LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/genome_node.c
// Function: gt_genome_node_cmp_generic
static inline int gt_genome_node_cmp_generic(GtGenomeNode *gn_a,
                                             GtGenomeNode *gn_b,
                                             bool numeric_cmp)
{
  GtRange range_a, range_b;
  int rval;
  const char *id_a, *id_b;
  gt_assert(gn_a && gn_b);
  /* ensure that region nodes come first and sequence nodes come last,
     otherwise we don't get a valid GFF3 stream */
  if ((rval = compare_genome_node_type(gn_a, gn_b)))
    return rval;

  id_a = gt_str_get(gt_genome_node_get_idstr(gn_a));
  id_b = gt_str_get(gt_genome_node_get_idstr(gn_b));
  if (numeric_cmp) {
    GtUword anum, bnum;
    int arval, brval;
    arval = gt_parse_uword(&anum, id_a);
    brval = gt_parse_uword(&bnum, id_b);
    if (arval == 0 && brval == 0)
      rval = anum-bnum;
    else if (arval == 0)
      return -1;
    else if (brval == 0)
      return 1;
    else
      rval = 0;
    if (rval)
      return rval;
  } else {
    if ((rval = gt_md5_seqid_cmp_seqids(id_a, id_b))) {
      return rval;
    }
  }
  range_a = gt_genome_node_get_range(gn_a),
  range_b = gt_genome_node_get_range(gn_b);
  return gt_range_compare(&range_a, &range_b);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x20, %rsp
testq %rdi, %rdi
je 0x41e35
movq %rsi, %rbx
testq %rsi, %rsi
je 0x41e35
movl %edx, %ebp
movq %rdi, %r14
movq %rbx, %rsi
callq 0x42b61
testl %eax, %eax
jne 0x41e28
movq %r14, %rdi
callq 0x41f60
movq %rax, %rdi
callq 0x3c40b
movq %rax, %r15
movq %rbx, %rdi
callq 0x41f60
movq %rax, %rdi
callq 0x3c40b
movq %rax, %r12
testb %bpl, %bpl
je 0x41dbf
leaq 0x10(%rsp), %rdi
movq %r15, %rsi
callq 0x39e0b
movl %eax, %ebp
movq %rsp, %rdi
movq %r12, %rsi
callq 0x39e0b
movl %ebp, %ecx
orl %eax, %ecx
jne 0x41dd0
movl 0x10(%rsp), %eax
subl (%rsp), %eax
jmp 0x41df1
movq %r15, %rdi
movq %r12, %rsi
callq 0x7a69b
testl %eax, %eax
jne 0x41e28
jmp 0x41dfa
testl %eax, %eax
sete %sil
xorl %ecx, %ecx
testl %ebp, %ebp
sete %dl
xorl %eax, %eax
orb %dl, %sil
je 0x41df1
movb %dl, %cl
negl %ecx
orl $0x1, %ecx
xorl %edx, %edx
movl %ecx, %eax
jmp 0x41df6
testl %eax, %eax
sete %dl
testb %dl, %dl
je 0x41e28
movq %r14, %rdi
callq 0x41f83
leaq 0x10(%rsp), %r14
movq %rax, (%r14)
movq %rdx, 0x8(%r14)
movq %rbx, %rdi
callq 0x41f83
movq %rsp, %rsi
movq %rax, (%rsi)
movq %rdx, 0x8(%rsi)
movq %r14, %rdi
callq 0x7df58
addq $0x20, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
callq 0x10ebf
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/genome_node.c
// Function: gt_genome_node_create
GtGenomeNode* gt_genome_node_create(const GtGenomeNodeClass *gnc)
{
  GtGenomeNode *gn;
  gt_assert(gnc && gnc->size);
  gn                     = gt_malloc(gnc->size);
  gn->c_class            = gnc;
  gn->filename           = NULL; /* means the node is generated */
  gn->line_number        = 0;
  gn->reference_count    = 0;
  gn->userdata           = NULL;
  gn->userdata_nof_items = 0;
#ifdef GT_THREADS_ENABLED
  gn->lock              = gt_rwlock_new();
#endif
  return gn;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x41e99
movq %rdi, %rbx
movq (%rdi), %rdi
testq %rdi, %rdi
je 0x41e99
leaq 0xa3b99(%rip), %rsi     # 0xe59f8
movl $0xdb, %edx
callq 0x35ee2
movq %rax, %r14
movq %rbx, (%rax)
movq $0x0, 0x20(%rax)
movl $0x0, 0x28(%rax)
xorps %xmm0, %xmm0
movups %xmm0, 0x8(%rax)
callq 0x3d8a7
movq %rax, 0x18(%r14)
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x10ef8
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/genome_node.c
// Function: gt_genome_node_set_origin
void gt_genome_node_set_origin(GtGenomeNode *gn, GtStr *filename,
                               unsigned int line_number)
{
  gt_assert(gn && filename && line_number);
  gt_str_delete(gn->filename);
  gn->filename = gt_str_ref(filename);
  gn->line_number = line_number;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0x41ed8
movq %rsi, %r15
testq %rsi, %rsi
je 0x41ed8
movl %edx, %ebx
testl %edx, %edx
je 0x41ed8
movq %rdi, %r14
movq 0x8(%rdi), %rdi
callq 0x3d1eb
movq %r15, %rdi
callq 0x3c561
movq %rax, 0x8(%r14)
movl %ebx, 0x20(%r14)
popq %rbx
popq %r14
popq %r15
retq
callq 0x10f31
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/genome_node.c
// Function: gt_genome_node_get_seqid
GtStr* gt_genome_node_get_seqid(GtGenomeNode *gn)
{
  gt_assert(gn && gn->c_class);
  if (gn->c_class->get_seqid)
    return gn->c_class->get_seqid(gn);
  return NULL;
}

// Assembly:
testq %rdi, %rdi
je 0x41f5a
movq (%rdi), %rax
testq %rax, %rax
je 0x41f5a
movq 0x10(%rax), %rax
testq %rax, %rax
je 0x41f57
jmpq *%rax
xorl %eax, %eax
retq
pushq %rax
callq 0x1104e
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/genome_node.c
// Function: gt_genome_node_get_length
GtUword gt_genome_node_get_length(GtGenomeNode *gn)
{
  GtRange range;
  gt_assert(gn && gn->c_class && gn->c_class->get_range);
  range = gt_genome_node_get_range(gn);
  return gt_range_length(&range);
}

// Assembly:
subq $0x18, %rsp
testq %rdi, %rdi
je 0x41fdf
movq (%rdi), %rax
testq %rax, %rax
je 0x41fdf
cmpq $0x0, 0x20(%rax)
je 0x41fdf
callq 0x41f83
leaq 0x8(%rsp), %rdi
movq %rax, (%rdi)
movq %rdx, 0x8(%rdi)
callq 0x7e05b
addq $0x18, %rsp
retq
callq 0x110f9
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/genome_node.c
// Function: gt_genome_node_set_range
void gt_genome_node_set_range(GtGenomeNode *gn, const GtRange *range)
{
  gt_assert(gn && gn->c_class);
  if (gn->c_class->set_range) {
    gt_assert(range->start <= range->end);
    gn->c_class->set_range(gn, range);
  }
}

// Assembly:
pushq %rax
testq %rdi, %rdi
je 0x42009
movq (%rdi), %rax
testq %rax, %rax
je 0x42009
movq 0x28(%rax), %rax
testq %rax, %rax
je 0x42007
movq (%rsi), %rcx
cmpq 0x8(%rsi), %rcx
ja 0x4200e
popq %rcx
jmpq *%rax
popq %rax
retq
callq 0x1116b
callq 0x11132
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/genome_node.c
// Function: gt_genome_nodes_show
void gt_genome_nodes_show(GtArray *nodes, GtFile *outfp)
{
  GtNodeVisitor *gff3_visitor;
  GtUword i;
  gt_assert(nodes);
  gff3_visitor = gt_gff3_visitor_new(outfp);
  for (i = 0; i < gt_array_size(nodes); i++) {
    GT_UNUSED int had_err;
    had_err = gt_genome_node_accept(*(GtGenomeNode**) gt_array_get(nodes, i),
                                    gff3_visitor, NULL);
    gt_assert(!had_err); /* should not happen */
  }
  gt_node_visitor_delete(gff3_visitor);
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0x422a3
movq %rdi, %rbx
movq %rsi, %rdi
callq 0x48588
movq %rax, %r14
movq %rbx, %rdi
callq 0x6ecda
testq %rax, %rax
je 0x42291
xorl %r15d, %r15d
movq %rbx, %rdi
movq %r15, %rsi
callq 0x6e9fa
movq (%rax), %rdi
movq %r14, %rsi
xorl %edx, %edx
callq 0x42036
testl %eax, %eax
jne 0x4229e
incq %r15
movq %rbx, %rdi
callq 0x6ecda
cmpq %rax, %r15
jb 0x42265
movq %r14, %rdi
popq %rbx
popq %r14
popq %r15
jmp 0x49e5e
callq 0x112c1
callq 0x112fa
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/genome_node.c
// Function: gt_genome_nodes_are_equal_region_nodes
bool gt_genome_nodes_are_equal_region_nodes(GtGenomeNode *gn_a,
                                            GtGenomeNode *gn_b)
{
  void *sr_a, *sr_b;

  sr_a = gn_a ? gt_region_node_try_cast(gn_a) : NULL;
  sr_b = gn_b ? gt_region_node_try_cast(gn_b) : NULL;

  if (sr_a && sr_b && !gt_str_cmp(gt_genome_node_get_seqid(gn_a),
                                  gt_genome_node_get_seqid(gn_b))) {
    return true;
  }
  return false;
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
movq %rsi, %rbx
movq %rdi, %r14
testq %rdi, %rdi
je 0x422c8
movq %r14, %rdi
callq 0x4a358
testq %rax, %rax
setne %bpl
jmp 0x422ca
xorl %ebp, %ebp
testq %rbx, %rbx
je 0x422df
movq %rbx, %rdi
callq 0x4a358
testq %rax, %rax
setne %al
jmp 0x422e1
xorl %eax, %eax
andb %al, %bpl
cmpb $0x1, %bpl
jne 0x4230c
movq %r14, %rdi
callq 0x41f3f
movq %rax, %r14
movq %rbx, %rdi
callq 0x41f3f
movq %r14, %rdi
movq %rax, %rsi
callq 0x3c4b0
testl %eax, %eax
je 0x42313
xorl %eax, %eax
popq %rbx
popq %r14
popq %rbp
retq
movb $0x1, %al
jmp 0x4230e
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/genome_node.c
// Function: gt_genome_nodes_are_sorted
bool gt_genome_nodes_are_sorted(const GtArray *nodes)
{
  GtUword i;
  gt_assert(nodes);
  for (i = 1; i < gt_array_size(nodes); i++) {
    if (gt_genome_node_compare(gt_array_get(nodes, i-1),
                               gt_array_get(nodes, i)) > 0) {
      return false;
    }
  }
  return true;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x423b7
movq %rdi, %rbx
callq 0x6ecda
cmpq $0x2, %rax
setb %bpl
jae 0x42346
movl %ebp, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
movq %rbx, %rdi
xorl %esi, %esi
callq 0x6e9fa
movq %rax, %r15
movl $0x1, %r14d
movl $0x1, %esi
movq %rbx, %rdi
callq 0x6e9fa
movq (%r15), %rdi
movq (%rax), %rsi
xorl %edx, %edx
callq 0x41d35
testl %eax, %eax
jg 0x42339
leaq 0x1(%r14), %r15
movq %rbx, %rdi
callq 0x6ecda
cmpq %rax, %r15
setae %bpl
jae 0x42339
movq %rbx, %rdi
movq %r14, %rsi
callq 0x6e9fa
movq %rax, %r14
movq %rbx, %rdi
movq %r15, %rsi
callq 0x6e9fa
movq (%r14), %rdi
movq (%rax), %rsi
xorl %edx, %edx
callq 0x41d35
movq %r15, %r14
jmp 0x42373
callq 0x11333
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/genome_node.c
// Function: gt_genome_node_add_user_data
void gt_genome_node_add_user_data(GtGenomeNode *gn, const char *key, void *data,
                                  GtFree free_func)
{
  GtGenomeNodeUserData *ud, *myud;
  gt_assert(gn && key);
  ud = gt_malloc(sizeof (GtGenomeNodeUserData));
  ud->ptr = data;
  ud->free_func = free_func;
  if (!gn->userdata) {
    gn->userdata = gt_hashmap_new(GT_HASH_STRING, gt_free_func,
                                  userdata_delete);
  }
  gt_assert(gn->userdata != NULL);
  /* remove old data entry first if there is one */
  if ((myud = gt_hashmap_get(gn->userdata, key)) != NULL) {
    gt_hashmap_remove(gn->userdata, key);
  } else {
    gn->userdata_nof_items++;
  }
  gt_hashmap_add(gn->userdata, gt_cstr_dup((char*) key), ud);
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
testq %rdi, %rdi
je 0x42471
movq %rsi, %rbx
testq %rsi, %rsi
je 0x42471
movq %rcx, %r12
movq %rdx, %r13
movq %rdi, %r14
leaq 0xa360e(%rip), %rsi     # 0xe59f8
movl $0x10, %edi
movl $0x1ab, %edx            # imm = 0x1AB
callq 0x35ee2
movq %rax, %r15
movq %r13, (%rax)
movq %r12, 0x8(%rax)
cmpq $0x0, 0x10(%r14)
jne 0x42426
leaq -0xc0b2(%rip), %rsi     # 0x3635f
leaq 0x63(%rip), %rdx        # 0x4247b
movl $0x1, %edi
callq 0x76f28
movq %rax, 0x10(%r14)
movq 0x10(%r14), %rdi
testq %rdi, %rdi
je 0x42476
movq %rbx, %rsi
callq 0x77109
testq %rax, %rax
je 0x4244a
movq 0x10(%r14), %rdi
movq %rbx, %rsi
callq 0x77182
jmp 0x4244e
incl 0x28(%r14)
movq 0x10(%r14), %r14
movq %rbx, %rdi
callq 0x722dc
movq %r14, %rdi
movq %rax, %rsi
movq %r15, %rdx
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
jmp 0x77144
callq 0x1136c
callq 0x113a5
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/genome_node.c
// Function: userdata_delete
static void userdata_delete(void *data)
{
  GtGenomeNodeUserData *ud;
  if (!data) return;
  ud = (GtGenomeNodeUserData*) data;
  if (ud->free_func)
    ud->free_func(ud->ptr);
  ud->free_func = ud->ptr = NULL;
  gt_free(ud);
}

// Assembly:
testq %rdi, %rdi
je 0x424ad
pushq %rbx
movq %rdi, %rbx
movq 0x8(%rdi), %rax
testq %rax, %rax
je 0x42492
movq (%rbx), %rdi
callq *%rax
xorps %xmm0, %xmm0
movups %xmm0, (%rbx)
leaq 0xa3559(%rip), %rsi     # 0xe59f8
movq %rbx, %rdi
movl $0x52, %edx
popq %rbx
jmp 0x362a0
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/genome_node.c
// Function: gt_genome_node_get_user_data
void* gt_genome_node_get_user_data(const GtGenomeNode *gn, const char *key)
{
  GtGenomeNodeUserData *ud;
  gt_assert(gn && key);
  if (!gn->userdata)
    return NULL;
  ud = (GtGenomeNodeUserData*) gt_hashmap_get(gn->userdata, key);
  return (ud ? ud->ptr : NULL);
}

// Assembly:
pushq %rax
testq %rdi, %rdi
je 0x424d5
testq %rsi, %rsi
je 0x424d5
movq 0x10(%rdi), %rdi
testq %rdi, %rdi
je 0x424d1
callq 0x77109
testq %rax, %rax
je 0x424d1
movq (%rax), %rax
jmp 0x424d3
xorl %eax, %eax
popq %rcx
retq
callq 0x113de
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/genome_node.c
// Function: gt_genome_node_release_user_data
void gt_genome_node_release_user_data(GtGenomeNode *gn, const char *key)
{
  GtGenomeNodeUserData *ud;
  gt_assert(gn && key);
  if (!gn->userdata)
    return;
  if ((ud = (GtGenomeNodeUserData*) gt_hashmap_get(gn->userdata, key))) {
    gt_hashmap_remove(gn->userdata, (char*) key);
    if (--gn->userdata_nof_items == 0) {
      gt_hashmap_delete(gn->userdata);
      gn->userdata = NULL;
    }
  }
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x4252e
movq %rsi, %r14
testq %rsi, %rsi
je 0x4252e
movq %rdi, %rbx
movq 0x10(%rdi), %rdi
testq %rdi, %rdi
je 0x42526
movq %r14, %rsi
callq 0x77109
testq %rax, %rax
je 0x42526
movq 0x10(%rbx), %rdi
movq %r14, %rsi
callq 0x77182
decl 0x28(%rbx)
jne 0x42526
movq 0x10(%rbx), %rdi
callq 0x77675
movq $0x0, 0x10(%rbx)
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x11417
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/genome_node.c
// Function: gt_genome_node_delete
void gt_genome_node_delete(GtGenomeNode *gn)
{
  if (!gn) return;
  gt_rwlock_wrlock(gn->lock);
  if (gn->reference_count) {
    gn->reference_count--;
    gt_rwlock_unlock(gn->lock);
    return;
  }
  gt_assert(gn->c_class);
  if (gn->c_class->free)
    gn->c_class->free(gn);
  gt_str_delete(gn->filename);
  if (gn->userdata)
    gt_hashmap_delete(gn->userdata);
  gt_rwlock_unlock(gn->lock);
#ifdef GT_THREADS_ENABLED
  gt_rwlock_delete(gn->lock);
#endif
  gt_free(gn);
}

// Assembly:
pushq %rbx
testq %rdi, %rdi
je 0x42b06
movq %rdi, %rbx
movq 0x18(%rdi), %rdi
callq 0x3d934
movl 0x24(%rbx), %eax
testl %eax, %eax
je 0x42b08
decl %eax
movl %eax, 0x24(%rbx)
movq 0x18(%rbx), %rdi
popq %rbx
jmp 0x3d94f
popq %rbx
retq
movq (%rbx), %rax
testq %rax, %rax
je 0x42b5c
movq 0x8(%rax), %rax
testq %rax, %rax
je 0x42b1e
movq %rbx, %rdi
callq *%rax
movq 0x8(%rbx), %rdi
callq 0x3d1eb
movq 0x10(%rbx), %rdi
testq %rdi, %rdi
je 0x42b35
callq 0x77675
movq 0x18(%rbx), %rdi
callq 0x3d94f
movq 0x18(%rbx), %rdi
callq 0x3d8f7
leaq 0xa2eaa(%rip), %rsi     # 0xe59f8
movq %rbx, %rdi
movl $0x21e, %edx            # imm = 0x21E
popq %rbx
jmp 0x362a0
callq 0x11489
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_in_stream.c
// Function: gt_gff3_in_stream_class
const GtNodeStreamClass* gt_gff3_in_stream_class(void)
{
  static const GtNodeStreamClass *nsc = NULL;
  gt_class_alloc_lock_enter();
  if (!nsc) {
    nsc = gt_node_stream_class_new(sizeof (GtGFF3InStream),
                                   gff3_in_stream_free,
                                   gff3_in_stream_next);
  }
  gt_class_alloc_lock_leave();
  return nsc;
}

// Assembly:
pushq %rax
callq 0x71d9b
cmpq $0x0, 0x10fdfe(%rip)    # 0x152b40
jne 0x42d63
leaq 0x26(%rip), %rsi        # 0x42d71
leaq 0x64(%rip), %rdx        # 0x42db6
movl $0x40, %edi
callq 0x498b0
movq %rax, 0x10fddd(%rip)    # 0x152b40
callq 0x71db1
movq 0x10fdd1(%rip), %rax    # 0x152b40
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_in_stream.c
// Function: gff3_in_stream_free
static void gff3_in_stream_free(GtNodeStream *ns)
{
  GtGFF3InStream *gff3_in_stream = gff3_in_stream_cast(ns);
  gt_node_stream_delete(gff3_in_stream->cds_check_stream);
  gt_node_stream_delete(gff3_in_stream->add_ids_stream);
  gt_node_stream_delete(gff3_in_stream->gff3_in_stream_plain);
  gt_node_stream_delete(gff3_in_stream->fix_region_stream);
  gt_node_stream_delete(gff3_in_stream->multi_sanitize_stream);
}

// Assembly:
pushq %rbx
movq %rdi, %rbx
callq 0x42d34
movq %rax, %rdi
movq %rbx, %rsi
callq 0x49b60
movq %rax, %rbx
movq 0x20(%rax), %rdi
callq 0x4996a
movq 0x18(%rbx), %rdi
callq 0x4996a
movq 0x10(%rbx), %rdi
callq 0x4996a
movq 0x28(%rbx), %rdi
callq 0x4996a
movq 0x38(%rbx), %rdi
popq %rbx
jmp 0x4996a
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_in_stream.c
// Function: gff3_in_stream_next
static int gff3_in_stream_next(GtNodeStream *ns, GtGenomeNode **gn,
                               GtError *err)
{
  GtGFF3InStream *is;
  gt_error_check(err);
  is = gff3_in_stream_cast(ns);
  return gt_node_stream_next(is->last_stream, gn, err);
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %rdx, %rbx
movq %rsi, %r14
movq %rdi, %r15
testq %rdx, %rdx
je 0x42dd5
movq %rbx, %rdi
callq 0x3566a
testb %al, %al
jne 0x42df9
callq 0x42d34
movq %rax, %rdi
movq %r15, %rsi
callq 0x49b60
movq 0x30(%rax), %rdi
movq %r14, %rsi
movq %rbx, %rdx
popq %rbx
popq %r14
popq %r15
jmp 0x499e4
callq 0x114c2
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_in_stream.c
// Function: gt_gff3_in_stream_set_type_checker
void gt_gff3_in_stream_set_type_checker(GtNodeStream *ns,
                                        GtTypeChecker *type_checker)
{
  GtGFF3InStream *is = gff3_in_stream_cast(ns);
  gt_assert(is);
  gt_gff3_in_stream_plain_set_type_checker(is->gff3_in_stream_plain,
                                           type_checker);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
callq 0x42d34
movq %rax, %rdi
movq %r14, %rsi
callq 0x49b60
testq %rax, %rax
je 0x42e58
movq 0x10(%rax), %rdi
movq %rbx, %rsi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x43577
callq 0x11567
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_in_stream.c
// Function: gt_gff3_in_stream_set_xrf_checker
void gt_gff3_in_stream_set_xrf_checker(GtNodeStream *ns,
                                       GtXRFChecker *xrf_checker)
{
  GtGFF3InStream *is = gff3_in_stream_cast(ns);
  gt_assert(is);
  gt_gff3_in_stream_plain_set_xrf_checker(is->gff3_in_stream_plain,
                                          xrf_checker);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
callq 0x42d34
movq %rax, %rdi
movq %r14, %rsi
callq 0x49b60
testq %rax, %rax
je 0x42e8f
movq 0x10(%rax), %rdi
movq %rbx, %rsi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x435ae
callq 0x1159e
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_in_stream.c
// Function: gt_gff3_in_stream_set_offsetfile
int gt_gff3_in_stream_set_offsetfile(GtNodeStream *ns, GtStr *offsetfile,
                                     GtError *err)
{
  GtGFF3InStream *is = gff3_in_stream_cast(ns);
  gt_assert(is);
  return gt_gff3_in_stream_plain_set_offsetfile(is->gff3_in_stream_plain,
                                                offsetfile, err);
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %rdx, %rbx
movq %rsi, %r14
movq %rdi, %r15
callq 0x42d34
movq %rax, %rdi
movq %r15, %rsi
callq 0x49b60
testq %rax, %rax
je 0x42f2a
movq 0x10(%rax), %rdi
movq %r14, %rsi
movq %rbx, %rdx
popq %rbx
popq %r14
popq %r15
jmp 0x43644
callq 0x11643
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_in_stream.c
// Function: gt_gff3_in_stream_enable_tidy_mode
void gt_gff3_in_stream_enable_tidy_mode(GtGFF3InStream *is)
{
  gt_assert(is);
  gt_gff3_in_stream_plain_enable_tidy_mode(is->gff3_in_stream_plain);
  gt_cds_check_stream_enable_tidy_mode((GtCDSCheckStream*)
                                       is->cds_check_stream);
}

// Assembly:
pushq %rbx
testq %rdi, %rdi
je 0x42f8c
movq %rdi, %rbx
movq 0x10(%rdi), %rdi
callq 0x436a8
movq 0x20(%rbx), %rdi
popq %rbx
jmp 0x84370
callq 0x116ec
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_in_stream.c
// Function: gt_gff3_in_stream_fix_region_boundaries
void gt_gff3_in_stream_fix_region_boundaries(GtGFF3InStream *is)
{
  gt_assert(is);
  gt_gff3_in_stream_plain_do_not_check_region_boundaries(
                               (GtGFF3InStreamPlain*) is->gff3_in_stream_plain);
  is->last_stream = is->fix_region_stream =
             gt_tidy_region_node_stream_new(is->last_stream);
}

// Assembly:
pushq %rbx
testq %rdi, %rdi
je 0x42fb6
movq %rdi, %rbx
movq 0x10(%rdi), %rdi
callq 0x43553
movq 0x30(%rbx), %rdi
callq 0x4bc4e
movq %rax, 0x28(%rbx)
movq %rax, 0x30(%rbx)
popq %rbx
retq
callq 0x11725
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_in_stream.c
// Function: gt_gff3_in_stream_new_unsorted
GtNodeStream* gt_gff3_in_stream_new_unsorted(int num_of_files,
                                             const char **filenames)
{
  GtNodeStream *ns = gt_node_stream_create(gt_gff3_in_stream_class(), false);
  GtGFF3InStream *is = gff3_in_stream_cast(ns);
  is->fix_region_stream = NULL;
  is->last_stream = is->gff3_in_stream_plain =
                  gt_gff3_in_stream_plain_new_unsorted(num_of_files, filenames);
  gt_gff3_in_stream_plain_check_region_boundaries(
                               (GtGFF3InStreamPlain*) is->gff3_in_stream_plain);
  is->last_stream = is->add_ids_stream = gt_add_ids_stream_new(is->last_stream);
  is->last_stream = is->multi_sanitize_stream =
       gt_visitor_stream_new(is->last_stream, gt_multi_sanitizer_visitor_new());
  is->last_stream = is->cds_check_stream =
                                       gt_cds_check_stream_new(is->last_stream);
  return ns;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %r15
movl %edi, %ebp
callq 0x42d34
movq %rax, %rdi
xorl %esi, %esi
callq 0x498e8
movq %rax, %rbx
callq 0x42d34
movq %rax, %rdi
movq %rbx, %rsi
callq 0x49b60
movq %rax, %r14
movq $0x0, 0x28(%rax)
movl %ebp, %edi
movq %r15, %rsi
callq 0x436d0
movq %rax, 0x10(%r14)
movq %rax, 0x30(%r14)
movq %rax, %rdi
callq 0x4353f
movq 0x30(%r14), %rdi
callq 0x83a80
movq %rax, %r15
movq %rax, 0x18(%r14)
movq %rax, 0x30(%r14)
callq 0x497f5
movq %r15, %rdi
movq %rax, %rsi
callq 0x4c337
movq %rax, 0x38(%r14)
movq %rax, 0x30(%r14)
movq %rax, %rdi
callq 0x84325
movq %rax, 0x20(%r14)
movq %rax, 0x30(%r14)
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_in_stream.c
// Function: gt_gff3_in_stream_new_sorted
GtNodeStream* gt_gff3_in_stream_new_sorted(const char *filename)
{
  GtNodeStream *ns = gt_node_stream_create(gt_gff3_in_stream_class(), true);
  GtGFF3InStream *is = gff3_in_stream_cast(ns);
  is->fix_region_stream = NULL;
  is->last_stream = is->gff3_in_stream_plain =
                                   gt_gff3_in_stream_plain_new_sorted(filename);
  gt_gff3_in_stream_plain_check_region_boundaries(
                               (GtGFF3InStreamPlain*) is->gff3_in_stream_plain);
  is->last_stream = is->add_ids_stream = gt_add_ids_stream_new(is->last_stream);
  is->last_stream = is->multi_sanitize_stream =
       gt_visitor_stream_new(is->last_stream, gt_multi_sanitizer_visitor_new());
  is->last_stream = is->cds_check_stream =
                                       gt_cds_check_stream_new(is->last_stream);
  return ns;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %rdi, %r15
callq 0x42d34
movq %rax, %rdi
movl $0x1, %esi
callq 0x498e8
movq %rax, %rbx
callq 0x42d34
movq %rax, %rdi
movq %rbx, %rsi
callq 0x49b60
movq %rax, %r14
movq $0x0, 0x28(%rax)
movq %r15, %rdi
callq 0x43786
movq %rax, 0x10(%r14)
movq %rax, 0x30(%r14)
movq %rax, %rdi
callq 0x4353f
movq 0x30(%r14), %rdi
callq 0x83a80
movq %rax, %r15
movq %rax, 0x18(%r14)
movq %rax, 0x30(%r14)
callq 0x497f5
movq %r15, %rdi
movq %rax, %rsi
callq 0x4c337
movq %rax, 0x38(%r14)
movq %rax, 0x30(%r14)
movq %rax, %rdi
callq 0x84325
movq %rax, 0x20(%r14)
movq %rax, 0x30(%r14)
movq %rbx, %rax
popq %rbx
popq %r14
popq %r15
retq
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_in_stream_plain.c
// Function: gt_gff3_in_stream_plain_class
const GtNodeStreamClass* gt_gff3_in_stream_plain_class(void)
{
  static const GtNodeStreamClass *nsc = NULL;
  gt_class_alloc_lock_enter();
  if (!nsc) {
    nsc = gt_node_stream_class_new(sizeof (GtGFF3InStreamPlain),
                                   gff3_in_stream_plain_free,
                                   gff3_in_stream_plain_next);
  }
  gt_class_alloc_lock_leave();
  return nsc;
}

// Assembly:
pushq %rax
callq 0x71d9b
cmpq $0x0, 0x10fa4a(%rip)    # 0x152b48
jne 0x4311f
leaq 0x26(%rip), %rsi        # 0x4312d
leaq 0x8e(%rip), %rdx        # 0x4319c
movl $0x58, %edi
callq 0x498b0
movq %rax, 0x10fa29(%rip)    # 0x152b48
callq 0x71db1
movq 0x10fa1d(%rip), %rax    # 0x152b48
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_in_stream_plain.c
// Function: gff3_in_stream_plain_free
static void gff3_in_stream_plain_free(GtNodeStream *ns)
{
  GtGFF3InStreamPlain *gff3_in_stream_plain = gff3_in_stream_plain_cast(ns);
  gt_str_array_delete(gff3_in_stream_plain->files);
  gt_str_delete(gff3_in_stream_plain->stdinstr);
  while (gt_queue_size(gff3_in_stream_plain->genome_node_buffer)) {
    gt_genome_node_delete(gt_queue_get(gff3_in_stream_plain
                                       ->genome_node_buffer));
  }
  gt_queue_delete(gff3_in_stream_plain->genome_node_buffer);
  gt_gff3_parser_delete(gff3_in_stream_plain->gff3_parser);
  gt_cstr_table_delete(gff3_in_stream_plain->used_types);
  gt_file_delete(gff3_in_stream_plain->fpin);
}

// Assembly:
pushq %rbx
movq %rdi, %rbx
callq 0x430f0
movq %rax, %rdi
movq %rbx, %rsi
callq 0x49b60
movq %rax, %rbx
movq 0x18(%rax), %rdi
callq 0x3d573
movq 0x20(%rbx), %rdi
callq 0x3d1eb
movq 0x40(%rbx), %rdi
callq 0x7c194
testq %rax, %rax
je 0x43177
movq 0x40(%rbx), %rdi
callq 0x7c132
movq %rax, %rdi
callq 0x42ade
jmp 0x43156
movq 0x40(%rbx), %rdi
callq 0x7c623
movq 0x48(%rbx), %rdi
callq 0x46cc0
movq 0x50(%rbx), %rdi
callq 0x72c9c
movq 0x30(%rbx), %rdi
popq %rbx
jmp 0x75b7c
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_in_stream_plain.c
// Function: gt_gff3_in_stream_plain_new_unsorted
GtNodeStream* gt_gff3_in_stream_plain_new_unsorted(int num_of_files,
                                                   const char **filenames)
{
  int i;
  GtStrArray *files = gt_str_array_new();
  for (i = 0; i < num_of_files; i++)
    gt_str_array_add_cstr(files, filenames[i]);
  return gff3_in_stream_plain_new(files, false);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movq %rsi, %rbx
movl %edi, %ebp
callq 0x3d23c
movq %rax, %r14
testl %ebp, %ebp
jle 0x43703
movl %ebp, %r15d
xorl %r12d, %r12d
movq (%rbx,%r12,8), %rsi
movq %r14, %rdi
callq 0x3d318
incq %r12
cmpq %r12, %r15
jne 0x436ef
movq %r14, %rdi
xorl %esi, %esi
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
jmp 0x43712
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_in_stream_plain.c
// Function: gff3_in_stream_plain_new
static GtNodeStream* gff3_in_stream_plain_new(GtStrArray *files,
                                              bool ensure_sorting)
{
  GtNodeStream *ns = gt_node_stream_create(gt_gff3_in_stream_plain_class(),
                                           ensure_sorting);
  GtGFF3InStreamPlain *gff3_in_stream_plain = gff3_in_stream_plain_cast(ns);
  gff3_in_stream_plain->files               = files;
  gff3_in_stream_plain->stdinstr            = gt_str_new_cstr("stdin");
  gff3_in_stream_plain->ensure_sorting      = ensure_sorting;
  gff3_in_stream_plain->genome_node_buffer  = gt_queue_new();
  gff3_in_stream_plain->gff3_parser         = gt_gff3_parser_new(NULL);
  gff3_in_stream_plain->used_types          = gt_cstr_table_new();
  return ns;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movl %esi, %ebp
movq %rdi, %r14
callq 0x430f0
movq %rax, %rdi
movl %ebp, %esi
callq 0x498e8
movq %rax, %rbx
callq 0x430f0
movq %rax, %rdi
movq %rbx, %rsi
callq 0x49b60
movq %rax, %r15
movq %r14, 0x18(%rax)
leaq 0xaa4e6(%rip), %rdi     # 0xedc34
callq 0x3c03d
movq %rax, 0x20(%r15)
movb %bpl, 0x28(%r15)
callq 0x7c028
movq %rax, 0x40(%r15)
xorl %edi, %edi
callq 0x4386c
movq %rax, 0x48(%r15)
callq 0x72918
movq %rax, 0x50(%r15)
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_in_stream_plain.c
// Function: gt_gff3_in_stream_plain_new_sorted
GtNodeStream* gt_gff3_in_stream_plain_new_sorted(const char *filename)
{
  GtStrArray *files = gt_str_array_new();
  if (filename)
    gt_str_array_add_cstr(files, filename);
  return gff3_in_stream_plain_new(files, true);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %r14
callq 0x3d23c
movq %rax, %rbx
testq %r14, %r14
je 0x437a5
movq %rbx, %rdi
movq %r14, %rsi
callq 0x3d318
movq %rbx, %rdi
movl $0x1, %esi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x43712
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_in_stream_plain.c
// Function: buffer_is_sorted
static int buffer_is_sorted(void **elem, void *info, GtError *err)
{
  GtGenomeNode *current_node, **last_node;

  gt_error_check(err);
  gt_assert(elem && info);

  current_node = *(GtGenomeNode**) elem,
  last_node = info;

  if (*last_node && gt_genome_node_compare(last_node, &current_node) > 0) {
    gt_assert(*last_node);
    gt_error_set(err, "the file %s is not sorted (example: line %u and %u)",
              gt_genome_node_get_filename(*last_node),
              gt_genome_node_get_line_number(*last_node),
              gt_genome_node_get_line_number(current_node));
    return -1;
  }
  else
    *last_node = current_node;
  return 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movq %rdx, %rbx
movq %rsi, %r14
movq %rdi, %r15
testq %rdx, %rdx
je 0x437de
movq %rbx, %rdi
callq 0x3566a
testb %al, %al
jne 0x43860
testq %r15, %r15
je 0x4385b
testq %r14, %r14
je 0x4385b
movq (%r15), %rax
movq %rax, (%rsp)
cmpq $0x0, (%r14)
je 0x43847
movq %rsp, %rsi
movq %r14, %rdi
callq 0x4208a
testl %eax, %eax
jle 0x43847
movq (%r14), %rdi
testq %rdi, %rdi
je 0x43865
callq 0x41f10
movq %rax, %r15
movq (%r14), %rdi
callq 0x41f30
movl %eax, %ebp
movq (%rsp), %rdi
callq 0x41f30
leaq 0xa2c66(%rip), %rsi     # 0xe6494
movq %rbx, %rdi
movq %r15, %rdx
movl %ebp, %ecx
movl %eax, %r8d
xorl %eax, %eax
callq 0x3559f
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
jmp 0x43850
movq (%rsp), %rax
movq %rax, (%r14)
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
callq 0x11b5a
callq 0x11b23
callq 0x11b91
nop
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_parser.c
// Function: gt_gff3_parser_new
GtGFF3Parser* gt_gff3_parser_new(GtTypeChecker *type_checker)
{
  GtGFF3Parser *parser;
  parser = gt_calloc(1, sizeof *parser);
  parser->feature_info = gt_feature_info_new();
  parser->seqid_to_ssr_mapping = gt_hashmap_new(GT_HASH_STRING, NULL,
                                        (GtFree) simple_sequence_region_delete);
  parser->source_to_str_mapping = gt_hashmap_new(GT_HASH_STRING, NULL,
                                                 (GtFree) gt_str_delete);
  parser->offset = GT_UNDEF_WORD;
  parser->orphanage = gt_orphanage_new();
  parser->type_checker = type_checker ? gt_type_checker_ref(type_checker)
                                      : NULL;
  parser->xrf_checker = NULL;
  return parser;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %rdi, %r14
leaq 0xa2c65(%rip), %rdx     # 0xe64e0
movl $0x1, %edi
movl $0x58, %esi
movl $0x66, %ecx
callq 0x3601f
movq %rax, %rbx
callq 0x85038
movq %rax, (%rbx)
leaq 0x66(%rip), %rdx        # 0x43907
xorl %r15d, %r15d
movl $0x1, %edi
xorl %esi, %esi
callq 0x76f28
movq %rax, 0x8(%rbx)
leaq -0x66d0(%rip), %rdx     # 0x3d1eb
movl $0x1, %edi
xorl %esi, %esi
callq 0x76f28
movq %rax, 0x10(%rbx)
movabsq $-0x8000000000000000, %rax # imm = 0x8000000000000000
movq %rax, 0x28(%rbx)
callq 0x49e9c
movq %rax, 0x38(%rbx)
testq %r14, %r14
je 0x438f2
movq %r14, %rdi
callq 0x4c135
movq %rax, %r15
movq %r15, 0x40(%rbx)
movq $0x0, 0x48(%rbx)
movq %rbx, %rax
popq %rbx
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_parser.c
// Function: gt_gff3_parser_set_offsetfile
int gt_gff3_parser_set_offsetfile(GtGFF3Parser *parser, GtStr *offsetfile,
                                  GtError *err)
{
  gt_error_check(err);
  gt_assert(parser);
  gt_assert(parser->offset == GT_UNDEF_WORD);
  parser->offset_mapping = gt_mapping_new(offsetfile, "offsets",
                                          GT_MAPPINGTYPE_INTEGER, err);
  if (parser->offset_mapping)
    return 0;
  return -1;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rdx, %r14
movq %rsi, %r15
movq %rdi, %rbx
testq %rdx, %rdx
je 0x43a09
movq %r14, %rdi
callq 0x3566a
testb %al, %al
jne 0x43a52
testq %rbx, %rbx
je 0x43a48
xorl %r12d, %r12d
cmpq 0x28(%rbx), %r12
jno 0x43a4d
leaq 0xa2c31(%rip), %rsi     # 0xe664f
movq %r15, %rdi
movl $0x1, %edx
movq %r14, %rcx
callq 0x48e48
movq %rax, 0x30(%rbx)
cmpq $0x1, %rax
sbbl %r12d, %r12d
movl %r12d, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
callq 0x11dc5
callq 0x11d8c
callq 0x11d53
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_parser.c
// Function: gt_gff3_parser_build_target_str
void gt_gff3_parser_build_target_str(GtStr *target, GtStrArray *target_ids,
                                     GtArray *target_ranges,
                                     GtArray *target_strands)
{
  GtUword i;
  gt_assert(target && target_ids && target_ranges && target_strands);
  for (i = 0; i < gt_str_array_size(target_ids); i++) {
    GtRange *range;
    GtStrand *strand;
    range = gt_array_get(target_ranges, i);
    strand = gt_array_get(target_strands, i);
    if (i)
      gt_str_append_char(target, ',');
    gt_str_append_cstr(target, gt_str_array_get(target_ids, i));
    gt_str_append_char(target, ' ');
    gt_str_append_uword(target, range->start);
    gt_str_append_char(target, ' ');
    gt_str_append_uword(target, range->end);
    if (*strand != GT_NUM_OF_STRAND_TYPES) {
      gt_str_append_char(target, ' ');
      gt_str_append_char(target, GT_STRAND_CHARS[*strand]);
    }
  }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, %xmm0
movq %rdi, %xmm1
punpcklqdq %xmm0, %xmm1    # xmm1 = xmm1[0],xmm0[0]
movq %rcx, (%rsp)
movq %rcx, %xmm0
movq %rdx, %xmm2
punpcklqdq %xmm0, %xmm2    # xmm2 = xmm2[0],xmm0[0]
pxor %xmm0, %xmm0
pcmpeqd %xmm0, %xmm2
pcmpeqd %xmm0, %xmm1
movdqa %xmm1, %xmm0
shufps $0xdd, %xmm2, %xmm0     # xmm0 = xmm0[1,3],xmm2[1,3]
shufps $0x88, %xmm2, %xmm1     # xmm1 = xmm1[0,2],xmm2[0,2]
andps %xmm0, %xmm1
movmskps %xmm1, %eax
testl %eax, %eax
jne 0x4405e
movq %rdx, %r14
movq %rsi, %r15
movq %rdi, %r12
movq %rsi, %rdi
callq 0x3d560
testq %rax, %rax
je 0x4404f
xorl %r13d, %r13d
movq %r14, %rdi
movq %r13, %rsi
callq 0x6e9fa
movq %rax, %rbx
movq (%rsp), %rdi
movq %r13, %rsi
callq 0x6e9fa
movq %rax, %rbp
testq %r13, %r13
je 0x43fcb
movq %r12, %rdi
movl $0x2c, %esi
callq 0x3c28d
movq %r15, %rdi
movq %r13, %rsi
callq 0x3d3e2
movq %r12, %rdi
movq %rax, %rsi
callq 0x3c067
movq %r12, %rdi
movl $0x20, %esi
callq 0x3c28d
movq (%rbx), %rsi
movq %r12, %rdi
callq 0x3c1dc
movq %r12, %rdi
movl $0x20, %esi
callq 0x3c28d
movq 0x8(%rbx), %rsi
movq %r12, %rdi
callq 0x3c1dc
cmpl $0x4, (%rbp)
je 0x4403b
movq %r12, %rdi
movl $0x20, %esi
callq 0x3c28d
movl (%rbp), %eax
leaq 0x9eb15(%rip), %rcx     # 0xe2b44
movsbl (%rax,%rcx), %esi
movq %r12, %rdi
callq 0x3c28d
incq %r13
movq %r15, %rdi
callq 0x3d560
cmpq %rax, %r13
jb 0x43f9c
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x11f54
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_parser.c
// Function: chomp_seqid
void chomp_seqid(char *seqid, const char *filename, unsigned int line_number)
{
  GtUword len;
  if (!seqid) return;
  len = strlen(seqid);
  if (len > 0) {
    if (seqid[len-1] == ' ') {
      gt_warning("seqid \"%s\" on line %u in file \"%s\" ends with a blank, "
                 "removing it", seqid, line_number, filename);
      (void) gt_cstr_rtrim(seqid, ' ');
    }
  }
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0x440ac
movl %edx, %ebp
movq %rsi, %r14
movq %rdi, %rbx
callq 0xb260
testq %rax, %rax
je 0x440ac
cmpb $0x20, -0x1(%rbx,%rax)
jne 0x440ac
leaq 0xa2697(%rip), %rdi     # 0xe6723
movq %rbx, %rsi
movl %ebp, %edx
movq %r14, %rcx
xorl %eax, %eax
callq 0x3da84
movq %rbx, %rdi
movl $0x20, %esi
popq %rbx
popq %r14
popq %rbp
jmp 0x72402
popq %rbx
popq %r14
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_parser.c
// Function: gt_gff3_parser_reset
void gt_gff3_parser_reset(GtGFF3Parser *parser)
{
  gt_assert(parser);
  parser->fasta_parsing = false;
  parser->eof_emitted = false;
  gt_feature_info_reset(parser->feature_info);
  gt_hashmap_reset(parser->seqid_to_ssr_mapping);
  gt_hashmap_reset(parser->source_to_str_mapping);
  gt_orphanage_reset(parser->orphanage);
  parser->last_terminator = 0;
}

// Assembly:
pushq %rbx
testq %rdi, %rdi
je 0x46cbb
movq %rdi, %rbx
movw $0x0, 0x1d(%rdi)
movq (%rdi), %rdi
callq 0x850c4
movq 0x8(%rbx), %rdi
callq 0x77249
movq 0x10(%rbx), %rdi
callq 0x77249
movq 0x38(%rbx), %rdi
callq 0x49f2d
movl $0x0, 0x50(%rbx)
popq %rbx
retq
callq 0x12959
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_parser.c
// Function: gt_gff3_parser_delete
void gt_gff3_parser_delete(GtGFF3Parser *parser)
{
  if (!parser) return;
  gt_feature_info_delete(parser->feature_info);
  gt_hashmap_delete(parser->seqid_to_ssr_mapping);
  gt_hashmap_delete(parser->source_to_str_mapping);
  gt_mapping_delete(parser->offset_mapping);
  gt_orphanage_delete(parser->orphanage);
  gt_type_checker_delete(parser->type_checker);
  gt_xrf_checker_delete(parser->xrf_checker);
  gt_free(parser);
}

// Assembly:
testq %rdi, %rdi
je 0x46d1c
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x85094
movq 0x8(%rbx), %rdi
callq 0x77675
movq 0x10(%rbx), %rdi
callq 0x77675
movq 0x30(%rbx), %rdi
callq 0x4905a
movq 0x38(%rbx), %rdi
callq 0x49ed5
movq 0x40(%rbx), %rdi
callq 0x4c1e7
movq 0x48(%rbx), %rdi
callq 0x4c719
leaq 0x9f7d2(%rip), %rsi     # 0xe64e0
movq %rbx, %rdi
movl $0x8ca, %edx            # imm = 0x8CA
popq %rbx
jmp 0x362a0
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_parser.c
// Function: verify_seqid
static int verify_seqid(const GtStr *seqid, const char *filename,
                        unsigned int line_number, GtError *err)
{
  int had_err = 0;
  gt_error_check(err);
  gt_assert(seqid);
  if (gt_md5_seqid_has_prefix(gt_str_get(seqid))) {
    if (gt_str_length(seqid) < GT_MD5_SEQID_PREFIX_LEN +
                               GT_MD5_SEQID_HASH_LEN) {
      gt_error_set(err, "MD5 sequence ID '%s' on line %u in file \"%s\" is too "
                   "short", gt_str_get(seqid), line_number, filename);
      had_err = -1;
    }
    if (!had_err && gt_str_length(seqid) >= GT_MD5_SEQID_TOTAL_LEN) {
      const char *sid = gt_str_get(seqid);
      if (sid[GT_MD5_SEQID_TOTAL_LEN-1] != GT_MD5_SEQID_SEPARATOR) {
        gt_error_set(err, "MD5 sequence ID '%s' on line %u in file \"%s\" has "
                     "wrong separator '%c' (must be '%c')",
                     gt_str_get(seqid), line_number, filename,
                     sid[GT_MD5_SEQID_TOTAL_LEN-1], GT_MD5_SEQID_SEPARATOR);
        had_err = -1;
      }
    }
    if (!had_err && gt_str_length(seqid) == GT_MD5_SEQID_TOTAL_LEN) {
      gt_error_set(err, "MD5 sequence ID '%s' on line %u in file \"%s\" has "
                   "missing sequence ID after separator '%c'",
                   gt_str_get(seqid), line_number, filename,
                   GT_MD5_SEQID_SEPARATOR);
      had_err = -1;
    }
  }
  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rcx, %r14
movl %edx, %ebp
movq %rsi, %rbx
movq %rdi, %r15
testq %rcx, %rcx
je 0x46d48
movq %r14, %rdi
callq 0x3566a
testb %al, %al
jne 0x46e36
testq %r15, %r15
je 0x46e31
movq %r15, %rdi
callq 0x3c40b
movq %rax, %rdi
callq 0x7a678
xorl %r12d, %r12d
testb %al, %al
je 0x46e1f
movq %r15, %rdi
callq 0x3c434
cmpq $0x23, %rax
jbe 0x46dc6
movq %r15, %rdi
callq 0x3c434
cmpq $0x25, %rax
jb 0x46d96
movq %r15, %rdi
callq 0x3c40b
cmpb $0x3a, 0x24(%rax)
jne 0x46de9
movq %r15, %rdi
callq 0x3c434
cmpq $0x25, %rax
jne 0x46e1f
movq %r15, %rdi
callq 0x3c40b
leaq 0x9fbab(%rip), %rsi     # 0xe695e
movq %r14, %rdi
movq %rax, %rdx
movl %ebp, %ecx
movq %rbx, %r8
movl $0x3a, %r9d
jmp 0x46e12
movq %r15, %rdi
callq 0x3c40b
leaq 0x9fafa(%rip), %rsi     # 0xe68cf
movq %r14, %rdi
movq %rax, %rdx
movl %ebp, %ecx
movq %rbx, %r8
xorl %eax, %eax
callq 0x3559f
jmp 0x46e19
movq %rax, %r13
movq %r15, %rdi
callq 0x3c40b
movsbl 0x24(%r13), %r9d
movl $0x3a, (%rsp)
leaq 0x9fb02(%rip), %rsi     # 0xe6909
movq %r14, %rdi
movq %rax, %rdx
movl %ebp, %ecx
movq %rbx, %r8
xorl %eax, %eax
callq 0x3559f
movl $0xffffffff, %r12d      # imm = 0xFFFFFFFF
movl %r12d, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x129cb
callq 0x12992
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_parser.c
// Function: add_offset_if_necessary
static int add_offset_if_necessary(GtRange *range, GtGFF3Parser *parser,
                                   const char *seqid, const char *filename,
                                   GtUword line_number, GtError *err)
{
  int had_err = 0;
  gt_error_check(err);
  if (parser->offset != GT_UNDEF_WORD) {
    had_err = offset_possible(range, parser->offset, filename, line_number,
                              err);
    if (!had_err)
      *range = gt_range_offset(range, parser->offset);
  }
  else if (parser->offset_mapping) {
    GtWord offset;
    had_err = gt_mapping_map_integer(parser->offset_mapping, &offset, seqid,
                                     err);
    if (!had_err)
      had_err = offset_possible(range, offset, filename, line_number, err);
    if (!had_err)
      *range = gt_range_offset(range, offset);
  }
  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r9, %r14
movq %r8, %r15
movq %rcx, %r12
movq %rdx, %rbp
movq %rsi, %r13
movq %rdi, %rbx
testq %r9, %r9
je 0x46e6d
movq %r14, %rdi
callq 0x3566a
testb %al, %al
jne 0x46f06
movq 0x28(%r13), %rsi
movq %rsi, %rax
negq %rax
jno 0x46ec6
movq 0x30(%r13), %rdi
testq %rdi, %rdi
je 0x46ef3
movq %rsp, %rsi
movq %rbp, %rdx
movq %r14, %rcx
callq 0x494ef
movl %eax, %ebp
testl %eax, %eax
jne 0x46ead
movq (%rsp), %rsi
movq %rbx, %rdi
movq %r12, %rdx
movl %r15d, %ecx
movq %r14, %r8
callq 0x472c3
movl %eax, %ebp
testl %ebp, %ebp
jne 0x46ef5
movq (%rsp), %rsi
movq %rbx, %rdi
callq 0x7e198
movq %rax, (%rbx)
movq %rdx, 0x8(%rbx)
jmp 0x46ef5
movq %rbx, %rdi
movq %r12, %rdx
movl %r15d, %ecx
movq %r14, %r8
callq 0x472c3
movl $0xffffffff, %ebp       # imm = 0xFFFFFFFF
testl %eax, %eax
jne 0x46ef5
movq 0x28(%r13), %rsi
movq %rbx, %rdi
callq 0x7e198
movq %rax, (%rbx)
movq %rdx, 0x8(%rbx)
xorl %ebp, %ebp
movl %ebp, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x12a04
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_parser.c
// Function: invalid_gff3_pragma
static bool invalid_gff3_pragma(const char *line)
{
  return (strncmp(line, GT_GFF_SPECIES, strlen(GT_GFF_SPECIES))
            && strncmp(line, GT_GFF_FEATURE_ONTOLOGY,
                       strlen(GT_GFF_FEATURE_ONTOLOGY))
            && strncmp(line, GT_GFF_ATTRIBUTE_ONTOLOGY,
                       strlen(GT_GFF_ATTRIBUTE_ONTOLOGY))
            && strncmp(line, GT_GFF_SOURCE_ONTOLOGY,
                       strlen(GT_GFF_SOURCE_ONTOLOGY))
            && strncmp(line, GT_GFF_GENOME_BUILD,
                       strlen(GT_GFF_GENOME_BUILD)));
}

// Assembly:
pushq %rbx
movq %rdi, %rbx
leaq 0xa00a5(%rip), %rsi     # 0xe6fbb
movl $0x9, %edx
callq 0xb2a0
testl %eax, %eax
je 0x46f87
leaq 0xa009a(%rip), %rsi     # 0xe6fc5
movl $0x12, %edx
movq %rbx, %rdi
callq 0xb2a0
testl %eax, %eax
je 0x46f87
leaq 0xa0095(%rip), %rsi     # 0xe6fd8
movl $0x14, %edx
movq %rbx, %rdi
callq 0xb2a0
testl %eax, %eax
je 0x46f87
leaq 0xa0092(%rip), %rsi     # 0xe6fed
movl $0x11, %edx
movq %rbx, %rdi
callq 0xb2a0
testl %eax, %eax
je 0x46f87
leaq 0xa008c(%rip), %rsi     # 0xe6fff
movl $0xe, %edx
movq %rbx, %rdi
callq 0xb2a0
testl %eax, %eax
setne %al
jmp 0x46f89
xorl %eax, %eax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/extended/gff3_parser.c
// Function: offset_possible
static int offset_possible(const GtRange *range, GtWord offset,
                           const char *filename, unsigned int line_number,
                           GtError *err)
{
  int had_err = 0;
  gt_error_check(err);
  if (offset < 0) {
    /* check for underflow */
    GtUword result = range->start + offset;
    if (result == 0) {
      gt_error_set(err, "==0");
      gt_error_set(err, "adding offset "GT_WD" to node on line %u in file "
                   "\"%s\" leads to start 0 (GFF3 files are 1-based)",
                   offset, line_number, filename);
      had_err = -1;
    }
    else if (result > range->start) {
      gt_error_set(err, "adding offset "GT_WD" to node on line %u in file "
                   "\"%s\" leads to underflow",
                   offset, line_number, filename);
      had_err = -1;
    }
  }
  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movq %r8, %r14
movl %ecx, %ebp
movq %rdx, %rbx
movq %rsi, %r15
movq %rdi, %r12
testq %r8, %r8
je 0x472ea
movq %r14, %rdi
callq 0x3566a
testb %al, %al
jne 0x47343
xorl %eax, %eax
testq %r15, %r15
jns 0x4733a
movq (%r12), %rcx
movq %rcx, %rdx
addq %r15, %rdx
je 0x4730b
cmpq %rcx, %rdx
jbe 0x4733a
leaq 0x9fc6d(%rip), %rsi     # 0xe6f76
jmp 0x47323
leaq 0xaa588(%rip), %rsi     # 0xf189a
movq %r14, %rdi
xorl %eax, %eax
callq 0x3559f
leaq 0x9fbf7(%rip), %rsi     # 0xe6f1a
movq %r14, %rdi
movq %r15, %rdx
movl %ebp, %ecx
movq %rbx, %r8
xorl %eax, %eax
callq 0x3559f
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
callq 0x12a3d