LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/match/xdrop.c
// Function: gt_xdrop_resources_new
GtXdropresources *gt_xdrop_resources_new(const GtXdropArbitraryscores *scores)
{
  GtXdropresources *res = gt_malloc(sizeof *res);

  res->arbitscores = scores;
  GT_INITARRAY (&res->fronts, GtXdropfrontvalue);
  GT_INITARRAY (&res->big_t, GtXdropscore);
  gt_calculatedistancesfromscores(scores,&res->arbitdistances);
  return res;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %r14
leaq 0x1a5cd0(%rip), %rsi    # 0x35d1f2
pushq $0x48
popq %rdi
movl $0xae, %edx
callq 0x93160
movq %r14, (%rax)
xorps %xmm0, %xmm0
movups %xmm0, 0x18(%rax)
movups %xmm0, 0x28(%rax)
movups %xmm0, 0x38(%rax)
movl (%r14), %ebp
testl %ebp, %ebp
jle 0x1b75fc
movq %rax, %rbx
testb $0x1, %bpl
jne 0x1b7563
movl 0x4(%r14), %edx
movl 0x8(%r14), %eax
movl 0xc(%r14), %ecx
jmp 0x1b7577
addl %ebp, %ebp
movl 0x4(%r14), %edx
movl 0x8(%r14), %eax
addl %edx, %edx
addl %eax, %eax
movl 0xc(%r14), %ecx
addl %ecx, %ecx
movl %ebp, %r14d
subl %edx, %r14d
jl 0x1b75ce
shrl %ebp
movl %ebp, %r15d
subl %eax, %r15d
jl 0x1b75ce
subl %ecx, %ebp
jl 0x1b75ce
movl %r14d, %edi
movl %r15d, %esi
callq 0x959b0
movl %eax, %edi
movl %ebp, %esi
callq 0x959b0
movl %eax, %ecx
movl %eax, 0x14(%rbx)
movl %r14d, %eax
cltd
idivl %ecx
movl %eax, 0x8(%rbx)
movl %r15d, %eax
cltd
idivl %ecx
movl %eax, 0xc(%rbx)
movl %ebp, %eax
cltd
idivl %ecx
movl %eax, 0x10(%rbx)
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
movq 0x280993(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x12da34(%rip), %rsi    # 0x2e5013
leaq 0x1a5f5a(%rip), %rdx    # 0x35d540
leaq 0x1a5f33(%rip), %rcx    # 0x35d520
leaq 0x1a5bfe(%rip), %r8     # 0x35d1f2
movl $0x95, %r9d
jmp 0x1b7628
movq 0x280965(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x12da06(%rip), %rsi    # 0x2e5013
leaq 0x1a5ef7(%rip), %rdx    # 0x35d50b
leaq 0x1a5f05(%rip), %rcx    # 0x35d520
leaq 0x1a5bd0(%rip), %r8     # 0x35d1f2
movl $0x87, %r9d
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/match/xdrop.c
// Function: gt_xdrop_resources_delete
void gt_xdrop_resources_delete(GtXdropresources *res)
{
  if (res != NULL)
  {
    GT_FREEARRAY (&res->fronts, GtXdropfrontvalue);
    GT_FREEARRAY (&res->big_t, GtXdropscore);
    gt_free(res);
  }
}

// Assembly:
testq %rdi, %rdi
je 0x1b76af
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq 0x18(%rdi), %rdi
testq %rdi, %rdi
je 0x1b766a
leaq 0x18(%rbx), %r14
leaq 0x1a5b9e(%rip), %rsi    # 0x35d1f2
movl $0xbb, %edx
callq 0x936f9
xorps %xmm0, %xmm0
movups %xmm0, (%r14)
andq $0x0, 0x10(%r14)
movq 0x30(%rbx), %rdi
testq %rdi, %rdi
je 0x1b7694
leaq 0x30(%rbx), %r14
leaq 0x1a5b74(%rip), %rsi    # 0x35d1f2
movl $0xbc, %edx
callq 0x936f9
xorps %xmm0, %xmm0
movups %xmm0, (%r14)
andq $0x0, 0x10(%r14)
leaq 0x1a5b57(%rip), %rsi    # 0x35d1f2
movq %rbx, %rdi
movl $0xbd, %edx
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x936f9
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x1b80a6
leaq 0x20(%r12), %rsi
movq %rsi, 0x20(%r14)
shlq $0x4, %rsi
leaq 0x1a515d(%rip), %rdx    # 0x35d1f2
movq %rax, %rdi
movl $0xda, %ecx
callq 0x93472
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_O2/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 0x1a5f19(%rip), %rdx    # 0x35e640
pushq $0x1
popq %rdi
pushq $0x40
popq %rsi
pushq $0x2b
popq %rcx
callq 0x9334a
movq %rax, %rbx
callq 0x9b6b4
movq %rax, 0x8(%rbx)
callq 0xacb84
movq %rax, 0x10(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x1b8785
pushq %rbx
movq %rdi, %rbx
movq 0x10(%rdi), %rdi
callq 0xae103
movq (%rbx), %rdi
callq 0x8da06
movq 0x8(%rbx), %rdi
callq 0x9ba24
leaq 0x1a5ec7(%rip), %rsi    # 0x35e640
pushq $0x38
popq %rdx
movq %rbx, %rdi
popq %rbx
jmp 0x936f9
retq
// File: /workspace/github_c_makefile_star2_O2/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 %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x1b884f
movq %rdi, %rbx
leaq 0x1a5edd(%rip), %rdi    # 0x35e67e
leaq 0x1a5efd(%rip), %rsi    # 0x35e6a5
callq 0x97df5
movq %rax, %r14
leaq 0x18(%rbx), %rdx
leaq 0x1a5f04(%rip), %rdi    # 0x35e6bf
leaq 0x1a5f04(%rip), %rsi    # 0x35e6c6
pushq $0x64
popq %r15
xorl %ecx, %ecx
xorl %r8d, %r8d
movq %r15, %r9
callq 0x9ac6b
movq %rax, %r12
movq %rax, %rdi
callq 0x9ae37
movq %r14, %rdi
movq %r12, %rsi
callq 0x97f31
leaq 0x20(%rbx), %rdx
leaq 0x1a5f4e(%rip), %rdi    # 0x35e742
leaq 0x1a5f4e(%rip), %rsi    # 0x35e749
xorl %ecx, %ecx
xorl %r8d, %r8d
movq %r15, %r9
callq 0x9ac6b
movq %rax, %r15
movq %rax, %rdi
callq 0x9ae37
movq %r14, %rdi
movq %r15, %rsi
callq 0x97f31
movq %r15, %rdi
callq 0x9ae37
movq 0x8(%rbx), %rdi
movq %r14, %rsi
movq %rbx, %rdx
callq 0x9b6d7
pushq $0x1
popq %rsi
movq %r14, %rdi
callq 0x98be7
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
movq 0x27f712(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x12c7b3(%rip), %rsi    # 0x2e5013
leaq 0x18fdec(%rip), %rdx    # 0x348653
leaq 0x1a5ded(%rip), %rcx    # 0x35e65b
leaq 0x1a5dcb(%rip), %r8     # 0x35e640
pushq $0x40
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x1b8a61
leaq 0x1a5d9e(%rip), %rdi    # 0x35e7f8
xorl %eax, %eax
callq 0xb2cd0
movq (%r14), %rdi
xorl %ebp, %ebp
testq %rdi, %rdi
je 0x1b8aa8
callq 0xad289
testq %rax, %rax
je 0x1b8aa8
movq (%r14), %rdi
callq 0xad1fa
movq %rax, %rdi
callq 0x8da98
testb %al, %al
jne 0x1b8aa8
movq (%r14), %rdi
callq 0xad1fa
leaq 0x1a5dd9(%rip), %rsi    # 0x35e871
movq %rbx, %rdi
movq %rax, %rdx
xorl %eax, %eax
callq 0x89dbb
pushq $-0x1
popq %rbp
movl %ebp, %eax
popq %rbx
popq %r14
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x1a5dac(%rip), %rdx    # 0x35e88b
pushq $0x1
popq %rdi
pushq $0x59
popq %rcx
movl $0x110, %esi            # imm = 0x110
callq 0x9334a
movq %rax, %rbx
movl $0x110, %edx            # imm = 0x110
movq %rax, %rdi
xorl %esi, %esi
callq 0x17380
callq 0xacb84
movq %rax, (%rbx)
callq 0xacb84
movq %rax, 0x8(%rbx)
callq 0xacb84
movq %rax, 0x10(%rbx)
callq 0x9b6b4
movq %rax, 0x20(%rbx)
callq 0xae154
movq %rax, 0x30(%rbx)
callq 0x116724
movq %rax, 0x38(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x1b8b95
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0xae103
movq 0x8(%rbx), %rdi
callq 0xae103
movq 0x10(%rbx), %rdi
callq 0xae103
movq 0x30(%rbx), %rdi
callq 0xae662
movq 0x28(%rbx), %rdi
callq 0x8da06
movq 0x20(%rbx), %rdi
callq 0x9ba24
movq 0x38(%rbx), %rdi
callq 0x116765
leaq 0x1a5d02(%rip), %rsi    # 0x35e88b
pushq $0x6f
popq %rdx
movq %rbx, %rdi
popq %rbx
jmp 0x936f9
retq
// File: /workspace/github_c_makefile_star2_O2/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 %r15
pushq %r14
pushq %rbx
leaq 0x1a5477(%rip), %rbx    # 0x35f053
pushq $0x1
popq %r14
movl $0xf8, %esi
movq %r14, %rdi
movq %rbx, %rdx
movl $0x93, %ecx
callq 0x9334a
movq %rax, %r15
callq 0x9b6b4
movq %rax, (%r15)
callq 0xacb84
movq %rax, 0x18(%r15)
callq 0xacb84
movq %rax, 0x20(%r15)
callq 0xacb84
movq %rax, 0x10(%r15)
callq 0xacb84
movq %rax, 0x28(%r15)
callq 0xacb84
movq %rax, 0x30(%r15)
callq 0xacb84
movq %rax, 0x38(%r15)
pushq $0x10
popq %rsi
movq %r14, %rdi
movq %rbx, %rdx
movl $0x9b, %ecx
callq 0x9334a
movq %rax, 0xf0(%r15)
movq %r15, %rax
popq %rbx
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x1b9d2a
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq 0x8(%rdi), %rdi
callq 0x8da06
movq (%rbx), %rdi
callq 0x9ba24
movq 0x18(%rbx), %rdi
callq 0xae103
movq 0x20(%rbx), %rdi
callq 0xae103
movq 0x10(%rbx), %rdi
callq 0xae103
movq 0x28(%rbx), %rdi
callq 0xae103
movq 0x30(%rbx), %rdi
callq 0xae103
movq 0x38(%rbx), %rdi
callq 0xae103
movq 0xe8(%rbx), %rdi
callq 0x9a8ea
movq 0xe0(%rbx), %rdi
callq 0x9a8ea
movq 0xd8(%rbx), %rdi
callq 0x9a8ea
movq 0xc0(%rbx), %rdi
callq 0x9a8ea
movq 0xc8(%rbx), %rdi
callq 0x9a8ea
movq 0xd0(%rbx), %rdi
callq 0x9a8ea
movq 0xf0(%rbx), %rdi
leaq 0x1a534d(%rip), %r14    # 0x35f053
movq %r14, %rsi
movl $0xb1, %edx
callq 0x936f9
movq %rbx, %rdi
movq %r14, %rsi
movl $0xb2, %edx
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x936f9
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x69e97
cmpq $0x0, 0x282bc6(%rip)    # 0x43d918
jne 0x1bad71
leaq 0x24(%rip), %rsi        # 0x1bad7f
leaq 0x76(%rip), %rdx        # 0x1badd8
pushq $0x50
popq %rdi
callq 0x102838
movq %rax, 0x282ba7(%rip)    # 0x43d918
callq 0x69ede
movq 0x282b9b(%rip), %rax    # 0x43d918
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x1bad44
movq %rax, %rdi
movq %rbx, %rsi
callq 0x102c81
movq %rax, %rbx
xorl %r14d, %r14d
movq 0x18(%rbx), %rdi
callq 0x586a4
movq 0x18(%rbx), %rdi
cmpq %rax, %r14
jae 0x1badc3
movq %r14, %rsi
callq 0x581aa
movq (%rax), %rdi
callq 0xde013
incq %r14
jmp 0x1bad9c
callq 0x58eb9
movq 0x10(%rbx), %rdi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x10297b
// File: /workspace/github_c_makefile_star2_O2/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 0x1bad44
movq %rax, %rdi
xorl %esi, %esi
callq 0x10289f
movq %rax, %rbp
callq 0x1bad44
movq %rax, %rdi
movq %rbp, %rsi
callq 0x102c81
movq %rax, %rbx
movq %r13, %rdi
callq 0x102934
movq %rax, 0x10(%rbx)
pushq $0x8
popq %rdi
callq 0x5809c
movq %rax, 0x18(%rbx)
movq %r12, 0x20(%rbx)
movb $0x1, 0x38(%rbx)
andq $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_O2/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 0x69e97
cmpq $0x0, 0x281e86(%rip)    # 0x43d920
jne 0x1bbabb
leaq 0x26(%rip), %rsi        # 0x1bbac9
leaq 0x93(%rip), %rdx        # 0x1bbb3d
movl $0x88, %edi
callq 0x102838
movq %rax, 0x281e65(%rip)    # 0x43d920
callq 0x69ede
movq 0x281e59(%rip), %rax    # 0x43d920
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x1bba8c
movq %rax, %rdi
movq %rbx, %rsi
callq 0x102c81
movq %rax, %rbx
movq 0x18(%rax), %rdi
callq 0x10327a
movq 0x28(%rbx), %rdi
callq 0x8f933
movq 0x30(%rbx), %rdi
callq 0xae662
xorl %r14d, %r14d
movq 0x20(%rbx), %rdi
callq 0x586a4
movq 0x20(%rbx), %rdi
cmpq %rax, %r14
jae 0x1bbb28
movq %r14, %rsi
callq 0x581aa
movq (%rax), %rdi
callq 0xde013
incq %r14
jmp 0x1bbb01
callq 0x58eb9
movq 0x10(%rbx), %rdi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x10297b
// File: /workspace/github_c_makefile_star2_O2/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 0x281145(%rip), %rax    # 0x43d928
testq %rax, %rax
je 0x1bc7e9
retq
pushq %rax
andq $0x0, (%rsp)
leaq 0x1e(%rip), %rcx        # 0x1bc814
pushq $0x18
popq %rdi
xorl %esi, %esi
xorl %edx, %edx
xorl %r8d, %r8d
xorl %r9d, %r9d
callq 0x102cd0
movq %rax, 0x281119(%rip)    # 0x43d928
addq $0x8, %rsp
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x1bc7dc
movq %rax, %rdi
callq 0x102da0
testq %rax, %rax
je 0x1bca62
movq %rax, %rbx
callq 0x1bc7dc
movq %rax, %rdi
movq %rbx, %rsi
callq 0x102dfe
movb $0x0, 0x10(%rax)
movq %rbx, %rax
popq %rbx
retq
movq 0x27b4ff(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x1285a0(%rip), %rsi    # 0x2e5013
leaq 0x1813e7(%rip), %rdx    # 0x33de61
leaq 0x1a304e(%rip), %rcx    # 0x35facf
leaq 0x1a3025(%rip), %r8     # 0x35faad
pushq $0x7f
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x69e97
cmpq $0x0, 0x280e8a(%rip)    # 0x43d930
jne 0x1bcac7
leaq 0x26(%rip), %rsi        # 0x1bcad5
leaq 0x49(%rip), %rdx        # 0x1bcaff
movl $0xa8, %edi
callq 0x102838
movq %rax, 0x280e69(%rip)    # 0x43d930
callq 0x69ede
movq 0x280e5d(%rip), %rax    # 0x43d930
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x69e97
cmpq $0x0, 0x28001e(%rip)    # 0x43d938
jne 0x1bd941
andq $0x0, (%rsp)
leaq 0x27(%rip), %rcx        # 0x1bd94f
pushq $0x18
popq %rdi
xorl %esi, %esi
xorl %edx, %edx
xorl %r8d, %r8d
xorl %r9d, %r9d
callq 0x102cd0
movq %rax, 0x27fff7(%rip)    # 0x43d938
callq 0x69ede
movq 0x27ffeb(%rip), %rax    # 0x43d938
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x69e97
cmpq $0x0, 0x27ed19(%rip)    # 0x43d940
jne 0x1bec48
leaq 0x26(%rip), %rsi        # 0x1bec56
leaq -0x1043(%rip), %rdx     # 0x1bdbf4
movl $0xe0, %edi
callq 0x102838
movq %rax, 0x27ecf8(%rip)    # 0x43d940
callq 0x69ede
movq 0x27ecec(%rip), %rax    # 0x43d940
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x1bec19
movq %rax, %rdi
movq %rbx, %rsi
callq 0x102c81
movq %rax, %rbx
movq 0x28(%rax), %rdi
testq %rdi, %rdi
je 0x1bec7b
callq 0x8da06
movq 0x30(%rbx), %rdi
testq %rdi, %rdi
je 0x1bec89
callq 0x8da06
movq 0x38(%rbx), %rdi
testq %rdi, %rdi
je 0x1bec97
callq 0x8da06
movq 0x40(%rbx), %rdi
testq %rdi, %rdi
je 0x1beca5
callq 0x8da06
movq 0x48(%rbx), %rdi
testq %rdi, %rdi
je 0x1becb3
callq 0x8da06
movq 0x50(%rbx), %rdi
testq %rdi, %rdi
je 0x1becc1
callq 0x8da06
movq 0x58(%rbx), %rdi
callq 0x10327a
movq 0x10(%rbx), %rdi
popq %rbx
jmp 0x10297b
// File: /workspace/github_c_makefile_star2_O2/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 0x1becf6
movq %rdi, %rbx
callq 0x1bec19
movq %rax, %rdi
movq %rbx, %rsi
callq 0x102c81
movb $0x1, 0xd8(%rax)
popq %rbx
retq
movq 0x27926b(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x12630c(%rip), %rsi    # 0x2e5013
leaq 0x1c1a28(%rip), %rdx    # 0x380736
leaq 0x1a1151(%rip), %rcx    # 0x35fe66
leaq 0x1a107f(%rip), %r8     # 0x35fd9b
movl $0x2a0, %r9d            # imm = 0x2A0
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x1bed50
movq %rdi, %rbx
callq 0x1bec19
movq %rax, %rdi
movq %rbx, %rsi
callq 0x102c81
movb $0x1, 0xd9(%rax)
popq %rbx
retq
movq 0x279211(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x1262b2(%rip), %rsi    # 0x2e5013
leaq 0x1c19ce(%rip), %rdx    # 0x380736
leaq 0x1a1131(%rip), %rcx    # 0x35fea0
leaq 0x1a1025(%rip), %r8     # 0x35fd9b
movl $0x2a8, %r9d            # imm = 0x2A8
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x27e49d(%rip), %rax    # 0x43d948
testq %rax, %rax
je 0x1bf4b1
retq
pushq %rax
andq $0x0, (%rsp)
leaq 0x25(%rip), %rsi        # 0x1bf4e3
leaq 0x42(%rip), %rcx        # 0x1bf507
movl $0x98, %edi
xorl %edx, %edx
xorl %r8d, %r8d
xorl %r9d, %r9d
callq 0x102cd0
movq %rax, 0x27e46a(%rip)    # 0x43d948
addq $0x8, %rsp
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x1bff29
cmpq $0x0, 0x88(%rsp)
je 0x1bff29
movq %rcx, %r15
movl %edx, %ebp
movl %esi, %r12d
movq %rdi, %r13
callq 0x1bf4a4
movq %rax, %rdi
callq 0x102da0
movq %rax, %rbx
callq 0x1bf4a4
movq %rax, %rdi
movq %rbx, %rsi
callq 0x102dfe
movq %rax, %r14
leaq 0x19f1a7(%rip), %rdi    # 0x35f044
callq 0xacbd1
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
movq 0x278038(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x1250d9(%rip), %rsi    # 0x2e5013
leaq 0x1a05b7(%rip), %rdx    # 0x3604f8
leaq 0x1a05c1(%rip), %rcx    # 0x360509
leaq 0x1a05d7(%rip), %r8     # 0x360526
movl $0x214, %r9d            # imm = 0x214
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x1c02c5
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
callq 0x1c02c6
movq %rax, %rdi
movq %rbx, %rsi
callq 0x102dfe
movq %rax, %rbx
pushq $-0x18
popq %r14
testq %r14, %r14
je 0x1c029a
movq 0x48(%rbx,%r14), %rdi
callq 0xae103
movq 0x60(%rbx,%r14), %rdi
callq 0xae103
addq $0x8, %r14
jmp 0x1c027b
movq 0x80(%rbx), %rdi
callq 0xae103
movq 0x88(%rbx), %rdi
callq 0xae103
movq 0x98(%rbx), %rdi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x6ca1b
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x27d683(%rip), %rax    # 0x43d950
testq %rax, %rax
je 0x1c02d3
retq
pushq %rax
andq $0x0, (%rsp)
leaq -0x88(%rip), %rsi       # 0x1c0258
leaq 0x1e(%rip), %rcx        # 0x1c0305
movl $0xa8, %edi
xorl %edx, %edx
xorl %r8d, %r8d
xorl %r9d, %r9d
callq 0x102cd0
movq %rax, 0x27d650(%rip)    # 0x43d950
addq $0x8, %rsp
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x17990
testl %eax, %eax
je 0x1c0d46
callq 0x17060
movl (%rax), %edi
callq 0x17220
leaq 0x19fbb5(%rip), %rsi    # 0x3608e9
movq %rbx, %rdi
movq %rax, %rdx
xorl %eax, %eax
callq 0x89dbb
pushq $-0x1
popq %rax
jmp 0x1c0d48
xorl %eax, %eax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/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
xorl %ebp, %ebp
pushq $0x4
popq %r15
cmpq $0x3, %rbp
je 0x1c0e66
leaq 0x3(%rsp), %r14
movq %r14, %rdi
leaq 0x19fbf9(%rip), %rsi    # 0x360991
movq %rbp, %rdx
pushq $0x2b
popq %rcx
xorl %eax, %eax
callq 0x17120
movq (%rbx), %rax
movl 0x4(%rax), %edi
movq %r14, %rsi
movq %r14, %r12
movq %r15, %rdx
callq 0x17250
movq (%rbx), %rax
movq 0x18(%rbx), %rcx
movl 0x4(%rax), %r13d
movq 0x30(%rcx,%rbp,8), %rdi
callq 0xad1fa
movq %rax, %r14
movq 0x18(%rbx), %rax
movq 0x30(%rax,%rbp,8), %rdi
callq 0xad289
movl %r13d, %edi
movq %r14, %rsi
movq %rax, %rdx
callq 0x17250
movq (%rbx), %rax
movl 0x4(%rax), %edi
leaq 0x19f6f5(%rip), %rsi    # 0x3604ef
pushq $0x1
popq %rdx
callq 0x17250
movq %r12, %rdi
leaq 0x19fb85(%rip), %rsi    # 0x360991
movq %rbp, %rdx
pushq $0x2d
popq %rcx
xorl %eax, %eax
callq 0x17120
movq (%rbx), %rax
movl 0x4(%rax), %edi
movq %r12, %rsi
movq %r15, %rdx
callq 0x17250
movq (%rbx), %rax
movq 0x18(%rbx), %rcx
movl 0x4(%rax), %r14d
movq 0x48(%rcx,%rbp,8), %rdi
callq 0xad1fa
movq %rax, %r13
movq 0x18(%rbx), %rax
movq 0x48(%rax,%rbp,8), %rdi
callq 0xad289
movl %r14d, %edi
movq %r13, %rsi
movq %rax, %rdx
callq 0x17250
incq %rbp
jmp 0x1c0d7f
movq (%rbx), %rax
movl (%rax), %edi
callq 0x17f20
movq (%rbx), %rax
movl 0x4(%rax), %edi
callq 0x17f20
movq 0x8(%rbx), %rax
movl 0x4(%rax), %edi
callq 0x17f20
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_O2/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 0x1c1c7f
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rdi, %rbx
xorl %r14d, %r14d
leaq 0x19eb34(%rip), %r15    # 0x3606e2
movq (%rbx), %rdi
callq 0x586a4
movq (%rbx), %rdi
cmpq %rax, %r14
jae 0x1c1bfc
movq %r14, %rsi
callq 0x581aa
movq (%rax), %r12
movq 0x50(%r12), %rdi
callq 0xae103
movq 0x58(%r12), %rdi
callq 0xae103
movq 0x40(%r12), %rdi
callq 0x58eb9
movq %r12, %rdi
movq %r15, %rsi
movl $0xd8, %edx
callq 0x936f9
incq %r14
jmp 0x1c1bae
callq 0x58eb9
xorl %r14d, %r14d
leaq 0x19ead7(%rip), %r15    # 0x3606e2
movq 0x8(%rbx), %rdi
callq 0x586a4
movq 0x8(%rbx), %rdi
cmpq %rax, %r14
jae 0x1c1c5b
movq %r14, %rsi
callq 0x581aa
movq (%rax), %r12
movq 0x50(%r12), %rdi
callq 0xae103
movq 0x58(%r12), %rdi
callq 0xae103
movq 0x40(%r12), %rdi
callq 0x58eb9
movq %r12, %rdi
movq %r15, %rsi
movl $0xe0, %edx
callq 0x936f9
incq %r14
jmp 0x1c1c0b
callq 0x58eb9
leaq 0x19ea7b(%rip), %rsi    # 0x3606e2
movq %rbx, %rdi
movl $0xe3, %edx
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
jmp 0x936f9
retq
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/ltr/ltrdigest_pdom_visitor.c
// Function: pdom_parser_get_next_line
static inline int pdom_parser_get_next_line(char *buf, FILE *instream,
                                            GtError *err) {
  int had_err = 0;
  char *bufp = buf;
  if (fgets(buf, GT_HMMER_BUF_LEN, instream) == NULL) {
    if (feof(instream)) {
      memset(buf, (int) '\0', (size_t) GT_HMMER_BUF_LEN);
      return 0;
    } else if (ferror(instream)) {
      gt_error_set(err, "error reading from input stream");
      return -1;
    }
  }
  while (!had_err && bufp && (buf[0] == '#' || buf[0] == '\n'))
    bufp = fgets(buf, GT_HMMER_BUF_LEN, instream);
  (void) gt_cstr_rtrim(buf, '\n');
  (void) gt_cstr_rtrim(buf, ' ');
  return 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movq %rdx, %r15
movq %rsi, %r14
movq %rdi, %rbx
movl $0xfa00, %esi           # imm = 0xFA00
movq %r14, %rdx
callq 0x17bc0
movq %rax, %rcx
movq %rbx, %rax
testq %rcx, %rcx
je 0x1c1ce6
testq %rax, %rax
je 0x1c1ccc
movzbl (%rbx), %eax
cmpl $0x23, %eax
je 0x1c1cba
cmpl $0xa, %eax
jne 0x1c1ccc
movq %rbx, %rdi
movl $0xfa00, %esi           # imm = 0xFA00
movq %r14, %rdx
callq 0x17bc0
jmp 0x1c1ca8
pushq $0xa
popq %rsi
movq %rbx, %rdi
callq 0x6c4c8
pushq $0x20
popq %rsi
movq %rbx, %rdi
callq 0x6c4c8
xorl %ebp, %ebp
jmp 0x1c1d2a
movq %r14, %rdi
callq 0x17b70
testl %eax, %eax
je 0x1c1d05
xorl %ebp, %ebp
movl $0xfa00, %edx           # imm = 0xFA00
movq %rbx, %rdi
xorl %esi, %esi
callq 0x17380
jmp 0x1c1d2a
movq %r14, %rdi
callq 0x17e70
movl %eax, %ecx
movq %rbx, %rax
testl %ecx, %ecx
je 0x1c1ca8
leaq 0x19ed13(%rip), %rsi    # 0x360a30
movq %r15, %rdi
xorl %eax, %eax
callq 0x89dbb
pushq $-0x1
popq %rbp
movl %ebp, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x298360
movq %rax, %r12
movq %r15, %rdi
callq 0x29816a
leaq 0x19ee55(%rip), %rdi    # 0x360dd9
movq %r12, %rsi
movq %rax, %rdx
xorl %eax, %eax
callq 0x92a82
pushq $0x8
popq %r13
xorl %ebp, %ebp
movq %r15, %rdi
callq 0x298360
cmpq %rax, %rbp
jae 0x1c1fee
movq %r15, %rdi
movq %rbp, %rsi
callq 0x2982ce
imulq $0x30, %rax, %rax
movq (%r14,%rax), %rsi
movq 0x8(%r14,%rax), %rdx
movq 0x10(%r14,%rax), %rcx
movq 0x18(%r14,%rax), %r8
movq 0x28(%r14,%rax), %r12
leaq 0x19ee36(%rip), %rdi    # 0x360e08
xorl %eax, %eax
callq 0x92a82
movq 0x40(%r12), %rdi
movq %rbx, %rsi
movq %r13, %rdx
callq 0x5851d
incq %rbp
jmp 0x1c1f97
incq (%rbx)
leaq 0x19e4f7(%rip), %rdi    # 0x3604ef
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x92a82
// File: /workspace/github_c_makefile_star2_O2/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 0x1c2359
movq %rdi, %rbx
movq (%rdi), %r15
cmpl $0x1, 0x28(%rdi)
movq 0x30(%rdi), %rcx
movl 0x88(%rsi), %eax
jne 0x1c2307
movq 0x10(%rcx), %r14
subq %r15, %r14
addq %rax, %r14
movq %rbx, %rdi
callq 0xa31ee
movq %r14, %r12
subq %rax, %r12
incq %r12
jmp 0x1c2322
addq 0x18(%rcx), %r15
subq %rax, %r15
leaq -0x2(%r15), %r12
movq %rbx, %rdi
callq 0xa31ee
leaq (%rax,%r15), %r14
addq $-0x3, %r14
leaq 0x8(%rsp), %rdi
movq %r14, 0x8(%rdi)
movq %r12, (%rdi)
callq 0xa31ee
movq %rax, %r14
movq %rbx, %rdi
callq 0xa31ee
cmpq %rax, %r14
jne 0x1c2385
movq 0x8(%rsp), %rax
movq 0x10(%rsp), %rdx
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
movq 0x275c08(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x122ca9(%rip), %rsi    # 0x2e5013
leaq 0x18a69f(%rip), %rdx    # 0x34ca10
leaq 0x19eb48(%rip), %rcx    # 0x360ec0
leaq 0x19eb57(%rip), %r8     # 0x360ed6
pushq $0x74
popq %r9
jmp 0x1c23b1
movq 0x275bdc(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x122c7d(%rip), %rsi    # 0x2e5013
leaq 0x19eb59(%rip), %rdx    # 0x360ef6
leaq 0x19eb1c(%rip), %rcx    # 0x360ec0
leaq 0x19eb2b(%rip), %r8     # 0x360ed6
movl $0x84, %r9d
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x1c244e
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq (%rdi), %rdi
testq %rdi, %rdi
je 0x1c242f
xorl %r14d, %r14d
leaq 0x19eaf3(%rip), %r15    # 0x360ed6
callq 0x586a4
movq (%rbx), %rdi
cmpq %rax, %r14
jae 0x1c242a
movq %r14, %rsi
callq 0x581aa
movq (%rax), %r12
movq 0x20(%r12), %rdi
testq %rdi, %rdi
je 0x1c2412
movq %r15, %rsi
movl $0x1ca, %edx            # imm = 0x1CA
callq 0x936f9
movq %r12, %rdi
movq %r15, %rsi
movl $0x1cb, %edx            # imm = 0x1CB
callq 0x936f9
incq %r14
movq (%rbx), %rdi
jmp 0x1c23e3
callq 0x58eb9
leaq 0x19eaa0(%rip), %rsi    # 0x360ed6
movq %rbx, %rdi
movl $0x1cf, %edx            # imm = 0x1CF
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
jmp 0x936f9
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x1c2487
pushq %rbx
movq %rdi, %rbx
callq 0x1c2488
movq %rax, %rdi
movq %rbx, %rsi
callq 0x102dfe
movq %rax, %rbx
movq 0x18(%rax), %rdi
callq 0xae103
movq 0x28(%rbx), %rdi
callq 0x568b5
movq 0x20(%rbx), %rdi
popq %rbx
jmp 0xee153
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x27b4c9(%rip), %rax    # 0x43d958
testq %rax, %rax
je 0x1c2495
retq
pushq %rax
andq $0x0, (%rsp)
leaq -0x53(%rip), %rsi       # 0x1c244f
leaq 0x1e(%rip), %rcx        # 0x1c24c7
movl $0x90, %edi
xorl %edx, %edx
xorl %r8d, %r8d
xorl %r9d, %r9d
callq 0x102cd0
movq %rax, 0x27b496(%rip)    # 0x43d958
addq $0x8, %rsp
retq