fd7f(%rip), %rdi    # 0x3511e2
xorl %eax, %eax
callq 0x17070
movq $0x0, 0x8(%rsp)
movq 0x48(%rsp), %rsi
leaq 0x8(%rsp), %rdi
callq 0x10ba28
movq 0x48(%rsp), %rax
movq 0x8(%rsp), %rcx
cmpq %rax, %rcx
jae 0xb14b5
incq %rcx
negq %rax
movsbl -0x1(%r12,%rcx), %edx
orl %edx, %r14d
movq %rcx, 0x8(%rsp)
leaq (%rax,%rcx), %rdx
incq %rdx
incq %rcx
cmpq $0x1, %rdx
jne 0xb1497
callq 0x10bf8a
movq 0x48(%rsp), %rsi
movq %r12, %rdi
callq 0x11fbe0
movq %rbp, %r12
movl 0x14(%rsp), %ebp
movl %r13d, %edi
callq 0x11faf8
incq %r15
cmpl %ebp, %r15d
jne 0xb13ec
testl %r14d, %r14d
jne 0xb14f3
leaq 0x29fd07(%rip), %rdi    # 0x3511f5
callq 0x17bd0
xorl %eax, %eax
addq $0xa8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x1cbc7
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_orffinder.c
// Function: gt_orffinder_arguments_new
static void* gt_orffinder_arguments_new(void)
{
  GtOrffinderArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->ofi = gt_output_file_info_new();
  arguments->types = gt_str_array_new();
  arguments->s2fi = gt_seqid2file_info_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x29fce7(%rip), %rdx    # 0x351223
movl $0x1, %edi
movl $0x30, %esi
movl $0x38, %ecx
callq 0x10436a
movq %rax, %rbx
callq 0x10ad60
movq %rax, 0x18(%rbx)
callq 0x11be10
movq %rax, 0x10(%rbx)
callq 0x172c40
movq %rax, 0x28(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_orffinder.c
// Function: gt_orffinder_arguments_delete
static void gt_orffinder_arguments_delete(void *tool_arguments)
{
  GtOrffinderArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_str_array_delete(arguments->types);
  gt_seqid2file_info_delete(arguments->s2fi);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xb15b4
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0xff22c
movq 0x18(%rbx), %rdi
callq 0x10b00c
movq 0x10(%rbx), %rdi
callq 0x11c144
movq 0x28(%rbx), %rdi
callq 0x172c87
leaq 0x29fc7d(%rip), %rsi    # 0x351223
movq %rbx, %rdi
movl $0x47, %edx
popq %rbx
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_orffinder.c
// Function: gt_orffinder_arguments_check
static int gt_orffinder_arguments_check(GT_UNUSED int rest_argc,
                                       void *tool_arguments, GtError *err)
{
  GtOrffinderArguments *arguments = tool_arguments;
  int had_err = 0;
  int diff;

  gt_error_check(err);
  gt_assert(arguments);

  diff = (arguments->max - arguments->min);
  if (diff < 0) {
    gt_error_set(err, "Value for -min must be larger than -max");
    had_err = -1;
  }

  return had_err;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdx, %rbx
movq %rsi, %r14
testq %rdx, %rdx
je 0xb16d9
movq %rbx, %rdi
callq 0xfcc32
testb %al, %al
jne 0xb170d
testq %r14, %r14
je 0xb1708
movl 0xc(%r14), %ecx
xorl %eax, %eax
cmpl 0x8(%r14), %ecx
jns 0xb1700
leaq 0x29fca5(%rip), %rsi    # 0x351396
movq %rbx, %rdi
xorl %eax, %eax
callq 0xfcb67
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x1cc6e
callq 0x1cc35
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_packedindex.c
// Function: gt_packedindex_arguments_new
static void* gt_packedindex_arguments_new(void)
{
  GtToolbox *packedindex_toolbox = gt_toolbox_new();
  gt_toolbox_add(packedindex_toolbox, "mkindex", gt_packedindex_make);
  gt_toolbox_add(packedindex_toolbox, "mkctxmap", gt_packedindex_mkctxmap);
  gt_toolbox_add(packedindex_toolbox, "trsuftab", gt_packedindex_trsuftab);
  gt_toolbox_add(packedindex_toolbox, "chkintegrity",
              gt_packedindex_chk_integrity );
  gt_toolbox_add(packedindex_toolbox, "chksearch", gt_packedindex_chk_search);
  return packedindex_toolbox;
}

// Assembly:
pushq %rbx
callq 0x11dc0a
movq %rax, %rbx
leaq 0x29fa07(%rip), %rsi    # 0x3513f6
leaq 0x1d8(%rip), %rdx       # 0xb1bce
movq %rax, %rdi
callq 0x11dd27
leaq 0x2a0304(%rip), %rsi    # 0x351d09
leaq 0xd54(%rip), %rdx       # 0xb2760
movq %rbx, %rdi
callq 0x11dd27
leaq 0x2a03ee(%rip), %rsi    # 0x351e09
leaq 0x109a(%rip), %rdx      # 0xb2abc
movq %rbx, %rdi
callq 0x11dd27
leaq 0x29f9cd(%rip), %rsi    # 0x3513fe
leaq 0x1a8(%rip), %rdx       # 0xb1be0
movq %rbx, %rdi
callq 0x11dd27
leaq 0x29f9c4(%rip), %rsi    # 0x35140b
leaq 0x42a(%rip), %rdx       # 0xb1e78
movq %rbx, %rdi
callq 0x11dd27
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_packedindex.c
// Function: gt_packedindex_option_parser_new
static GtOptionParser* gt_packedindex_option_parser_new(void *tool_arguments)
{
  GtToolbox *index_toolbox = tool_arguments;
  GtOptionParser *op;
  gt_assert(index_toolbox);
  op = gt_option_parser_new("[option ...] index_tool [argument ...]",
                         "Call apacked index 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, 1);
  gt_option_parser_refer_to_manual(op);
  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xb1ab9
movq %rdi, %rbx
leaq 0x29f9e7(%rip), %rdi    # 0x35145f
leaq 0x29fa07(%rip), %rsi    # 0x351486
callq 0x107bfe
movq %rax, %r14
leaq 0x6c310(%rip), %rsi     # 0x11dd9e
movq %rax, %rdi
movq %rbx, %rdx
callq 0x107d3d
movq %r14, %rdi
movl $0x1, %esi
callq 0x10872d
movq %r14, %rdi
callq 0x107d2d
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x1cd19
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_packedindex.c
// Function: gt_packedindex_runner
static int gt_packedindex_runner(int argc, const char **argv, int parsed_args,
                                 void *tool_arguments, GtError *err)
{
  GtToolbox *index_toolbox = tool_arguments;
  GtToolfunc toolfunc;
  GtTool *tool = NULL;
  char **nargv = NULL;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(index_toolbox);

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

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

  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 0xb1aec
movq %rbx, %rdi
callq 0xfcc32
testb %al, %al
jne 0xb1bc4
testq %r15, %r15
je 0xb1bbf
movslq %r14d, %r13
movq (%r12,%r13,8), %rsi
movq %r15, %rdi
callq 0x11dd07
movq (%r12,%r13,8), %rdx
testb %al, %al
je 0xb1b2d
leaq (%r12,%r13,8), %r13
movq %r15, %rdi
movq %rdx, %rsi
callq 0x11dd77
movq %rax, %r12
testq %rax, %rax
je 0xb1b48
movq $0x0, (%rsp)
jmp 0xb1b5d
leaq 0x29f99f(%rip), %rsi    # 0x3514d3
xorl %r15d, %r15d
movq %rbx, %rdi
xorl %eax, %eax
callq 0xfcb67
movl $0xffffffff, %ebx       # imm = 0xFFFFFFFF
jmp 0xb1ba6
movq (%r13), %rsi
movq %r15, %rdi
callq 0x11dce1
movq %rax, (%rsp)
testq %rax, %rax
je 0xb1bc9
movq %rbx, %rdi
callq 0xfccba
movq %r13, %rdi
movq %rax, %rsi
callq 0xe464a
movq %rax, %r15
movq (%rax), %rsi
movq %rbx, %rdi
callq 0xfcc72
subl %r14d, %ebp
testq %r12, %r12
je 0xb1b93
movl %ebp, %edi
movq %r15, %rsi
movq %rbx, %rdx
callq *%r12
jmp 0xb1ba4
movq (%rsp), %rdi
movl %ebp, %esi
movq %r15, %rdx
movq %rbx, %rcx
callq 0x11d751
movl %eax, %ebx
movq %r15, %rdi
callq 0xe487c
movl %ebx, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x1cdbe
callq 0x1cd50
callq 0x1cd87
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_packedindex_mkctxmap.c
// Function: parseMkCtxMapOptions
static GtOPrval
parseMkCtxMapOptions(int *parsed_args, int argc, const char **argv,
                     struct mkCtxMapOptions *params, GtError *err)
{
  GtOptionParser *op;
  GtOPrval oprval;
  GtOption *option;

  gt_error_check(err);
  op = gt_option_parser_new("indexname",
                         "Build BWT packedindex for project <indexname>.");
  gt_registerCtxMapOptions(op, &params->mapIntervalLog2);

  option = gt_option_new_bool("v",
                           "print verbose progress information",
                           &params->verboseOutput,
                           false);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_min_max_args(op, 1, 1);
  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);

  gt_option_parser_delete(op);

  return oprval;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r8, %rbx
movq %rcx, %r13
movq %rdx, %r14
movl %esi, %ebp
movq %rdi, %r15
testq %r8, %r8
je 0xb2a27
movq %rbx, %rdi
callq 0xfcc32
testb %al, %al
jne 0xb2ab6
leaq 0x2b30ff(%rip), %rdi    # 0x365b2d
leaq 0x29f396(%rip), %rsi    # 0x351dcb
callq 0x107bfe
movq %rax, %r12
movq %rax, %rdi
movq %r13, %rsi
callq 0x1993e8
addq $0x4, %r13
leaq 0x2dcddf(%rip), %rdi    # 0x38f832
leaq 0x29ebce(%rip), %rsi    # 0x351628
movq %r13, %rdx
xorl %ecx, %ecx
callq 0x10a235
movq %r12, %rdi
movq %rax, %rsi
callq 0x107cc0
movq %r12, %rdi
movl $0x1, %esi
movl $0x1, %edx
callq 0x10874b
leaq 0x6cb84(%rip), %r8      # 0x11f60c
movq %r12, %rdi
movq %r15, %rsi
movl %ebp, %edx
movq %r14, %rcx
movq %rbx, %r9
callq 0x10875d
movl %eax, %ebx
movq %r12, %rdi
callq 0x10a0b4
movl %ebx, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x1d02d
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_packedindex_trsuftab.c
// Function: gt_packedindex_trsuftab
extern int
gt_packedindex_trsuftab(int argc, const char *argv[], GtError *err)
{
  struct trSufTabOptions params;
  BWTSeq *bwtSeq = NULL;
  GtStr *inputProject = NULL;
  int parsedArgs;
  bool had_err = false;
  GtLogger *logger = NULL;
  inputProject = gt_str_new();

  do {
    gt_error_check(err);
    {
      bool exitNow = false;
      switch (parseTrSufTabOptions(&parsedArgs, argc, argv, &params,
                                   inputProject, err))
      {
      case GT_OPTION_PARSER_OK:
        break;
      case GT_OPTION_PARSER_ERROR:
        had_err = true;
        exitNow = true;
        break;
      case GT_OPTION_PARSER_REQUESTS_EXIT:
        exitNow = true;
        break;
      }
      if (exitNow)
        break;
    }
    gt_str_set(inputProject, argv[parsedArgs]);
    logger = gt_logger_new(params.verboseOutput,
                           GT_LOGGER_DEFLT_PREFIX, stdout);
    bwtSeq = gt_trSuftab2BWTSeq(&params.idx.final, logger, err);
    had_err = bwtSeq == NULL;
    if (had_err)
      break;
  } while (0);
  if (bwtSeq) gt_deleteBWTSeq(bwtSeq);
  if (logger) gt_logger_delete(logger);
  if (inputProject) gt_str_delete(inputProject);
  return had_err?-1:0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x50, %rsp
movq %rdx, %r14
movq %rsi, %r15
movl %edi, %ebp
callq 0x11ac6c
movq %rax, %rbx
testq %r14, %r14
je 0xb2b04
movq %r14, %rdi
callq 0xfcc32
testb %al, %al
jne 0xb2bb2
leaq 0xc(%rsp), %rdi
leaq 0x10(%rsp), %rcx
movl %ebp, %esi
movq %r15, %rdx
movq %rbx, %r8
movq %r14, %r9
jmp 0xb2b19
leaq 0xc(%rsp), %rdi
leaq 0x10(%rsp), %rcx
movl %ebp, %esi
movq %r15, %rdx
movq %rbx, %r8
xorl %r9d, %r9d
callq 0xb2bb7
cmpl $0x1, %eax
je 0xb2b2c
cmpl $0x2, %eax
jne 0xb2b31
xorl %ebp, %ebp
jmp 0xb2b92
movb $0x1, %bpl
jmp 0xb2b92
movslq 0xc(%rsp), %rax
movq (%r15,%rax,8), %rsi
movq %rbx, %rdi
callq 0x11ad62
leaq 0x10(%rsp), %r12
movzbl 0x38(%r12), %edi
movq 0x406384(%rip), %rax    # 0x4b8ed8
movq (%rax), %rdx
leaq 0x293d76(%rip), %rsi    # 0x3468d4
callq 0x103e40
movq %rax, %r15
movq %r12, %rdi
movq %rax, %rsi
movq %r14, %rdx
callq 0x198f5a
testq %rax, %rax
sete %bpl
je 0xb2b85
movq %rax, %rdi
callq 0x19bd88
testq %r15, %r15
je 0xb2b92
movq %r15, %rdi
callq 0x1040e0
testq %rbx, %rbx
je 0xb2b9f
movq %rbx, %rdi
callq 0x11bdbf
movzbl %bpl, %eax
negl %eax
addq $0x50, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
callq 0x1d066