LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/xdrop.c
// Function: gt_xdrop_frontvalue_set
static void gt_xdrop_frontvalue_set(GtXdropresources *res, GtWord d, GtWord k,
                                    GtXdropfrontvalue value)
{
  const GtUword frontidx = GT_XDROP_FRONTIDX(d, k);

  if (frontidx >= res->fronts.allocatedGtXdropfrontvalue)
  {
    res->fronts.allocatedGtXdropfrontvalue = frontidx + 32UL;
    res->fronts.spaceGtXdropfrontvalue
      = gt_realloc_mem(res->fronts.spaceGtXdropfrontvalue,
                       sizeof (*res->fronts.spaceGtXdropfrontvalue) *
                       res->fronts.allocatedGtXdropfrontvalue,
                       __FILE__, __LINE__);
  }
  res->fronts.spaceGtXdropfrontvalue[frontidx] = value;
  res->fronts.nextfreeGtXdropfrontvalue = frontidx + 1;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movl %r8d, %ebx
movq %rcx, %r15
movq %rdi, %r14
leaq 0x1(%rsi), %r12
imulq %rsi, %r12
addq %rdx, %r12
movq 0x18(%rdi), %rax
cmpq 0x20(%rdi), %r12
jb 0x203eb5
leaq 0x20(%r12), %rsi
movq %rsi, 0x20(%r14)
shlq $0x4, %rsi
leaq 0x1b8efa(%rip), %rdx    # 0x3bcd9e
movq %rax, %rdi
movl $0xda, %ecx
callq 0x104461
movq %rax, 0x18(%r14)
movq %r12, %rcx
shlq $0x4, %rcx
movq %r15, (%rax,%rcx)
movb %bl, 0x8(%rax,%rcx)
incq %r12
movq %r12, 0x28(%r14)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/gt_ltrclustering.c
// Function: gt_ltrclustering_arguments_new
static void* gt_ltrclustering_arguments_new(void)
{
  GtLTRClusteringArguments *arguments = gt_calloc((size_t) 1,
                                                  sizeof (*arguments));
  arguments->ofi = gt_output_file_info_new();
  arguments->file_prefix = gt_str_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x1b9d75(%rip), %rdx    # 0x3be1f0
movl $0x1, %edi
movl $0x40, %esi
movl $0x2b, %ecx
callq 0x10436a
movq %rax, %rbx
callq 0x10ad60
movq %rax, 0x8(%rbx)
callq 0x11ac6c
movq %rax, 0x10(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/gt_ltrclustering.c
// Function: gt_ltrclustering_arguments_delete
static void gt_ltrclustering_arguments_delete(void *tool_arguments)
{
  GtLTRClusteringArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->file_prefix);
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0x2044e1
pushq %rbx
movq %rdi, %rbx
movq 0x10(%rdi), %rdi
callq 0x11bdbf
movq (%rbx), %rdi
callq 0xff22c
movq 0x8(%rbx), %rdi
callq 0x10b00c
leaq 0x1b9d1d(%rip), %rsi    # 0x3be1f0
movq %rbx, %rdi
movl $0x38, %edx
popq %rbx
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/gt_ltrclustering.c
// Function: gt_ltrclustering_option_parser_new
static GtOptionParser* gt_ltrclustering_option_parser_new(void *tool_arguments)
{
  GtLTRClusteringArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] indexname [GFF3_file ...]",
                            "Cluster features of LTRs.");

  /* -psmall */
  option = gt_option_new_uword_min_max("psmall", "specify how many percent of"
                                       " the smaller sequence a match needs to"
                                       " cover in order to cluster the two"
                                       " sequences of the match.",
                                       &arguments->psmall, 0, 0, 100UL);

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

  /* -plarge */
  option = gt_option_new_uword_min_max("plarge", "specify how many percent of"
                                       " the larger sequence a match needs to"
                                       " cover in order to cluster the two"
                                       " sequences of the match.",
                                       &arguments->plarge, 0, 0, 100UL);
  gt_option_is_mandatory(option);
  gt_option_parser_add_option(op, option);

  gt_option_is_mandatory(option);

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

  gt_option_parser_set_min_args(op, 1U);

  return op;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0x2045a6
movq %rdi, %rbx
leaq 0x1b9d34(%rip), %rdi    # 0x3be22e
leaq 0x1b9d54(%rip), %rsi    # 0x3be255
callq 0x107bfe
movq %rax, %r14
leaq 0x18(%rbx), %rdx
leaq 0x1b9d5b(%rip), %rdi    # 0x3be26f
leaq 0x1b9d5b(%rip), %rsi    # 0x3be276
movl $0x64, %r9d
xorl %ecx, %ecx
xorl %r8d, %r8d
callq 0x10a5ff
movq %rax, %r15
movq %rax, %rdi
callq 0x10a87b
movq %r14, %rdi
movq %r15, %rsi
callq 0x107cc0
leaq 0x20(%rbx), %rdx
leaq 0x1b9da6(%rip), %rdi    # 0x3be2f2
leaq 0x1b9da6(%rip), %rsi    # 0x3be2f9
movl $0x64, %r9d
xorl %ecx, %ecx
xorl %r8d, %r8d
callq 0x10a5ff
movq %rax, %r15
movq %rax, %rdi
callq 0x10a87b
movq %r14, %rdi
movq %r15, %rsi
callq 0x107cc0
movq %r15, %rdi
callq 0x10a87b
movq 0x8(%rbx), %rdi
movq %r14, %rsi
movq %rbx, %rdx
callq 0x10ad87
movq %r14, %rdi
movl $0x1, %esi
callq 0x10872d
movq %r14, %rax
popq %rbx
popq %r14
popq %r15
retq
callq 0x7fe9c
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/gt_ltrdigest.c
// Function: gt_ltrdigest_arguments_check
int gt_ltrdigest_arguments_check(GT_UNUSED int rest_argc, void *tool_arguments,
                                 GtError* err)
{
  GtLTRdigestOptions *arguments = tool_arguments;
  int had_err  = 0;

  if (arguments->nthreads > 0) {
    gt_warning("The '-threads' option is deprecated. Please use the '-j'"
               "option of the 'gt' call instead, e.g.:\n"
               "  gt -j "GT_WU" ltrdigest ...", arguments->nthreads);
  }

  /* -trnas */
  if (!had_err && arguments->trna_lib && gt_str_length(arguments->trna_lib) > 0)
  {
    if (!gt_file_exists(gt_str_get(arguments->trna_lib)))
    {
      gt_error_set(err, "File '%s' does not exist!",
                        gt_str_get(arguments->trna_lib));
      had_err = -1;
    }
  }
  return had_err;
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
movq %rdx, %rbx
movq %rsi, %r14
movq 0x50(%rsi), %rsi
testq %rsi, %rsi
je 0x204735
leaq 0x1b9c7a(%rip), %rdi    # 0x3be3a8
xorl %eax, %eax
callq 0x11f68c
movq (%r14), %rdi
xorl %ebp, %ebp
testq %rdi, %rdi
je 0x20477e
callq 0x11b0ca
testq %rax, %rax
je 0x20477e
movq (%r14), %rdi
callq 0x11b0a1
movq %rax, %rdi
callq 0xff28c
testb %al, %al
jne 0x20477e
movq (%r14), %rdi
callq 0x11b0a1
leaq 0x1b9cb5(%rip), %rsi    # 0x3be421
movq %rbx, %rdi
movq %rax, %rdx
xorl %eax, %eax
callq 0xfcb67
movl $0xffffffff, %ebp       # imm = 0xFFFFFFFF
movl %ebp, %eax
popq %rbx
popq %r14
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/gt_ltrdigest.c
// Function: gt_ltrdigest_arguments_new
static void* gt_ltrdigest_arguments_new(void)
{
  GtLTRdigestOptions *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  memset(arguments, 0, sizeof *arguments);
  arguments->trna_lib = gt_str_new();
  arguments->prefix = gt_str_new();
  arguments->cutoffs = gt_str_new();
  arguments->ofi = gt_output_file_info_new();
  arguments->hmm_files = gt_str_array_new();
  arguments->s2fi = gt_seqid2file_info_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x1b9c86(%rip), %rdx    # 0x3be43b
movl $0x1, %edi
movl $0x110, %esi            # imm = 0x110
movl $0x59, %ecx
callq 0x10436a
movq %rax, %rbx
movl $0x110, %edx            # imm = 0x110
movq %rax, %rdi
xorl %esi, %esi
callq 0x173a0
callq 0x11ac6c
movq %rax, (%rbx)
callq 0x11ac6c
movq %rax, 0x8(%rbx)
callq 0x11ac6c
movq %rax, 0x10(%rbx)
callq 0x10ad60
movq %rax, 0x20(%rbx)
callq 0x11be10
movq %rax, 0x30(%rbx)
callq 0x172c40
movq %rax, 0x38(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/gt_ltrdigest.c
// Function: gt_ltrdigest_arguments_delete
static void gt_ltrdigest_arguments_delete(void *tool_arguments)
{
  GtLTRdigestOptions *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->trna_lib);
  gt_str_delete(arguments->prefix);
  gt_str_delete(arguments->cutoffs);
  gt_str_array_delete(arguments->hmm_files);
  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 0x204871
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x11bdbf
movq 0x8(%rbx), %rdi
callq 0x11bdbf
movq 0x10(%rbx), %rdi
callq 0x11bdbf
movq 0x30(%rbx), %rdi
callq 0x11c144
movq 0x28(%rbx), %rdi
callq 0xff22c
movq 0x20(%rbx), %rdi
callq 0x10b00c
movq 0x38(%rbx), %rdi
callq 0x172c87
leaq 0x1b9bd8(%rip), %rsi    # 0x3be43b
movq %rbx, %rdi
movl $0x6f, %edx
popq %rbx
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/gt_ltrharvest.c
// Function: gt_ltrharvest_arguments_new
static void* gt_ltrharvest_arguments_new(void)
{
  LTRharvestArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->ofi = gt_output_file_info_new();
  arguments->str_motif = gt_str_new();
  arguments->str_overlaps = gt_str_new();
  arguments->str_indexname = gt_str_new();
  arguments->str_fastaoutputfilename = gt_str_new();
  arguments->str_fastaoutputfilenameinnerregion = gt_str_new();
  arguments->str_gff3filename = gt_str_new();
  arguments->motif = gt_calloc((size_t) 1, sizeof (GtLTRFourCharMotif));
  return arguments;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
leaq 0x1b9358(%rip), %rbx    # 0x3bec03
movl $0x1, %edi
movl $0xf8, %esi
movq %rbx, %rdx
movl $0x93, %ecx
callq 0x10436a
movq %rax, %r14
callq 0x10ad60
movq %rax, (%r14)
callq 0x11ac6c
movq %rax, 0x18(%r14)
callq 0x11ac6c
movq %rax, 0x20(%r14)
callq 0x11ac6c
movq %rax, 0x10(%r14)
callq 0x11ac6c
movq %rax, 0x28(%r14)
callq 0x11ac6c
movq %rax, 0x30(%r14)
callq 0x11ac6c
movq %rax, 0x38(%r14)
movl $0x1, %edi
movl $0x10, %esi
movq %rbx, %rdx
movl $0x9b, %ecx
callq 0x10436a
movq %rax, 0xf0(%r14)
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/gt_ltrharvest.c
// Function: gt_ltrharvest_arguments_delete
static void gt_ltrharvest_arguments_delete(void *tool_arguments)
{
  LTRharvestArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_str_delete(arguments->str_motif);
  gt_str_delete(arguments->str_overlaps);
  gt_str_delete(arguments->str_indexname);
  gt_str_delete(arguments->str_fastaoutputfilename);
  gt_str_delete(arguments->str_fastaoutputfilenameinnerregion);
  gt_str_delete(arguments->str_gff3filename);
  gt_option_delete(arguments->optiongff3);
  gt_option_delete(arguments->optionoutinner);
  gt_option_delete(arguments->optionout);
  gt_option_delete(arguments->optionmotif);
  gt_option_delete(arguments->optionmotifmis);
  gt_option_delete(arguments->optionoverlaps);
  gt_free(arguments->motif);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0x2059fd
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq 0x8(%rdi), %rdi
callq 0xff22c
movq (%rbx), %rdi
callq 0x10b00c
movq 0x18(%rbx), %rdi
callq 0x11bdbf
movq 0x20(%rbx), %rdi
callq 0x11bdbf
movq 0x10(%rbx), %rdi
callq 0x11bdbf
movq 0x28(%rbx), %rdi
callq 0x11bdbf
movq 0x30(%rbx), %rdi
callq 0x11bdbf
movq 0x38(%rbx), %rdi
callq 0x11bdbf
movq 0xe8(%rbx), %rdi
callq 0x10a16a
movq 0xe0(%rbx), %rdi
callq 0x10a16a
movq 0xd8(%rbx), %rdi
callq 0x10a16a
movq 0xc0(%rbx), %rdi
callq 0x10a16a
movq 0xc8(%rbx), %rdi
callq 0x10a16a
movq 0xd0(%rbx), %rdi
callq 0x10a16a
movq 0xf0(%rbx), %rdi
leaq 0x1b922a(%rip), %r14    # 0x3bec03
movq %r14, %rsi
movl $0xb1, %edx
callq 0x1045eb
movq %rbx, %rdi
movq %r14, %rsi
movl $0xb2, %edx
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltr_classify_stream.c
// Function: gt_ltr_classify_stream_class
const GtNodeStreamClass* gt_ltr_classify_stream_class(void)
{
  static const GtNodeStreamClass *nsc;
  gt_class_alloc_lock_enter();
  if (!nsc) {
    nsc = gt_node_stream_class_new(sizeof(GtLTRClassifyStream),
                                   gt_ltr_classify_stream_free,
                                   gt_ltr_classify_stream_next);
  }
  gt_class_alloc_lock_leave();
  return nsc;
}

// Assembly:
pushq %rax
callq 0xe252f
cmpq $0x0, 0x2b7fc2(%rip)    # 0x4be968
jne 0x2069c7
leaq 0x26(%rip), %rsi        # 0x2069d5
leaq 0x88(%rip), %rdx        # 0x206a3e
movl $0x50, %edi
callq 0x162d34
movq %rax, 0x2b7fa1(%rip)    # 0x4be968
callq 0xe2545
movq 0x2b7f95(%rip), %rax    # 0x4be968
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltr_classify_stream.c
// Function: gt_ltr_classify_stream_free
static void gt_ltr_classify_stream_free(GtNodeStream *ns)
{
  GtUword i;
  GtLTRClassifyStream *lcs = gt_ltr_classify_stream_cast(ns);
  for (i = 0; i < gt_array_size(lcs->nodes); i++)
    gt_genome_node_delete(*(GtGenomeNode**) gt_array_get(lcs->nodes, i));
  gt_array_delete(lcs->nodes);
  gt_node_stream_delete(lcs->in_stream);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
callq 0x206998
movq %rax, %rdi
movq %rbx, %rsi
callq 0x162ff7
movq %rax, %rbx
movq 0x18(%rax), %rdi
callq 0xd24e0
testq %rax, %rax
je 0x206a25
xorl %r14d, %r14d
movq 0x18(%rbx), %rdi
movq %r14, %rsi
callq 0xd2207
movq (%rax), %rdi
callq 0x1451a0
incq %r14
movq 0x18(%rbx), %rdi
callq 0xd24e0
cmpq %rax, %r14
jb 0x206a00
movq 0x18(%rbx), %rdi
callq 0xd2938
movq 0x10(%rbx), %rdi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x162dee
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltr_classify_stream.c
// Function: gt_ltr_classify_stream_new
GtNodeStream* gt_ltr_classify_stream_new(GtNodeStream *in_stream,
                                         GtHashmap *features,
                                         const char *famprefix,
                                         char **current_state,
                                         GtUword *progress,
                                         GT_UNUSED GtError *err)
{
  GtNodeStream *ns;
  GtLTRClassifyStream *lcs;
  ns = gt_node_stream_create(gt_ltr_classify_stream_class(), false);
  lcs = gt_ltr_classify_stream_cast(ns);
  lcs->in_stream = gt_node_stream_ref(in_stream);
  lcs->nodes = gt_array_new(sizeof(GtGenomeNode*));
  lcs->features = features;
  lcs->first_next = true;
  lcs->next_index = 0;
  lcs->famprefix = famprefix;
  lcs->progress = progress;
  lcs->current_state = current_state;
  return ns;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r8, %r14
movq %rcx, (%rsp)
movq %rdx, %r15
movq %rsi, %r12
movq %rdi, %r13
callq 0x206998
movq %rax, %rdi
xorl %esi, %esi
callq 0x162d6c
movq %rax, %rbp
callq 0x206998
movq %rax, %rdi
movq %rbp, %rsi
callq 0x162ff7
movq %rax, %rbx
movq %r13, %rdi
callq 0x162dd8
movq %rax, 0x10(%rbx)
movl $0x8, %edi
callq 0xd214c
movq %rax, 0x18(%rbx)
movq %r12, 0x20(%rbx)
movb $0x1, 0x38(%rbx)
movq $0x0, 0x40(%rbx)
movq %r15, 0x28(%rbx)
movq %r14, 0x48(%rbx)
movq (%rsp), %rax
movq %rax, 0x30(%rbx)
movq %rbp, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltr_cluster_stream.c
// Function: gt_ltr_cluster_stream_class
const GtNodeStreamClass* gt_ltr_cluster_stream_class(void)
{
  static const GtNodeStreamClass *nsc;
  gt_class_alloc_lock_enter();
  if (!nsc) {
    nsc = gt_node_stream_class_new(sizeof(GtLTRClusterStream),
                                   gt_ltr_cluster_stream_free,
                                   gt_ltr_cluster_stream_next);
  }
  gt_class_alloc_lock_leave();
  return nsc;
}

// Assembly:
pushq %rax
callq 0xe252f
cmpq $0x0, 0x2b7352(%rip)    # 0x4be970
jne 0x20763f
leaq 0x26(%rip), %rsi        # 0x20764d
leaq 0xa3(%rip), %rdx        # 0x2076d1
movl $0x88, %edi
callq 0x162d34
movq %rax, 0x2b7331(%rip)    # 0x4be970
callq 0xe2545
movq 0x2b7325(%rip), %rax    # 0x4be970
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltr_cluster_stream.c
// Function: gt_ltr_cluster_stream_free
static void gt_ltr_cluster_stream_free(GtNodeStream *ns)
{
  GtUword i;
  GtLTRClusterStream *lcs = gt_ltr_cluster_stream_cast(ns);
  gt_node_visitor_delete((GtNodeVisitor*) lcs->lcv);
  gt_hashmap_delete(lcs->feat_to_encseq);
  gt_str_array_delete(lcs->feat_to_encseq_keys);
  for (i = 0; i < gt_array_size(lcs->nodes); i++)
    gt_genome_node_delete(*(GtGenomeNode**) gt_array_get(lcs->nodes, i));
  gt_array_delete(lcs->nodes);
  gt_node_stream_delete(lcs->in_stream);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
callq 0x207610
movq %rax, %rdi
movq %rbx, %rsi
callq 0x162ff7
movq %rax, %rbx
movq 0x18(%rax), %rdi
callq 0x1632f2
movq 0x28(%rbx), %rdi
callq 0x10109b
movq 0x30(%rbx), %rdi
callq 0x11c144
movq 0x20(%rbx), %rdi
callq 0xd24e0
testq %rax, %rax
je 0x2076b8
xorl %r14d, %r14d
movq 0x20(%rbx), %rdi
movq %r14, %rsi
callq 0xd2207
movq (%rax), %rdi
callq 0x1451a0
incq %r14
movq 0x20(%rbx), %rdi
callq 0xd24e0
cmpq %rax, %r14
jb 0x207693
movq 0x20(%rbx), %rdi
callq 0xd2938
movq 0x10(%rbx), %rdi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x162dee
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltr_input_check_visitor.c
// Function: gt_ltr_input_check_visitor_class
const GtNodeVisitorClass* gt_ltr_input_check_visitor_class(void)
{
  static const GtNodeVisitorClass *nvc = NULL;
  if (!nvc) {
    nvc = gt_node_visitor_class_new(sizeof (GtLTRInputCheckVisitor),
                                    NULL,
                                    NULL,
                                    gt_ltr_input_check_visitor_feature_node,
                                    NULL,
                                    NULL,
                                    NULL);
  }
  return nvc;
}

// Assembly:
movq 0x2b652d(%rip), %rax    # 0x4be978
testq %rax, %rax
je 0x208451
retq
pushq %rax
movq $0x0, (%rsp)
leaq 0x20(%rip), %rcx        # 0x208481
movl $0x18, %edi
xorl %esi, %esi
xorl %edx, %edx
xorl %r8d, %r8d
xorl %r9d, %r9d
callq 0x163010
movq %rax, 0x2b64fc(%rip)    # 0x4be978
addq $0x8, %rsp
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltr_input_check_visitor.c
// Function: gt_ltr_input_check_visitor_new
GtNodeVisitor* gt_ltr_input_check_visitor_new(void)
{
  GtNodeVisitor *nv = NULL;
  GtLTRInputCheckVisitor *lv;
  nv = gt_node_visitor_create(gt_ltr_input_check_visitor_class());
  gt_assert(nv);
  lv = gt_ltr_input_check_visitor_cast(nv);
  lv->only_ltrs = false;
  return nv;
}

// Assembly:
pushq %rbx
callq 0x208444
movq %rax, %rdi
callq 0x163080
testq %rax, %rax
je 0x20868c
movq %rax, %rbx
callq 0x208444
movq %rax, %rdi
movq %rbx, %rsi
callq 0x1630b1
movb $0x0, 0x10(%rax)
movq %rbx, %rax
popq %rbx
retq
callq 0x80571
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltr_refseq_match_stream.c
// Function: gt_ltr_refseq_match_stream_class
const GtNodeStreamClass* gt_ltr_refseq_match_stream_class(void)
{
  static const GtNodeStreamClass *gsc = NULL;
  gt_class_alloc_lock_enter();
  if (!gsc) {
    gsc = gt_node_stream_class_new(sizeof (GtLTRRefseqMatchStream),
                                   gt_ltr_refseq_match_stream_free,
                                   gt_ltr_refseq_match_stream_next);
  }
  gt_class_alloc_lock_leave();
  return gsc;
}

// Assembly:
pushq %rax
callq 0xe252f
cmpq $0x0, 0x2b62de(%rip)    # 0x4be980
jne 0x2086c3
leaq 0x26(%rip), %rsi        # 0x2086d1
leaq 0x49(%rip), %rdx        # 0x2086fb
movl $0xa8, %edi
callq 0x162d34
movq %rax, 0x2b62bd(%rip)    # 0x4be980
callq 0xe2545
movq 0x2b62b1(%rip), %rax    # 0x4be980
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrdigest_file_out_stream.c
// Function: gt_ltr_visitor_class
const GtNodeVisitorClass* gt_ltr_visitor_class(void)
{
  static const GtNodeVisitorClass *nvc = NULL;
  gt_class_alloc_lock_enter();
  if (!nvc) {
    nvc = gt_node_visitor_class_new(sizeof (GtLTRVisitor),
                                    NULL,
                                    NULL,
                                    gt_ltr_visitor_feature_node,
                                    NULL,
                                    NULL,
                                    NULL);
  }
  gt_class_alloc_lock_leave();
  return nvc;
}

// Assembly:
pushq %rax
callq 0xe252f
cmpq $0x0, 0x2b5592(%rip)    # 0x4be988
jne 0x209422
movq $0x0, (%rsp)
leaq 0x29(%rip), %rcx        # 0x209430
movl $0x18, %edi
xorl %esi, %esi
xorl %edx, %edx
xorl %r8d, %r8d
xorl %r9d, %r9d
callq 0x163010
movq %rax, 0x2b5566(%rip)    # 0x4be988
callq 0xe2545
movq 0x2b555a(%rip), %rax    # 0x4be988
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrdigest_file_out_stream.c
// Function: gt_ltrdigest_file_out_stream_class
const GtNodeStreamClass* gt_ltrdigest_file_out_stream_class(void)
{
  static const GtNodeStreamClass *nsc;
  gt_class_alloc_lock_enter();
  if (!nsc) {
    nsc = gt_node_stream_class_new(sizeof (GtLTRdigestFileOutStream),
                                   gt_ltrfileout_stream_free,
                                   gt_ltrfileout_stream_next );
  }
  gt_class_alloc_lock_leave();
  return nsc;
}

// Assembly:
pushq %rax
callq 0xe252f
cmpq $0x0, 0x2b43b1(%rip)    # 0x4be990
jne 0x20a600
leaq 0x26(%rip), %rsi        # 0x20a60e
leaq -0xf6a(%rip), %rdx      # 0x209685
movl $0xe0, %edi
callq 0x162d34
movq %rax, 0x2b4390(%rip)    # 0x4be990
callq 0xe2545
movq 0x2b4384(%rip), %rax    # 0x4be990
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrdigest_file_out_stream.c
// Function: gt_ltrfileout_stream_free
void gt_ltrfileout_stream_free(GtNodeStream *ns)
{
  GtLTRdigestFileOutStream *ls = gt_ltrdigest_file_out_stream_cast(ns);
  if (ls->tabout_file != NULL)
    gt_file_delete(ls->tabout_file);
  if (ls->pbsout_file != NULL)
    gt_file_delete(ls->pbsout_file);
  if (ls->pptout_file != NULL)
    gt_file_delete(ls->pptout_file);
  if (ls->ltr5out_file != NULL)
    gt_file_delete(ls->ltr5out_file);
  if (ls->ltr3out_file != NULL)
    gt_file_delete(ls->ltr3out_file);
  if (ls->elemout_file != NULL)
    gt_file_delete(ls->elemout_file);
  gt_node_visitor_delete((GtNodeVisitor*) ls->lv);
  gt_node_stream_delete(ls->in_stream);
}

// Assembly:
pushq %rbx
movq %rdi, %rbx
callq 0x20a5d1
movq %rax, %rdi
movq %rbx, %rsi
callq 0x162ff7
movq %rax, %rbx
movq 0x28(%rax), %rdi
testq %rdi, %rdi
je 0x20a633
callq 0xff22c
movq 0x30(%rbx), %rdi
testq %rdi, %rdi
je 0x20a641
callq 0xff22c
movq 0x38(%rbx), %rdi
testq %rdi, %rdi
je 0x20a64f
callq 0xff22c
movq 0x40(%rbx), %rdi
testq %rdi, %rdi
je 0x20a65d
callq 0xff22c
movq 0x48(%rbx), %rdi
testq %rdi, %rdi
je 0x20a66b
callq 0xff22c
movq 0x50(%rbx), %rdi
testq %rdi, %rdi
je 0x20a679
callq 0xff22c
movq 0x58(%rbx), %rdi
callq 0x1632f2
movq 0x10(%rbx), %rdi
popq %rbx
jmp 0x162dee
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrdigest_file_out_stream.c
// Function: gt_ltrdigest_file_out_stream_enable_pdom_alignment_output
void gt_ltrdigest_file_out_stream_enable_pdom_alignment_output(GtNodeStream *ns)
{
  GtLTRdigestFileOutStream *ls;
  gt_assert(ns);
  ls = gt_ltrdigest_file_out_stream_cast(ns);
  ls->write_pdom_alignments = true;
}

// Assembly:
pushq %rbx
testq %rdi, %rdi
je 0x20a6ae
movq %rdi, %rbx
callq 0x20a5d1
movq %rax, %rdi
movq %rbx, %rsi
callq 0x162ff7
movb $0x1, 0xd8(%rax)
popq %rbx
retq
callq 0x809a4
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrdigest_file_out_stream.c
// Function: gt_ltrdigest_file_out_stream_enable_aa_sequence_output
void gt_ltrdigest_file_out_stream_enable_aa_sequence_output(GtNodeStream *ns)
{
  GtLTRdigestFileOutStream *ls;
  gt_assert(ns);
  ls = gt_ltrdigest_file_out_stream_cast(ns);
  ls->write_pdom_aaseqs = true;
}

// Assembly:
pushq %rbx
testq %rdi, %rdi
je 0x20a6d5
movq %rdi, %rbx
callq 0x20a5d1
movq %rax, %rdi
movq %rbx, %rsi
callq 0x162ff7
movb $0x1, 0xd9(%rax)
popq %rbx
retq
callq 0x809dd
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrdigest_pbs_visitor.c
// Function: gt_ltrdigest_pbs_visitor_class
const GtNodeVisitorClass* gt_ltrdigest_pbs_visitor_class(void)
{
  static const GtNodeVisitorClass *nvc = NULL;
  if (!nvc) {
    nvc = gt_node_visitor_class_new(sizeof (GtLTRdigestPBSVisitor),
                                   gt_ltrdigest_pbs_visitor_free,
                                   NULL,
                                   gt_ltrdigest_pbs_visitor_feature_node,
                                   NULL,
                                   NULL,
                                   NULL);
  }
  return nvc;
}

// Assembly:
movq 0x2b3c25(%rip), %rax    # 0x4be998
testq %rax, %rax
je 0x20ad79
retq
pushq %rax
movq $0x0, (%rsp)
leaq 0x25(%rip), %rsi        # 0x20adae
leaq 0x42(%rip), %rcx        # 0x20add2
movl $0x98, %edi
xorl %edx, %edx
xorl %r8d, %r8d
xorl %r9d, %r9d
callq 0x163010
movq %rax, 0x2b3bef(%rip)    # 0x4be998
addq $0x8, %rsp
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrdigest_pbs_visitor.c
// Function: gt_ltrdigest_pbs_visitor_new
GtNodeVisitor* gt_ltrdigest_pbs_visitor_new(GtRegionMapping *rmap,
                                            unsigned int radius,
                                            unsigned int max_edist,
                                            GtRange alilen,
                                            GtRange offsetlen,
                                            GtRange trnaoffsetlen,
                                            int ali_score_match,
                                            int ali_score_mismatch,
                                            int ali_score_insertion,
                                            int ali_score_deletion,
                                            GtBioseq *trna_lib,
                                            GT_UNUSED GtError *err)
{
  GtNodeVisitor *nv = NULL;
  GtLTRdigestPBSVisitor *lv;
  gt_assert(rmap && trna_lib);
  nv = gt_node_visitor_create(gt_ltrdigest_pbs_visitor_class());
  lv = gt_ltrdigest_pbs_visitor_cast(nv);
  lv->tag = gt_str_new_cstr(GT_LTRDIGEST_TAG);
  lv->rmap = rmap;
  lv->radius = radius;
  lv->max_edist = max_edist;
  lv->alilen = alilen;
  lv->offsetlen = offsetlen;
  lv->trnaoffsetlen = trnaoffsetlen;
  lv->ali_score_match = ali_score_match;
  lv->ali_score_mismatch = ali_score_mismatch;
  lv->ali_score_insertion = ali_score_insertion;
  lv->ali_score_deletion = ali_score_deletion;
  lv->trna_lib = trna_lib;
  return nv;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movl %r9d, 0xc(%rsp)
movq %r8, 0x10(%rsp)
testq %rdi, %rdi
je 0x20b75c
cmpq $0x0, 0x88(%rsp)
je 0x20b75c
movq %rcx, %r15
movl %edx, %ebp
movl %esi, %r12d
movq %rdi, %r13
callq 0x20ad6c
movq %rax, %rdi
callq 0x163080
movq %rax, %rbx
callq 0x20ad6c
movq %rax, %rdi
movq %rbx, %rsi
callq 0x1630b1
movq %rax, %r14
leaq 0x1b3524(%rip), %rdi    # 0x3bebf4
callq 0x11acc9
movq %rax, 0x18(%r14)
movq %r13, 0x10(%r14)
movl %r12d, 0x48(%r14)
movl %ebp, 0x4c(%r14)
movq %r15, 0x50(%r14)
movq 0x10(%rsp), %rax
movq %rax, 0x58(%r14)
leaq 0x50(%rsp), %rax
movups (%rax), %xmm0
movups %xmm0, 0x60(%r14)
leaq 0x60(%rsp), %rax
movups (%rax), %xmm0
movups %xmm0, 0x70(%r14)
movl 0xc(%rsp), %eax
movl %eax, 0x80(%r14)
movl 0x70(%rsp), %eax
movl %eax, 0x84(%r14)
movl 0x78(%rsp), %eax
movl %eax, 0x88(%r14)
movl 0x80(%rsp), %eax
movl %eax, 0x8c(%r14)
movq 0x88(%rsp), %rax
movq %rax, 0x90(%r14)
movq %rbx, %rax
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x80c15
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrdigest_pdom_visitor.c
// Function: gt_ltrdigest_pdom_visitor_free
void gt_ltrdigest_pdom_visitor_free(GtNodeVisitor *nv)
{
  GtLTRdigestPdomVisitor *lv;
  GtUword i;
  if (!nv) return;
  lv = gt_ltrdigest_pdom_visitor_cast(nv);
  for (i = 0UL; i < 3UL; i++) {
    gt_str_delete(lv->fwd[i]);
    gt_str_delete(lv->rev[i]);
  }
  gt_str_delete(lv->cmdline);
  gt_str_delete(lv->tag);
  gt_cstr_array_delete(lv->args);
}

// Assembly:
testq %rdi, %rdi
je 0x20ba2f
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
callq 0x20ba30
movq %rax, %rdi
movq %rbx, %rsi
callq 0x1630b1
movq %rax, %rbx
movq $-0x18, %r14
movq 0x48(%rbx,%r14), %rdi
callq 0x11bdbf
movq 0x60(%rbx,%r14), %rdi
callq 0x11bdbf
addq $0x8, %r14
jne 0x20b9ea
movq 0x80(%rbx), %rdi
callq 0x11bdbf
movq 0x88(%rbx), %rdi
callq 0x11bdbf
movq 0x98(%rbx), %rdi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0xe487c
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrdigest_pdom_visitor.c
// Function: gt_ltrdigest_pdom_visitor_class
const GtNodeVisitorClass* gt_ltrdigest_pdom_visitor_class(void)
{
  static const GtNodeVisitorClass *nvc = NULL;
  if (!nvc) {
    nvc = gt_node_visitor_class_new(sizeof (GtLTRdigestPdomVisitor),
                                   gt_ltrdigest_pdom_visitor_free,
                                   NULL,
                                   gt_ltrdigest_pdom_visitor_feature_node,
                                   NULL,
                                   NULL,
                                   NULL);
  }
  return nvc;
}

// Assembly:
movq 0x2b2f69(%rip), %rax    # 0x4be9a0
testq %rax, %rax
je 0x20ba3d
retq
pushq %rax
movq $0x0, (%rsp)
leaq -0x89(%rip), %rsi       # 0x20b9c4
leaq 0x1e(%rip), %rcx        # 0x20ba72
movl $0xa8, %edi
xorl %edx, %edx
xorl %r8d, %r8d
xorl %r9d, %r9d
callq 0x163010
movq %rax, 0x2b2f33(%rip)    # 0x4be9a0
addq $0x8, %rsp
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrdigest_pdom_visitor.c
// Function: gt_ltrdigest_checkpipe
static int gt_ltrdigest_checkpipe(int *fdpair, GtError *err)
{
  int had_err = 0;
  if (pipe(fdpair)) {
    gt_error_set(err, "could not create pipe, please check for number of "
                      "allowed file descriptors: %s", strerror(errno));
    had_err = -1;
  }
  return had_err;
}

// Assembly:
pushq %rbx
movq %rsi, %rbx
callq 0x179f0
testl %eax, %eax
je 0x20c36f
callq 0x17060
movl (%rax), %edi
callq 0x17240
leaq 0x1b4178(%rip), %rsi    # 0x3c04d3
movq %rbx, %rdi
movq %rax, %rdx
xorl %eax, %eax
callq 0xfcb67
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
jmp 0x20c371
xorl %eax, %eax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrdigest_pdom_visitor.c
// Function: gt_ltrdigest_hmmscan_send_thread
static void* gt_ltrdigest_hmmscan_send_thread(void *data) {
  GtUword i;
  GtLTRdigestHMMscanThreadData *d = (GtLTRdigestHMMscanThreadData*) data;
  for (i = 0UL; i < 3UL; i++) {
    char buf[5];
    GT_UNUSED ssize_t written;
    (void) sprintf(buf, ">"GT_WU"%c\n", i, '+');
    written = write(d->pc[1], buf, 4 * sizeof (char));
    written = write(d->pc[1], gt_str_get(d->lv->fwd[i]),
                   (size_t) gt_str_length(d->lv->fwd[i]) * sizeof (char));
    written = write(d->pc[1], "\n", 1 * sizeof (char));
    (void) sprintf(buf, ">"GT_WU"%c\n", i, '-');
    written = write(d->pc[1], buf, 4 * sizeof (char));
    written = write(d->pc[1], gt_str_get(d->lv->rev[i]),
                   (size_t) gt_str_length(d->lv->rev[i]) * sizeof (char));
  }
  (void) close(d->pc[0]);
  (void) close(d->pc[1]);
  (void) close(d->cp[1]);
  return NULL;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rdi, %rbx
leaq 0x1b41e1(%rip), %r14    # 0x3c057b
leaq 0x3(%rsp), %r15
xorl %r13d, %r13d
movq %r15, %rdi
movq %r14, %rsi
movq %r13, %rdx
movl $0x2b, %ecx
xorl %eax, %eax
callq 0x17130
movq (%rbx), %rax
movl 0x4(%rax), %edi
movl $0x4, %edx
movq %r15, %rsi
callq 0x17270
movq (%rbx), %rax
movq 0x18(%rbx), %rcx
movl 0x4(%rax), %ebp
movq 0x30(%rcx,%r13,8), %rdi
callq 0x11b0a1
movq %rax, %r12
movq 0x18(%rbx), %rax
movq 0x30(%rax,%r13,8), %rdi
callq 0x11b0ca
movl %ebp, %edi
movq %r12, %rsi
movq %rax, %rdx
callq 0x17270
movq (%rbx), %rax
movl 0x4(%rax), %edi
movl $0x1, %edx
leaq 0x1b3c91(%rip), %rsi    # 0x3c009f
callq 0x17270
movq %r15, %rdi
movq %r14, %rsi
movq %r13, %rdx
movl $0x2d, %ecx
xorl %eax, %eax
callq 0x17130
movq (%rbx), %rax
movl 0x4(%rax), %edi
movl $0x4, %edx
movq %r15, %rsi
callq 0x17270
movq (%rbx), %rax
movq 0x18(%rbx), %rcx
movl 0x4(%rax), %ebp
movq 0x48(%rcx,%r13,8), %rdi
callq 0x11b0a1
movq %rax, %r12
movq 0x18(%rbx), %rax
movq 0x48(%rax,%r13,8), %rdi
callq 0x11b0ca
movl %ebp, %edi
movq %r12, %rsi
movq %rax, %rdx
callq 0x17270
incq %r13
cmpq $0x3, %r13
jne 0x20c3a2
movq (%rbx), %rax
movl (%rax), %edi
callq 0x17fc0
movq (%rbx), %rax
movl 0x4(%rax), %edi
callq 0x17fc0
movq 0x8(%rbx), %rax
movl 0x4(%rax), %edi
callq 0x17fc0
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrdigest_pdom_visitor.c
// Function: gt_hmmer_model_hit_delete
static void gt_hmmer_model_hit_delete(GtHMMERModelHit *mh)
{
  GtUword i;
  if (!mh) return;
  for (i = 0; i < gt_array_size(mh->fwd_hits); i++) {
    GtHMMERSingleHit *h = *(GtHMMERSingleHit**)  gt_array_get(mh->fwd_hits, i);
    gt_str_delete(h->alignment);
    gt_str_delete(h->aastring);
    gt_array_delete(h->chains);
    gt_free(h);
  }
  gt_array_delete(mh->fwd_hits);
  for (i = 0; i < gt_array_size(mh->rev_hits); i++) {
    GtHMMERSingleHit *h = *(GtHMMERSingleHit**)  gt_array_get(mh->rev_hits, i);
    gt_str_delete(h->alignment);
    gt_str_delete(h->aastring);
    gt_array_delete(h->chains);
    gt_free(h);
  }
  gt_array_delete(mh->rev_hits);
  gt_free(mh);
}

// Assembly:
testq %rdi, %rdi
je 0x20d7c6
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0xd24e0
testq %rax, %rax
je 0x20d730
xorl %r14d, %r14d
leaq 0x1b2be8(%rip), %r15    # 0x3c02cc
movq (%rbx), %rdi
movq %r14, %rsi
callq 0xd2207
movq (%rax), %r12
movq 0x50(%r12), %rdi
callq 0x11bdbf
movq 0x58(%r12), %rdi
callq 0x11bdbf
movq 0x40(%r12), %rdi
callq 0xd2938
movq %r12, %rdi
movq %r15, %rsi
movl $0xd8, %edx
callq 0x1045eb
incq %r14
movq (%rbx), %rdi
callq 0xd24e0
cmpq %rax, %r14
jb 0x20d6e4
movq (%rbx), %rdi
callq 0xd2938
movq 0x8(%rbx), %rdi
callq 0xd24e0
testq %rax, %rax
je 0x20d79e
xorl %r14d, %r14d
leaq 0x1b2b7c(%rip), %r15    # 0x3c02cc
movq 0x8(%rbx), %rdi
movq %r14, %rsi
callq 0xd2207
movq (%rax), %r12
movq 0x50(%r12), %rdi
callq 0x11bdbf
movq 0x58(%r12), %rdi
callq 0x11bdbf
movq 0x40(%r12), %rdi
callq 0xd2938
movq %r12, %rdi
movq %r15, %rsi
movl $0xe0, %edx
callq 0x1045eb
incq %r14
movq 0x8(%rbx), %rdi
callq 0xd24e0
cmpq %rax, %r14
jb 0x20d750
movq 0x8(%rbx), %rdi
callq 0xd2938
leaq 0x1b2b1e(%rip), %rsi    # 0x3c02cc
movq %rbx, %rdi
movl $0xe3, %edx
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrdigest_pdom_visitor.c
// Function: gt_ltrdigest_pdom_visitor_chainproc
static void gt_ltrdigest_pdom_visitor_chainproc(GtChain *c, GtFragment *f,
                                             GT_UNUSED GtUword nof_frags,
                                             GT_UNUSED GtUword gap_length,
                                             void *data)
{
  GtUword i,
                *chainno = (GtUword*) data;
  gt_log_log("resulting chain has "GT_WD" GtFragments, score "GT_WD"",
             gt_chain_size(c),
             gt_chain_get_score(c));
  for (i = 0; i < gt_chain_size(c); i++) {
    GtFragment frag;
    frag = f[gt_chain_get_fragnum(c, i)];
    gt_log_log("("GT_WU" "GT_WU") ("GT_WU" "GT_WU")", frag.startpos1,
               frag.endpos1, frag.startpos2, frag.endpos2);
    gt_array_add(((GtHMMERSingleHit*) frag.data)->chains, *chainno);
  }
  (*chainno)++;
  gt_log_log("\n");
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r8, %rbx
movq %rsi, %r14
movq %rdi, %r15
callq 0x2fbd01
movq %rax, %r12
movq %r15, %rdi
callq 0x2fbc48
leaq 0x1b2ff9(%rip), %rdi    # 0x3c09c3
movq %r12, %rsi
movq %rax, %rdx
xorl %eax, %eax
callq 0x103d72
movq %r15, %rdi
callq 0x2fbd01
testq %rax, %rax
je 0x20da44
leaq 0x1b3007(%rip), %r12    # 0x3c09f2
xorl %r13d, %r13d
movq %r15, %rdi
movq %r13, %rsi
callq 0x2fbcc5
leaq (%rax,%rax,2), %rax
shlq $0x4, %rax
movq (%r14,%rax), %rsi
movq 0x8(%r14,%rax), %rdx
movq 0x10(%r14,%rax), %rcx
movq 0x18(%r14,%rax), %r8
movq 0x28(%r14,%rax), %rbp
movq %r12, %rdi
xorl %eax, %eax
callq 0x103d72
movq 0x40(%rbp), %rdi
movl $0x8, %edx
movq %rbx, %rsi
callq 0xd2410
incq %r13
movq %r15, %rdi
callq 0x2fbd01
cmpq %rax, %r13
jb 0x20d9ee
incq (%rbx)
leaq 0x1b2651(%rip), %rdi    # 0x3c009f
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x103d72
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrdigest_ppt_visitor.c
// Function: gt_ppt_hit_get_coords
GtRange gt_ppt_hit_get_coords(const GtPPTHit *h,
                                     GtLTRdigestPPTVisitor *lv)
{
  GtRange rng;
  gt_assert(h);
  rng.start = h->rng.start;
  rng.end = h->rng.end;
  switch (h->strand)
  {
    case GT_STRAND_FORWARD:
    default:
      rng.start = h->res->rightltrrng.start - 2 - lv->radius
                    + rng.start;
      rng.end = rng.start + (gt_range_length(&h->rng) - 1);
      break;
    case GT_STRAND_REVERSE:
      rng.end = h->res->leftltrrng.end + lv->radius - rng.start;
      rng.start = rng.end - (gt_range_length(&h->rng) - 1);
      break;
  }
  gt_assert(gt_range_length(&rng) == gt_range_length(&h->rng));
  return rng;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x18, %rsp
testq %rdi, %rdi
je 0x20dd5d
movq %rdi, %rbx
movq (%rdi), %r15
cmpl $0x1, 0x28(%rdi)
movq 0x30(%rdi), %rcx
movl 0x88(%rsi), %eax
jne 0x20dd0b
movq 0x10(%rcx), %r14
subq %r15, %r14
addq %rax, %r14
movq %rbx, %rdi
callq 0x112233
movq %r14, %r12
subq %rax, %r12
incq %r12
jmp 0x20dd26
addq 0x18(%rcx), %r15
subq %rax, %r15
leaq -0x2(%r15), %r12
movq %rbx, %rdi
callq 0x112233
leaq (%rax,%r15), %r14
addq $-0x3, %r14
leaq 0x8(%rsp), %rdi
movq %r14, 0x8(%rdi)
movq %r12, (%rdi)
callq 0x112233
movq %rax, %r14
movq %rbx, %rdi
callq 0x112233
cmpq %rax, %r14
jne 0x20dd62
movq 0x8(%rsp), %rax
movq 0x10(%rsp), %rdx
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
callq 0x814e5
callq 0x814ac
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrdigest_ppt_visitor.c
// Function: gt_ppt_results_delete
void gt_ppt_results_delete(GtPPTResults *results)
{
  GtUword i;
  if (results == NULL) return;

  if (results->hits != NULL)
  {
    for (i=0;i<gt_array_size(results->hits);i++)
    {
      GtPPTHit * hit = *(GtPPTHit**) gt_array_get(results->hits,i);
      if (hit->ubox != NULL)
        gt_free(hit->ubox);
      gt_free(hit);
    }
    gt_array_delete(results->hits);
  }
  gt_free(results);
}

// Assembly:
testq %rdi, %rdi
je 0x20de03
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq (%rdi), %rdi
testq %rdi, %rdi
je 0x20dde4
callq 0xd24e0
testq %rax, %rax
je 0x20dddc
xorl %r14d, %r14d
leaq 0x1b2d2f(%rip), %r15    # 0x3c0ac6
movq (%rbx), %rdi
movq %r14, %rsi
callq 0xd2207
movq (%rax), %r12
movq 0x20(%r12), %rdi
testq %rdi, %rdi
je 0x20ddbc
movq %r15, %rsi
movl $0x1ca, %edx            # imm = 0x1CA
callq 0x1045eb
movq %r12, %rdi
movq %r15, %rsi
movl $0x1cb, %edx            # imm = 0x1CB
callq 0x1045eb
incq %r14
movq (%rbx), %rdi
callq 0xd24e0
cmpq %rax, %r14
jb 0x20dd97
movq (%rbx), %rdi
callq 0xd2938
leaq 0x1b2cdb(%rip), %rsi    # 0x3c0ac6
movq %rbx, %rdi
movl $0x1cf, %edx            # imm = 0x1CF
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrdigest_ppt_visitor.c
// Function: gt_ltrdigest_ppt_visitor_free
void gt_ltrdigest_ppt_visitor_free(GtNodeVisitor *nv)
{
  GT_UNUSED GtLTRdigestPPTVisitor *lv;
  if (!nv) return;
  lv = gt_ltrdigest_ppt_visitor_cast(nv);
  gt_str_delete(lv->tag);
  gt_alphabet_delete(lv->alpha);
  gt_hmm_delete(lv->hmm);
}

// Assembly:
testq %rdi, %rdi
je 0x20de3c
pushq %rbx
movq %rdi, %rbx
callq 0x20de3d
movq %rax, %rdi
movq %rbx, %rsi
callq 0x1630b1
movq %rax, %rbx
movq 0x18(%rax), %rdi
callq 0x11bdbf
movq 0x28(%rbx), %rdi
callq 0xd0e1c
movq 0x20(%rbx), %rdi
popq %rbx
jmp 0x1522ad
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrdigest_ppt_visitor.c
// Function: gt_ltrdigest_ppt_visitor_class
const GtNodeVisitorClass* gt_ltrdigest_ppt_visitor_class(void)
{
  static const GtNodeVisitorClass *nvc = NULL;
  if (!nvc) {
    nvc = gt_node_visitor_class_new(sizeof (GtLTRdigestPPTVisitor),
                                   gt_ltrdigest_ppt_visitor_free,
                                   NULL,
                                   gt_ltrdigest_ppt_visitor_feature_node,
                                   NULL,
                                   NULL,
                                   NULL);
  }
  return nvc;
}

// Assembly:
movq 0x2b0b64(%rip), %rax    # 0x4be9a8
testq %rax, %rax
je 0x20de4a
retq
pushq %rax
movq $0x0, (%rsp)
leaq -0x56(%rip), %rsi       # 0x20de04
leaq 0x1e(%rip), %rcx        # 0x20de7f
movl $0x90, %edi
xorl %edx, %edx
xorl %r8d, %r8d
xorl %r9d, %r9d
callq 0x163010
movq %rax, 0x2b0b2e(%rip)    # 0x4be9a8
addq $0x8, %rsp
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrdigest_ppt_visitor.c
// Function: gt_ppt_hit_new
static GtPPTHit* gt_ppt_hit_new(GtStrand strand, GtPPTResults *r)
{
  GtPPTHit *h = gt_calloc((size_t) 1, sizeof (GtPPTHit));
  gt_assert(h);
  h->strand = strand;
  h->res = r;
  h->score = 0.0;
  return h;
}

// Assembly:
pushq %rbp
pushq %rbx
pushq %rax
movq %rsi, %rbx
movl %edi, %ebp
leaq 0x1b1d02(%rip), %rdx    # 0x3c0ac6
movl $0x1, %edi
movl $0x38, %esi
movl $0x68, %ecx
callq 0x10436a
testq %rax, %rax
je 0x20edf3
movl %ebp, 0x28(%rax)
movq %rbx, 0x30(%rax)
movq $0x0, 0x10(%rax)
addq $0x8, %rsp
popq %rbx
popq %rbp
retq
callq 0x816e4
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrdigest_strand_assign_visitor.c
// Function: gt_ltrdigest_strand_assign_visitor_class
const GtNodeVisitorClass* gt_ltrdigest_strand_assign_visitor_class(void)
{
  static const GtNodeVisitorClass *nvc = NULL;
  if (!nvc) {
    nvc = gt_node_visitor_class_new(sizeof (GtLTRdigestStrandAssignVisitor),
                                NULL,
                                NULL,
                                gt_ltrdigest_strand_assign_visitor_feature_node,
                                NULL,
                                NULL,
                                NULL);
  }
  return nvc;
}

// Assembly:
movq 0x2afb7e(%rip), %rax    # 0x4be9b0
testq %rax, %rax
je 0x20ee38
retq
pushq %rax
movq $0x0, (%rsp)
leaq 0x20(%rip), %rcx        # 0x20ee68
movl $0x18, %edi
xorl %esi, %esi
xorl %edx, %edx
xorl %r8d, %r8d
xorl %r9d, %r9d
callq 0x163010
movq %rax, 0x2afb4d(%rip)    # 0x4be9b0
addq $0x8, %rsp
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrdigest_strand_assign_visitor.c
// Function: gt_ltrdigest_strand_assign_visitor_new
GtNodeVisitor* gt_ltrdigest_strand_assign_visitor_new()
{
  GtNodeVisitor *nv = NULL;
  GtLTRdigestStrandAssignVisitor *sav;
  nv = gt_node_visitor_create(gt_ltrdigest_strand_assign_visitor_class());
  sav = gt_ltrdigest_strand_assign_visitor_cast(nv);
  sav->strand = GT_STRAND_UNKNOWN;
  return nv;
}

// Assembly:
pushq %rbx
callq 0x20ee2b
movq %rax, %rdi
callq 0x163080
movq %rax, %rbx
callq 0x20ee2b
movq %rax, %rdi
movq %rbx, %rsi
callq 0x1630b1
movl $0x3, 0x10(%rax)
movq %rbx, %rax
popq %rbx
retq
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrharvest_fasta_out_visitor.c
// Function: gt_ltrharvest_fasta_out_visitor_class
const GtNodeVisitorClass* gt_ltrharvest_fasta_out_visitor_class(void)
{
  static const GtNodeVisitorClass *nvc = NULL;
  gt_class_alloc_lock_enter();
  if (!nvc) {
    nvc = gt_node_visitor_class_new(sizeof (GtLTRharvestFastaOutVisitor),
                                   NULL,
                                   NULL,
                                   gt_ltrharvest_fasta_out_visitor_feature_node,
                                   NULL,
                                   NULL,
                                   NULL);
  }
  gt_class_alloc_lock_leave();
  return nvc;
}

// Assembly:
pushq %rax
callq 0xe252f
cmpq $0x0, 0x2af98e(%rip)    # 0x4be9b8
jne 0x20f056
movq $0x0, (%rsp)
leaq 0x29(%rip), %rcx        # 0x20f064
movl $0x30, %edi
xorl %esi, %esi
xorl %edx, %edx
xorl %r8d, %r8d
xorl %r9d, %r9d
callq 0x163010
movq %rax, 0x2af962(%rip)    # 0x4be9b8
callq 0xe2545
movq 0x2af956(%rip), %rax    # 0x4be9b8
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrharvest_fasta_out_visitor.c
// Function: gt_ltrharvest_fasta_out_visitor_new
GtNodeVisitor* gt_ltrharvest_fasta_out_visitor_new(const GtEncseq *encseq,
                                                   bool inner,
                                                   GtUword width,
                                                   GtFile *outfp)
{
  GtNodeVisitor *nv;
  GtLTRharvestFastaOutVisitor *lv;
  gt_assert(encseq && outfp);
  nv = gt_node_visitor_create(gt_ltrharvest_fasta_out_visitor_class());
  lv = gt_ltrharvest_fasta_out_visitor_cast(nv);
  gt_assert(lv);
  lv->inner = inner;
  lv->outfp = outfp;
  lv->width = width;
  lv->encseq = encseq;
  return nv;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
testq %rdi, %rdi
je 0x20f496
movq %rcx, %r14
testq %rcx, %rcx
je 0x20f496
movq %rdx, %rbx
movl %esi, %ebp
movq %rdi, %r15
callq 0x20f01c
movq %rax, %rdi
callq 0x163080
movq %rax, %r12
callq 0x20f01c
movq %rax, %rdi
movq %r12, %rsi
callq 0x1630b1
testq %rax, %rax
je 0x20f49b
movb %bpl, 0x20(%rax)
movq %r14, 0x10(%rax)
movq %rbx, 0x18(%rax)
movq %r15, 0x28(%rax)
movq %r12, %rax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
callq 0x818d7
callq 0x81910
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrharvest_stream.c
// Function: gt_ltrharvest_stream_class
const GtNodeStreamClass* gt_ltrharvest_stream_class(void)
{
  static const GtNodeStreamClass *nsc = NULL;
  gt_class_alloc_lock_enter();
  if (!nsc) {
    nsc = gt_node_stream_class_new(sizeof (GtLTRharvestStream),
                                   gt_ltrharvest_stream_free,
                                   gt_ltrharvest_stream_next);
  }
  gt_class_alloc_lock_leave();
  return nsc;
}

// Assembly:
pushq %rax
callq 0xe252f
cmpq $0x0, 0x2af512(%rip)    # 0x4be9c0
jne 0x20f4cf
leaq 0x26(%rip), %rsi        # 0x20f4dd
leaq 0xb1(%rip), %rdx        # 0x20f56f
movl $0x100, %edi            # imm = 0x100
callq 0x162d34
movq %rax, 0x2af4f1(%rip)    # 0x4be9c0
callq 0xe2545
movq 0x2af4e5(%rip), %rax    # 0x4be9c0
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/ltr/ltrharvest_stream.c
// Function: gt_ltrharvest_stream_free
static void gt_ltrharvest_stream_free(GtNodeStream *ns)
{
  GtLTRharvestStream *ltrh_stream = gt_ltrharvest_stream_cast(ns);
  GT_FREEARRAY(&ltrh_stream->arrayLTRboundaries, LTRboundaries);
  if (ltrh_stream->ssar != NULL)
    gt_freeSequentialsuffixarrayreader(&ltrh_stream->ssar);
  if (ltrh_stream->bdptrtab != NULL)
    gt_free(ltrh_stream->bdptrtab);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
callq 0x20f4a0
movq %rax, %rdi
movq %rbx, %rsi
callq 0x162ff7
movq %rax, %rbx
movq 0xc0(%rax), %rdi
testq %rdi, %rdi
je 0x20f52a
leaq 0xc0(%rbx), %r14
leaq 0x1b1a83(%rip), %rsi    # 0x3c0f94
movl $0x666, %edx            # imm = 0x666
callq 0x1045eb
xorps %xmm0, %xmm0
movups %xmm0, (%r14)
movq $0x0, 0x10(%r14)
cmpq $0x0, 0xe0(%rbx)
je 0x20f543
movq %rbx, %rdi
addq $0xe0, %rdi
callq 0x1a5698
movq 0xb8(%rbx), %rdi
testq %rdi, %rdi
je 0x20f567
leaq 0x1b1a3e(%rip), %rsi    # 0x3c0f94
movl $0x66a, %edx            # imm = 0x66A
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x1045eb
addq $0x8, %rsp
popq %rbx
popq %r14
retq