LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/bed_parser.c
// Function: parse_bed_range
static int parse_bed_range(GtRange *range, GtStr *start, GtStr *end,
                           GtWord offset, GtIO *bed_file, bool thick,
                           GtError *err)
{
  int had_err;
  gt_error_check(err);
  had_err = gt_parse_range(range, gt_str_get(start), gt_str_get(end),
                           gt_io_get_line_number(bed_file),
                           gt_io_get_filename(bed_file), err);
  /* BED has a weird numbering scheme: positions are 0-based, but the end
     position is not part of the feature. Transform to 1-based coordinates. */
  range->start++;
  /* Ranges defining a 'thick' region sometimes come with length 0 to
     designate that there are no thick regions. So do not fail here and
     handle that case later. */
  if (!thick) {
    if (!had_err && range->start > range->end) {
      gt_error_set(err, "file \"%s\": line "GT_WU": BED feature has length 0",
                   gt_io_get_filename(bed_file),
                   gt_io_get_line_number(bed_file));
      had_err = -1;
    }
  }
  if (offset)
    *range = gt_range_offset(range, offset);
  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movl %r9d, 0xc(%rsp)
movq %r8, %r12
movq %rcx, 0x10(%rsp)
movq %rdx, %r13
movq %rsi, %r15
movq %rdi, %rbx
movq 0x50(%rsp), %rbp
testq %rbp, %rbp
je 0x12796d
movq %rbp, %rdi
callq 0xfcc32
testb %al, %al
jne 0x127a29
movq %r15, %rdi
callq 0x11b0a1
movq %rax, %r15
movq %r13, %rdi
callq 0x11b0a1
movq %rax, %r13
movq %r12, %rdi
callq 0x103bde
movq %rax, %r14
movq %r12, %rdi
callq 0x103bee
movq %rbx, %rdi
movq %r15, %rsi
movq %r13, %rdx
movl %r14d, %ecx
movq %rax, %r8
movq %rbp, %r9
callq 0x10b328
movl %eax, %r13d
movq (%rbx), %rax
incq %rax
movq %rax, (%rbx)
testl %r13d, %r13d
setne %cl
orb 0xc(%rsp), %cl
jne 0x1279fe
xorl %r13d, %r13d
cmpq 0x8(%rbx), %rax
jbe 0x1279fe
movq %r12, %rdi
callq 0x103bee
movq %rax, %r14
movq %r12, %rdi
callq 0x103bde
leaq 0x24fec1(%rip), %rsi    # 0x3778a9
movq %rbp, %rdi
movq %r14, %rdx
movq %rax, %rcx
xorl %eax, %eax
callq 0xfcb67
movl $0xffffffff, %r13d      # imm = 0xFFFFFFFF
movq 0x10(%rsp), %rsi
testq %rsi, %rsi
je 0x127a17
movq %rbx, %rdi
callq 0x112370
movq %rax, (%rbx)
movq %rdx, 0x8(%rbx)
movl %r13d, %eax
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x3b7f6
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/blast_process_call.c
// Function: gt_blast_process_call_new_all_nucl
GtBlastProcessCall *gt_blast_process_call_new_all_nucl(void)
{
  GtBlastProcessCall *call =
    gt_blast_process_call_new("blastall -p blastn");
  call->nucl = call->all = true;
  call->version_call = "blastall -";
  return call;
}

// Assembly:
pushq %rax
leaq 0x25011a(%rip), %rdi    # 0x377ba6
callq 0x127aa6
movb $0x1, %cl
movb %cl, 0x10(%rax)
movb %cl, 0x15(%rax)
leaq 0x250119(%rip), %rcx    # 0x377bb9
movq %rcx, 0x8(%rax)
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/blast_process_call.c
// Function: gt_blast_process_call_new
static
GtBlastProcessCall *gt_blast_process_call_new(const char *which)
{
  GtBlastProcessCall *call = gt_malloc(sizeof (*call));
  char *env;

  env = getenv("GT_BLAST_PATH");
  if (env != NULL) {
    call->str = gt_str_new_cstr(env);
    gt_str_append_cstr(call->str, "/");
    gt_str_append_cstr(call->str, which);
  }
  else
    call->str = gt_str_new_cstr(which);
  call->all = false;
  call->db = false;
  call->evalue = false;
  call->gapextend = false;
  call->gapopen = false;
  call->nucl = false;
  call->num_threads = false;
  call->outfmt = false;
  call->penalty = false;
  call->query = false;
  call->reward = false;
  call->word_size = false;
  call->xdrop_gap_final = false;
  return call;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %r14
leaq 0x250170(%rip), %rsi    # 0x377c24
movl $0x20, %edi
movl $0x36, %edx
callq 0x104226
movq %rax, %rbx
leaq 0x25053f(%rip), %rdi    # 0x37800c
callq 0x17950
testq %rax, %rax
je 0x127afe
movq %rax, %rdi
callq 0x11acc9
movq %rax, (%rbx)
leaq 0x2376b9(%rip), %rsi    # 0x35f1a2
movq %rax, %rdi
callq 0x11acf3
movq (%rbx), %rdi
movq %r14, %rsi
callq 0x11acf3
jmp 0x127b09
movq %r14, %rdi
callq 0x11acc9
movq %rax, (%rbx)
xorl %eax, %eax
movq %rax, 0x15(%rbx)
movq %rax, 0x10(%rbx)
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/blast_process_call.c
// Function: gt_blast_process_call_new_nucl
GtBlastProcessCall *gt_blast_process_call_new_nucl(void)
{
  GtBlastProcessCall *call =
    gt_blast_process_call_new("blastn");
  call->version_call = "blastn -version";
  call->nucl = true;
  call->all = false;
  return call;
}

// Assembly:
pushq %rax
leaq 0x25008c(%rip), %rdi    # 0x377bb2
callq 0x127aa6
leaq 0x250092(%rip), %rcx    # 0x377bc4
movq %rcx, 0x8(%rax)
movb $0x1, 0x15(%rax)
movb $0x0, 0x10(%rax)
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/blast_process_call.c
// Function: gt_blast_process_call_new_all_prot
GtBlastProcessCall *gt_blast_process_call_new_all_prot(void)
{
  GtBlastProcessCall *call =
    gt_blast_process_call_new("blastall -p blastp");
  call->version_call = "blastall -";
  call->nucl = false;
  call->all = true;
  return call;
}

// Assembly:
pushq %rax
leaq 0x25008c(%rip), %rdi    # 0x377bd4
callq 0x127aa6
leaq 0x250065(%rip), %rcx    # 0x377bb9
movq %rcx, 0x8(%rax)
movb $0x0, 0x15(%rax)
movb $0x1, 0x10(%rax)
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/blast_process_call.c
// Function: gt_blast_process_call_new_prot
GtBlastProcessCall *gt_blast_process_call_new_prot(void)
{
  GtBlastProcessCall *call =
    gt_blast_process_call_new("blastp");
  call->version_call = "blastp -version";
  call->nucl = call->all = false;
  return call;
}

// Assembly:
pushq %rax
leaq 0x250076(%rip), %rdi    # 0x377be0
callq 0x127aa6
leaq 0x250071(%rip), %rcx    # 0x377be7
movq %rcx, 0x8(%rax)
xorl %ecx, %ecx
movb %cl, 0x10(%rax)
movb %cl, 0x15(%rax)
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/blast_process_call.c
// Function: gt_blast_process_call_set_query
void gt_blast_process_call_set_query(GtBlastProcessCall *call,
                                     const char *query)
{
  gt_assert(!call->query);
  call->query = true;
  if (call->all)
    gt_str_append_cstr(call->str, " -i ");
  else
    gt_str_append_cstr(call->str, " -query ");
  gt_str_append_cstr(call->str, query);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
cmpb $0x1, 0x19(%rdi)
je 0x127bc9
movq %rsi, %rbx
movq %rdi, %r14
movb $0x1, 0x19(%rdi)
movq (%rdi), %rdi
leaq 0x2500a4(%rip), %rax    # 0x377c46
leaq 0x2500a2(%rip), %rsi    # 0x377c4b
cmpb $0x0, 0x10(%r14)
cmovneq %rax, %rsi
callq 0x11acf3
movq (%r14), %rdi
movq %rbx, %rsi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x11acf3
callq 0x3b868
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/blast_process_call.c
// Function: gt_blast_process_call_set_db
void gt_blast_process_call_set_db(GtBlastProcessCall *call, const char *db)
{
  gt_assert(!call->db);
  call->db = true;
  if (call->all)
    gt_str_append_cstr(call->str, " -d ");
  else
    gt_str_append_cstr(call->str, " -db ");
  gt_str_append_cstr(call->str, db);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
cmpb $0x1, 0x11(%rdi)
je 0x127c13
movq %rsi, %rbx
movq %rdi, %r14
movb $0x1, 0x11(%rdi)
movq (%rdi), %rdi
leaq 0x25008f(%rip), %rax    # 0x377c7b
leaq 0x25008d(%rip), %rsi    # 0x377c80
cmpb $0x0, 0x10(%r14)
cmovneq %rax, %rsi
callq 0x11acf3
movq (%r14), %rdi
movq %rbx, %rsi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x11acf3
callq 0x3b89f
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/blast_process_call.c
// Function: gt_blast_process_call_set_evalue
void gt_blast_process_call_set_evalue(GtBlastProcessCall *call, double evalue)
{
  gt_assert(!call->evalue);
  call->evalue = true;
  if (call->all)
    gt_str_append_cstr(call->str, " -e ");
  else
    gt_str_append_cstr(call->str, " -evalue ");
  gt_str_append_sci_double(call->str, evalue, 6);
}

// Assembly:
pushq %rbx
subq $0x10, %rsp
movsd %xmm0, 0x8(%rsp)
cmpb $0x1, 0x12(%rdi)
je 0x127c66
movq %rdi, %rbx
movb $0x1, 0x12(%rdi)
movq (%rdi), %rdi
leaq 0x25007b(%rip), %rax    # 0x377cb5
leaq 0x250079(%rip), %rsi    # 0x377cba
cmpb $0x0, 0x10(%rbx)
cmovneq %rax, %rsi
callq 0x11acf3
movq (%rbx), %rdi
movsd 0x8(%rsp), %xmm0
movl $0x6, %esi
addq $0x10, %rsp
popq %rbx
jmp 0x11af6d
callq 0x3b8d8
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/blast_process_call.c
// Function: gt_blast_process_call_set_wordsize
void gt_blast_process_call_set_wordsize(GtBlastProcessCall *call, int word_size)
{
  gt_assert(!call->word_size);
  call->word_size = true;
  if (call->all)
    gt_str_append_cstr(call->str, " -W ");
  else
    gt_str_append_cstr(call->str, " -word_size ");
  gt_str_append_int(call->str, word_size);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
cmpb $0x1, 0x1b(%rdi)
je 0x127cae
movl %esi, %ebx
movq %rdi, %r14
movb $0x1, 0x1b(%rdi)
movq (%rdi), %rdi
leaq 0x250070(%rip), %rax    # 0x377cf8
leaq 0x25006e(%rip), %rsi    # 0x377cfd
cmpb $0x0, 0x10(%r14)
cmovneq %rax, %rsi
callq 0x11acf3
movq (%r14), %rdi
movl %ebx, %esi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x11b007
callq 0x3b911
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/blast_process_call.c
// Function: gt_blast_process_call_set_gapopen
void gt_blast_process_call_set_gapopen(GtBlastProcessCall *call, int gapopen)
{
  gt_assert(!call->gapopen);
  call->gapopen = true;
  if (call->all)
    gt_str_append_cstr(call->str, " -G ");
  else
    gt_str_append_cstr(call->str, " -gapopen ");
  gt_str_append_int(call->str, gapopen);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
cmpb $0x1, 0x14(%rdi)
je 0x127cf6
movl %esi, %ebx
movq %rdi, %r14
movb $0x1, 0x14(%rdi)
movq (%rdi), %rdi
leaq 0x25006b(%rip), %rax    # 0x377d3b
leaq 0x250069(%rip), %rsi    # 0x377d40
cmpb $0x0, 0x10(%r14)
cmovneq %rax, %rsi
callq 0x11acf3
movq (%r14), %rdi
movl %ebx, %esi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x11b007
callq 0x3b94a
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/blast_process_call.c
// Function: gt_blast_process_call_set_gapextend
void gt_blast_process_call_set_gapextend(GtBlastProcessCall *call,
                                         int gapextend)
{
  gt_assert(!call->gapextend);
  call->gapextend = true;
  if (call->all)
    gt_str_append_cstr(call->str, " -E ");
  else
    gt_str_append_cstr(call->str, " -gapextend ");
  gt_str_append_int(call->str, gapextend);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
cmpb $0x1, 0x13(%rdi)
je 0x127d3e
movl %esi, %ebx
movq %rdi, %r14
movb $0x1, 0x13(%rdi)
movq (%rdi), %rdi
leaq 0x250068(%rip), %rax    # 0x377d80
leaq 0x250066(%rip), %rsi    # 0x377d85
cmpb $0x0, 0x10(%r14)
cmovneq %rax, %rsi
callq 0x11acf3
movq (%r14), %rdi
movl %ebx, %esi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x11b007
callq 0x3b983
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/blast_process_call.c
// Function: gt_blast_process_call_set_penalty
void gt_blast_process_call_set_penalty(GtBlastProcessCall *call, int penalty)
{
  gt_assert(!call->penalty);
  call->penalty = true;
  gt_assert(call->nucl);
  if (call->all)
    gt_str_append_cstr(call->str, " -q ");
  else
    gt_str_append_cstr(call->str, " -penalty ");
  gt_str_append_int(call->str, penalty);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
cmpb $0x1, 0x18(%rdi)
je 0x127d8c
movq %rdi, %r14
movb $0x1, 0x18(%rdi)
cmpb $0x0, 0x15(%rdi)
je 0x127d91
movl %esi, %ebx
movq (%r14), %rdi
leaq 0x250068(%rip), %rax    # 0x377dce
leaq 0x250066(%rip), %rsi    # 0x377dd3
cmpb $0x0, 0x10(%r14)
cmovneq %rax, %rsi
callq 0x11acf3
movq (%r14), %rdi
movl %ebx, %esi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x11b007
callq 0x3b9f5
callq 0x3b9bc
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/blast_process_call.c
// Function: gt_blast_process_call_set_reward
void gt_blast_process_call_set_reward(GtBlastProcessCall *call, int reward)
{
  gt_assert(!call->reward);
  call->reward = true;
  gt_assert(call->nucl);
  if (call->all)
    gt_str_append_cstr(call->str, " -r ");
  else
    gt_str_append_cstr(call->str, " -reward ");
  gt_str_append_int(call->str, reward);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
cmpb $0x1, 0x1a(%rdi)
je 0x127ddf
movq %rdi, %r14
movb $0x1, 0x1a(%rdi)
cmpb $0x0, 0x15(%rdi)
je 0x127de4
movl %esi, %ebx
movq (%r14), %rdi
leaq 0x250054(%rip), %rax    # 0x377e0d
leaq 0x250052(%rip), %rsi    # 0x377e12
cmpb $0x0, 0x10(%r14)
cmovneq %rax, %rsi
callq 0x11acf3
movq (%r14), %rdi
movl %ebx, %esi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x11b007
callq 0x3ba67
callq 0x3ba2e
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/blast_process_call.c
// Function: gt_blast_process_call_set_num_threads
void gt_blast_process_call_set_num_threads(GtBlastProcessCall *call,
                                           int num_threads)
{
  gt_assert(!call->num_threads);
  call->num_threads = true;
  if (call->all)
    gt_str_append_cstr(call->str, " -a ");
  else
    gt_str_append_cstr(call->str, " -num_threads ");
  gt_str_append_int(call->str, num_threads);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
cmpb $0x1, 0x16(%rdi)
je 0x127e2c
movl %esi, %ebx
movq %rdi, %r14
movb $0x1, 0x16(%rdi)
movq (%rdi), %rdi
leaq 0x25004f(%rip), %rax    # 0x377e55
leaq 0x25004d(%rip), %rsi    # 0x377e5a
cmpb $0x0, 0x10(%r14)
cmovneq %rax, %rsi
callq 0x11acf3
movq (%r14), %rdi
movl %ebx, %esi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x11b007
callq 0x3baa0
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/blast_process_call.c
// Function: gt_blast_process_call_set_xdrop_gap_final
void gt_blast_process_call_set_xdrop_gap_final(GtBlastProcessCall *call,
                                               double xdrop_gap_final)
{
  gt_assert(!call->xdrop_gap_final);
  call->xdrop_gap_final = true;
  gt_assert(call->nucl);
  if (call->all)
    gt_str_append_cstr(call->str, " -Z ");
  else
    gt_str_append_cstr(call->str, " -xdrop_gap_final ");
  gt_str_append_double(call->str, xdrop_gap_final, 2);
}

// Assembly:
pushq %rbx
subq $0x10, %rsp
cmpb $0x1, 0x1c(%rdi)
je 0x127e85
movq %rdi, %rbx
movsd %xmm0, 0x8(%rsp)
movb $0x1, 0x1c(%rdi)
cmpb $0x0, 0x15(%rdi)
je 0x127e8a
movq (%rbx), %rdi
leaq 0x250051(%rip), %rax    # 0x377eaa
leaq 0x25004f(%rip), %rsi    # 0x377eaf
cmpb $0x0, 0x10(%rbx)
cmovneq %rax, %rsi
callq 0x11acf3
movq (%rbx), %rdi
movsd 0x8(%rsp), %xmm0
movl $0x2, %esi
addq $0x10, %rsp
popq %rbx
jmp 0x11afba
callq 0x3bb12
callq 0x3bad9
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/blast_process_call.c
// Function: gt_blast_process_call_set_outfmt
void gt_blast_process_call_set_outfmt(GtBlastProcessCall *call,
                                      int outfmt)
{
  gt_assert(!call->outfmt);
  call->outfmt = true;
  if (call->all)
    gt_str_append_cstr(call->str, " -m ");
  else
    gt_str_append_cstr(call->str, " -outfmt ");
  gt_str_append_int(call->str, outfmt);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
cmpb $0x1, 0x17(%rdi)
je 0x127ed2
movl %esi, %ebx
movq %rdi, %r14
movb $0x1, 0x17(%rdi)
movq (%rdi), %rdi
leaq 0x250045(%rip), %rax    # 0x377ef1
leaq 0x250043(%rip), %rsi    # 0x377ef6
cmpb $0x0, 0x10(%r14)
cmovneq %rax, %rsi
callq 0x11acf3
movq (%r14), %rdi
movl %ebx, %esi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x11b007
callq 0x3bb4b
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/check_boundaries_visitor.c
// Function: gt_check_boundaries_visitor_class
const GtNodeVisitorClass* gt_check_boundaries_visitor_class()
{
  static GtNodeVisitorClass *nvc = NULL;
  gt_class_alloc_lock_enter();
  if (!nvc) {
    nvc = gt_node_visitor_class_new(sizeof (GtCheckBoundariesVisitor),
                                    NULL,
                                    NULL,
                                    check_boundaries_visitor_feature_node,
                                    NULL,
                                    NULL,
                                    NULL);
  }
  gt_class_alloc_lock_leave();
  return nvc;
}

// Assembly:
pushq %rax
callq 0xe252f
cmpq $0x0, 0x395b06(%rip)    # 0x4be6d0
jne 0x128bf6
movq $0x0, (%rsp)
leaq 0x29(%rip), %rcx        # 0x128c04
movl $0x10, %edi
xorl %esi, %esi
xorl %edx, %edx
xorl %r8d, %r8d
xorl %r9d, %r9d
callq 0x163010
movq %rax, 0x395ada(%rip)    # 0x4be6d0
callq 0xe2545
movq 0x395ace(%rip), %rax    # 0x4be6d0
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/check_boundaries_visitor.c
// Function: check_boundaries_visitor_feature_node
static int check_boundaries_visitor_feature_node(GT_UNUSED GtNodeVisitor *nv,
                                                 GtFeatureNode *fn,
                                                 GT_UNUSED GtError *err)
{
  GtFeatureNodeIterator *fni;
  GtFeatureNode *node;
  int had_err = 0;

  fni = gt_feature_node_iterator_new_direct(fn);
  while (!had_err && (node = gt_feature_node_iterator_next(fni))) {
    had_err = check_boundaries_visitor_check_rec(fn, node, err);
  }
  gt_feature_node_iterator_delete(fni);

  return 0;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rsi, %rdi
callq 0x144041
movq %rax, %r14
movq %rax, %rdi
callq 0x1440ea
testq %rax, %rax
je 0x128c33
movq %rbx, %rdi
movq %rax, %rsi
callq 0x128c54
movq %r14, %rdi
jmp 0x128c19
movq %r14, %rdi
callq 0x14417c
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/check_boundaries_visitor.c
// Function: check_boundaries_visitor_check_rec
static int check_boundaries_visitor_check_rec(GtFeatureNode *parent,
                                              GtFeatureNode *child,
                                              GtError *err)
{
  GtFeatureNodeIterator *fni;
  GtFeatureNode *node;
  GtRange range,
          p_range;
  int had_err = 0;

  range = gt_genome_node_get_range((GtGenomeNode*) child);
  p_range = gt_genome_node_get_range((GtGenomeNode*) parent);

  if (range.start < p_range.start || range.end > p_range.end) {
    gt_warning("%s child range " GT_WU "-" GT_WU " (file %s, line %u) not "
               "contained in %s parent range " GT_WU "-" GT_WU " (file %s, "
               "line %u)",
               gt_feature_node_get_type(child),
               range.start, range.end,
               gt_genome_node_get_filename((GtGenomeNode*) child),
               gt_genome_node_get_line_number((GtGenomeNode*) child),
               gt_feature_node_get_type(parent),
               p_range.start, p_range.end,
               gt_genome_node_get_filename((GtGenomeNode*) parent),
               gt_genome_node_get_line_number((GtGenomeNode*) parent));
  }

  fni = gt_feature_node_iterator_new_direct(child);
  while ((node = gt_feature_node_iterator_next(fni))) {
    had_err = check_boundaries_visitor_check_rec(child, node, err);
  }
  gt_feature_node_iterator_delete(fni);

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq %rsi, %rbx
movq %rdi, %rbp
movq %rsi, %rdi
callq 0x144679
movq %rax, %r12
movq %rdx, %r13
movq %rbp, %rdi
callq 0x144679
movq %rax, %r14
cmpq %rax, %r12
setb %al
cmpq %rdx, %r13
seta %cl
orb %al, %cl
cmpb $0x1, %cl
jne 0x128d1f
movq %rdx, %r15
movq %rbx, %rdi
callq 0x142988
movq %rax, 0x20(%rsp)
movq %rbx, %rdi
callq 0x144606
movq %rax, 0x10(%rsp)
movq %rbx, %rdi
callq 0x144626
movl %eax, 0x4(%rsp)
movq %rbp, %rdi
callq 0x142988
movq %rax, 0x18(%rsp)
movq %rbp, %rdi
callq 0x144606
movq %rax, 0x8(%rsp)
movq %rbp, %rdi
callq 0x144626
movl %eax, %r10d
subq $0x8, %rsp
leaq 0x24f4cc(%rip), %rdi    # 0x3781bd
movq 0x28(%rsp), %rsi
movq %r12, %rdx
movq %r13, %rcx
movq 0x18(%rsp), %r8
movl 0xc(%rsp), %r9d
xorl %eax, %eax
pushq %r10
pushq 0x18(%rsp)
pushq %r15
pushq %r14
pushq 0x40(%rsp)
callq 0x11f68c
addq $0x30, %rsp
movq %rbx, %rdi
callq 0x144041
movq %rax, %r14
movq %rax, %rdi
callq 0x1440ea
testq %rax, %rax
je 0x128d47
movq %rbx, %rdi
movq %rax, %rsi
callq 0x128c54
movq %r14, %rdi
jmp 0x128d2d
movq %r14, %rdi
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x14417c
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/chseqids_stream.c
// Function: gt_chseqids_stream_class
const GtNodeStreamClass* gt_chseqids_stream_class(void)
{
  static const GtNodeStreamClass *nsc = NULL;
  gt_class_alloc_lock_enter();
  if (!nsc) {
    nsc = gt_node_stream_class_new(sizeof (GtChseqidsStream),
                                   chseqids_stream_free,
                                   chseqids_stream_next);
  }
  gt_class_alloc_lock_leave();
  return nsc;
}

// Assembly:
pushq %rax
callq 0xe252f
cmpq $0x0, 0x39596a(%rip)    # 0x4be6d8
jne 0x128d8f
leaq 0x26(%rip), %rsi        # 0x128d9d
leaq 0x8a(%rip), %rdx        # 0x128e08
movl $0x38, %edi
callq 0x162d34
movq %rax, 0x395949(%rip)    # 0x4be6d8
callq 0xe2545
movq 0x39593d(%rip), %rax    # 0x4be6d8
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/chseqids_stream.c
// Function: chseqids_stream_free
static void chseqids_stream_free(GtNodeStream *ns)
{
  GtChseqidsStream *cs;
  GtUword i;
  cs = chseqids_stream_cast(ns);
  gt_mapping_delete(cs->chseqids_mapping);
  for (i = cs->buffer_index; i < gt_array_size(cs->node_buffer); i++)
    gt_genome_node_delete(*(GtGenomeNode**) gt_array_get(cs->node_buffer, i));
  gt_array_delete(cs->node_buffer);
  gt_node_stream_delete(cs->in_stream);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
callq 0x128d60
movq %rax, %rdi
movq %rbx, %rsi
callq 0x162ff7
movq %rax, %rbx
movq 0x18(%rax), %rdi
callq 0x15d2e1
movq 0x20(%rbx), %rdi
movq 0x28(%rbx), %r14
callq 0xd24e0
cmpq %rax, %r14
jae 0x128def
movq 0x20(%rbx), %rdi
movq %r14, %rsi
callq 0xd2207
movq (%rax), %rdi
callq 0x1451a0
incq %r14
movq 0x20(%rbx), %rdi
jmp 0x128dc8
movq 0x20(%rbx), %rdi
callq 0xd2938
movq 0x10(%rbx), %rdi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x162dee
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/chseqids_stream.c
// Function: gt_chseqids_stream_new
GtNodeStream* gt_chseqids_stream_new(GtNodeStream *in_stream,
                                     GtStr *chseqids_file, GtError *err)
{
  GtNodeStream *ns;
  GtChseqidsStream *cs;
  gt_error_check(err);
  gt_assert(in_stream && chseqids_file);
  gt_assert(gt_node_stream_is_sorted(in_stream));
  ns = gt_node_stream_create(gt_chseqids_stream_class(), false);
  cs = chseqids_stream_cast(ns);
  cs->in_stream = gt_node_stream_ref(in_stream);
  cs->chseqids_mapping = gt_mapping_new(chseqids_file, "chseqids",
                                        GT_MAPPINGTYPE_STRING, err);
  if (!cs->chseqids_mapping) {
    gt_node_stream_delete(ns);
    return NULL;
  }
  cs->node_buffer = gt_array_new(sizeof (GtGenomeNode*));
  return ns;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
movq %rdx, %rbx
movq %rsi, %r14
movq %rdi, %r15
testq %rdx, %rdx
je 0x12912c
movq %rbx, %rdi
callq 0xfcc32
testb %al, %al
jne 0x1291ca
testq %r15, %r15
je 0x1291c0
testq %r14, %r14
je 0x1291c0
movq %r15, %rdi
callq 0x162fe4
testb %al, %al
je 0x1291c5
callq 0x128d60
movq %rax, %rdi
xorl %esi, %esi
callq 0x162d6c
movq %rax, %r12
callq 0x128d60
movq %rax, %rdi
movq %r12, %rsi
callq 0x162ff7
movq %rax, %r13
movq %r15, %rdi
callq 0x162dd8
movq %rax, 0x10(%r13)
leaq 0x21c549(%rip), %rsi    # 0x3456cb
movq %r14, %rdi
xorl %edx, %edx
movq %rbx, %rcx
callq 0x15d0e4
movq %rax, 0x18(%r13)
testq %rax, %rax
je 0x1291a8
movl $0x8, %edi
callq 0xd214c
movq %rax, 0x20(%r13)
jmp 0x1291b3
movq %r12, %rdi
callq 0x162dee
xorl %r12d, %r12d
movq %r12, %rax
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
callq 0x3c08d
callq 0x3c0c6
callq 0x3c054
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/chseqids_stream.c
// Function: change_sequence_id
static int change_sequence_id(GtFeatureNode *fn, void *data,
                              GT_UNUSED GtError *err)
{
  GtStr *changed_seqid = data;
  gt_error_check(err);
  gt_assert(changed_seqid);
  gt_genome_node_change_seqid((GtGenomeNode*) fn, changed_seqid);
  return 0;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
testq %rdx, %rdx
je 0x1291ea
movq %rdx, %rdi
callq 0xfcc32
testb %al, %al
jne 0x129209
testq %rbx, %rbx
je 0x129204
movq %r14, %rdi
movq %rbx, %rsi
callq 0x144709
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x3c136
callq 0x3c0ff
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/collect_ids_visitor.c
// Function: gt_collect_ids_visitor_class
const GtNodeVisitorClass* gt_collect_ids_visitor_class()
{
  static const GtNodeVisitorClass *nvc = NULL;
  gt_class_alloc_lock_enter();
  if (!nvc) {
    nvc = gt_node_visitor_class_new(sizeof (GtCollectIDsVisitor),
                                    NULL,
                                    NULL,
                                    collect_ids_visitor_feature_node,
                                    collect_ids_visitor_region_node,
                                    NULL,
                                    NULL);
  }
  gt_class_alloc_lock_leave();
  return nvc;
}

// Assembly:
pushq %rax
callq 0xe252f
cmpq $0x0, 0x3954c2(%rip)    # 0x4be6e0
jne 0x12924e
movq $0x0, (%rsp)
leaq 0x2d(%rip), %rcx        # 0x12925c
leaq 0x7d(%rip), %r8         # 0x1292b3
movl $0x18, %edi
xorl %esi, %esi
xorl %edx, %edx
xorl %r9d, %r9d
callq 0x163010
movq %rax, 0x395492(%rip)    # 0x4be6e0
callq 0xe2545
movq 0x395486(%rip), %rax    # 0x4be6e0
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/collect_ids_visitor.c
// Function: collect_ids_visitor_feature_node
static int collect_ids_visitor_feature_node(GtNodeVisitor *nv,
                                            GtFeatureNode *fn,
                                            GT_UNUSED GtError *err)
{
  GtCollectIDsVisitor *civ;
  const char *seqid;
  civ = collect_ids_visitor_cast(nv);
  seqid = gt_str_get(gt_genome_node_get_seqid((GtGenomeNode*) fn));
  if (!gt_cstr_table_get(civ->seqids, seqid))
    gt_cstr_table_add(civ->seqids, seqid);
  return 0;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %r14
movq %rdi, %rbx
callq 0x129210
movq %rax, %rdi
movq %rbx, %rsi
callq 0x1630b1
movq %rax, %rbx
movq %r14, %rdi
callq 0x144635
movq %rax, %rdi
callq 0x11b0a1
movq %rax, %r14
movq 0x10(%rbx), %rdi
movq %rax, %rsi
callq 0xe4995
testq %rax, %rax
jne 0x1292a9
movq 0x10(%rbx), %rdi
movq %r14, %rsi
callq 0xe4936
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/collect_ids_visitor.c
// Function: collect_ids_visitor_region_node
static int collect_ids_visitor_region_node(GtNodeVisitor *nv, GtRegionNode *rn,
                                           GT_UNUSED GtError *err)
{
  GtCollectIDsVisitor *civ;
  const char *seqid;
  int had_err = 0;
  gt_error_check(err);
  civ = collect_ids_visitor_cast(nv);
  seqid = gt_str_get(gt_genome_node_get_seqid((GtGenomeNode*) rn));
  if (!gt_cstr_table_get(civ->seqids, seqid))
    gt_cstr_table_add(civ->seqids, seqid);
  return had_err;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
testq %rdx, %rdx
je 0x1292ce
movq %rdx, %rdi
callq 0xfcc32
testb %al, %al
jne 0x12931b
callq 0x129210
movq %rax, %rdi
movq %r14, %rsi
callq 0x1630b1
movq %rax, %r14
movq %rbx, %rdi
callq 0x144635
movq %rax, %rdi
callq 0x11b0a1
movq %rax, %rbx
movq 0x10(%r14), %rdi
movq %rax, %rsi
callq 0xe4995
testq %rax, %rax
jne 0x129311
movq 0x10(%r14), %rdi
movq %rbx, %rsi
callq 0xe4936
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x3c16d
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/collect_ids_visitor.c
// Function: gt_collect_ids_visitor_new
GtNodeVisitor* gt_collect_ids_visitor_new(GtCstrTable *cst)
{
  GtNodeVisitor *nv = gt_node_visitor_create(gt_collect_ids_visitor_class());
  GtCollectIDsVisitor *collect_ids_visitor = collect_ids_visitor_cast(nv);
  collect_ids_visitor->seqids = cst;
  return nv;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
callq 0x129210
movq %rax, %rdi
callq 0x163080
movq %rax, %r14
callq 0x129210
movq %rax, %rdi
movq %r14, %rsi
callq 0x1630b1
movq %rbx, 0x10(%rax)
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/compressed_bitsequence.c
// Function: gt_compressed_bitsequence_access
int gt_compressed_bitsequence_access(GtCompressedBitsequence *cbs,
                                     GtUword position)
{
  int bit;
  unsigned int pos_in_block;
  GtUword block;
  GtCompressedBitsequenceBlockInfo *cbs_bi;

  gt_assert(cbs != NULL);
  gt_assert(position < cbs->num_of_bits);

  pos_in_block = (unsigned int) position % cbs->blocksize;

  gt_compressed_bitsequence_calc_block_info(cbs, position);
  cbs_bi = cbs->cbs_bi;
  if (cbs_bi->class == 0 || cbs_bi->class == cbs->blocksize)
    return cbs_bi->class == 0 ? 0 : 1;

  block = gt_popcount_tab_get(cbs->popcount_tab,
                              cbs_bi->class,
                              cbs_bi->block_offset);

  /* account for shorter blocks at the end */
  block <<= (cbs->blocksize - cbs_bi->block_len);

  bit = (int) ((block >> (cbs->blocksize - pos_in_block - 1)) & 1UL);
  return bit;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0x129d81
movq %rdi, %rbx
cmpq %rsi, 0xb0(%rdi)
jbe 0x129d86
movl %esi, %eax
xorl %edx, %edx
divl 0xd8(%rbx)
movl %edx, %r14d
movq %rbx, %rdi
callq 0x129d8b
movq 0x90(%rbx), %r15
movl 0x18(%r15), %esi
testl %esi, %esi
je 0x129d45
cmpl 0xd8(%rbx), %esi
jne 0x129d4e
xorl %eax, %eax
testl %esi, %esi
setne %al
jmp 0x129d7b
movq 0x68(%rbx), %rdi
movq (%r15), %rdx
callq 0x164278
movq %rax, %rdx
movl 0xd8(%rbx), %eax
movl %eax, %ecx
subl 0x1c(%r15), %ecx
shlq %cl, %rdx
notl %r14d
addl %eax, %r14d
xorl %eax, %eax
btq %r14, %rdx
setb %al
popq %rbx
popq %r14
popq %r15
retq
callq 0x3c5a6
callq 0x3c56d
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/compressed_bitsequence.c
// Function: gt_compressed_bitsequence_rank_1
GtUword gt_compressed_bitsequence_rank_1(GtCompressedBitsequence *cbs,
                                         GtUword position)
{
  unsigned int pos_in_block;
  GtCompressedBitsequenceBlockInfo *cbs_bi;

  gt_assert(cbs != NULL);
  gt_assert(position < cbs->num_of_bits);

  pos_in_block = (unsigned int) position % cbs->blocksize;

  gt_compressed_bitsequence_calc_block_info(cbs, position);
  cbs_bi = cbs->cbs_bi;

  pos_in_block += cbs->blocksize - cbs_bi->block_len;
  if (cbs_bi->class == 0)
    return cbs_bi->rank_sum;
  if (cbs_bi->class == cbs->blocksize)
    return cbs_bi->rank_sum + pos_in_block + 1;

  return cbs_bi->rank_sum + gt_popcount_tab_rank_1(cbs->popcount_tab,
                                                   cbs_bi->class,
                                                   cbs_bi->block_offset,
                                                   pos_in_block);
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0x12a007
movq %rdi, %rbx
cmpq %rsi, 0xb0(%rdi)
jbe 0x12a00c
movl %esi, %eax
xorl %edx, %edx
divl 0xd8(%rbx)
movl %edx, %ebp
movq %rbx, %rdi
callq 0x129d8b
movq 0x90(%rbx), %rax
movl 0x18(%rax), %esi
testl %esi, %esi
je 0x129fe8
movl 0xd8(%rbx), %edx
movl %edx, %ecx
subl 0x1c(%rax), %ecx
addl %ebp, %ecx
movq 0x10(%rax), %r14
cmpl %edx, %esi
jne 0x129fee
movl %ecx, %eax
addq %rax, %r14
incq %r14
jmp 0x129fff
movq 0x10(%rax), %r14
jmp 0x129fff
movq 0x68(%rbx), %rdi
movq (%rax), %rdx
callq 0x164436
movl %eax, %eax
addq %rax, %r14
movq %r14, %rax
popq %rbx
popq %r14
popq %rbp
retq
callq 0x3c6c3
callq 0x3c68a
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/compressed_bitsequence.c
// Function: gt_compressed_bitsequence_rank_0
GtUword gt_compressed_bitsequence_rank_0(GtCompressedBitsequence *cbs,
                                         GtUword position)
{
  unsigned int pos_in_block;
  GtUword rank_sum0;
  GtCompressedBitsequenceBlockInfo *cbs_bi;

  gt_assert(cbs != NULL);
  gt_assert(position < cbs->num_of_bits);

  pos_in_block = (unsigned int) position % cbs->blocksize;

  gt_compressed_bitsequence_calc_block_info(cbs, position);
  cbs_bi = cbs->cbs_bi;

  pos_in_block += cbs->blocksize - cbs_bi->block_len;
  rank_sum0 = ((cbs_bi->idx) * cbs->blocksize) - cbs_bi->rank_sum;
  rank_sum0 -= cbs->blocksize - cbs_bi->block_len;
  if (cbs_bi->class == 0)
    return rank_sum0 + pos_in_block + 1;
  if (cbs_bi->class == cbs->blocksize)
    return rank_sum0;
  return rank_sum0 + gt_popcount_tab_rank_0(cbs->popcount_tab,
                                            cbs_bi->class,
                                            cbs_bi->block_offset,
                                            pos_in_block);
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0x12a08d
movq %rdi, %rbx
cmpq %rsi, 0xb0(%rdi)
jbe 0x12a092
movl %esi, %eax
xorl %edx, %edx
divl 0xd8(%rbx)
movl %edx, %ebp
movq %rbx, %rdi
callq 0x129d8b
movq 0x90(%rbx), %rax
movl 0xd8(%rbx), %ecx
movl %ecx, %edx
subl 0x1c(%rax), %edx
addl %edx, %ebp
movq %rcx, %r14
imulq 0x8(%rax), %r14
addq 0x10(%rax), %rdx
subq %rdx, %r14
movl 0x18(%rax), %esi
testl %esi, %esi
je 0x12a07d
cmpl %ecx, %esi
je 0x12a085
movq 0x68(%rbx), %rdi
movq (%rax), %rdx
movl %ebp, %ecx
callq 0x164545
movl %eax, %eax
addq %rax, %r14
jmp 0x12a085
movl %ebp, %eax
addq %rax, %r14
incq %r14
movq %r14, %rax
popq %rbx
popq %r14
popq %rbp
retq
callq 0x3c735
callq 0x3c6fc
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/compressed_bitsequence.c
// Function: gt_compressed_bitsequence_get_class
static inline unsigned int
gt_compressed_bitsequence_get_class(GtCompressedBitsequence *cbs,
                                    GtUword idx)
{
  gt_assert(cbs != NULL);
  gt_assert(cbs->classes != NULL);
  return (unsigned int)
    gt_compressed_bitsequence_get_variable_field(cbs->classes,
                                                 idx * cbs->class_bits,
                                                 cbs->class_bits);
}

// Assembly:
pushq %rax
testq %rdi, %rdi
je 0x12a527
movq 0x78(%rdi), %r8
testq %r8, %r8
je 0x12a52c
movl 0xdc(%rdi), %edx
cmpq $0x41, %rdx
jae 0x12a531
testq %rdx, %rdx
je 0x12a523
imulq %rdx, %rsi
movq %rsi, %rdi
shrq $0x6, %rdi
movq (%r8,%rdi,8), %rax
movl %esi, %ecx
shlq %cl, %rax
movl %esi, %ecx
andl $0x3f, %ecx
leal (%rcx,%rdx), %esi
cmpl $0x41, %esi
jb 0x12a51a
movq 0x8(%r8,%rdi,8), %rsi
negb %cl
shrq %cl, %rsi
orq %rsi, %rax
negb %dl
movl %edx, %ecx
shrq %cl, %rax
jmp 0x12a525
xorl %eax, %eax
popq %rcx
retq
callq 0x3c9a8
callq 0x3c96f
callq 0x3c936
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/compressed_bitsequence.c
// Function: gt_compressed_bitsequence_file_size
size_t gt_compressed_bitsequence_file_size(const GtCompressedBitsequence *cbs)
{
  size_t size = gt_compressed_bitsequence_header_size(cbs);

  size += sizeof (cbs->c_offsets[0]) * cbs->c_offsets_size;
  size += sizeof (cbs->classes[0]) * cbs->classes_size;
  size += sizeof (cbs->superblockoffsets[0]) * cbs->superblockoffsets_size;
  size += sizeof (cbs->superblockranks[0]) * cbs->superblockranks_size;

  return size;
}

// Assembly:
pushq %rbx
movq %rdi, %rbx
callq 0x12aa39
movq 0xa8(%rbx), %rax
addq 0xa0(%rbx), %rax
addq 0xc8(%rbx), %rax
addq 0xd0(%rbx), %rax
leaq 0x50(,%rax,8), %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/compressed_bitsequence.c
// Function: gt_compressed_bitsequence_size
size_t gt_compressed_bitsequence_size(const GtCompressedBitsequence *cbs)
{
  size_t size =  sizeof (cbs) +
    gt_popcount_tab_calculate_size(cbs->blocksize) +
    sizeof (cbs->cbs_bi) +
    sizeof (cbs->c_offsets[0]) * cbs->c_offsets_size +
    sizeof (cbs->classes[0]) * cbs->classes_size +
    sizeof (cbs->superblockoffsets[0]) * cbs->superblockoffsets_size +
    sizeof (cbs->superblockranks[0]) * cbs->superblockranks_size;

  return size;
}

// Assembly:
pushq %rbx
movq %rdi, %rbx
movl 0xd8(%rdi), %edi
callq 0x164314
movq 0xa8(%rbx), %rcx
addq 0xa0(%rbx), %rcx
addq 0xc8(%rbx), %rcx
addq 0xd0(%rbx), %rcx
leaq (%rax,%rcx,8), %rax
addq $0x10, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/compressed_bitsequence.c
// Function: gt_compressed_bitsequence_write
int gt_compressed_bitsequence_write(GtCompressedBitsequence *cbs,
                                    char *filename,
                                    GtError *err)
{
  int had_err = 0;
  GtUword expectedsize = 0;
  FILE *fp = NULL;

  fp = gt_fa_fopen(filename, "w", err);
  if (fp == NULL)
    had_err = -1;

  if (!had_err) {
    expectedsize = (GtUword) gt_compressed_bitsequence_file_size(cbs);
    had_err = gt_mapspec_write(gt_compressed_bitsequence_data_setup_mapspec,
                               fp, cbs, expectedsize, err);
  }
  if (!had_err) {
    gt_log_log("blocksize: %u\n"
           "class_offsets_size: " GT_WU "\n"
           "class_bits: %u\n"
           "classes_size: " GT_WU "\n"
           "last_block_len: %u\n"
           "num_of_bits: " GT_WU "\n"
           "num_of_blocks: " GT_WU "\n"
           "num_of_superblocks: " GT_WU "\n"
           "superblocksize: %u\n"
           "size: " GT_WU "\n",
           cbs->blocksize,
           cbs->c_offsets_size,
           cbs->class_bits,
           cbs->classes_size,
           cbs->last_block_len,
           cbs->num_of_bits,
           cbs->num_of_blocks,
           cbs->num_of_superblocks,
           cbs->superblocksize,
           expectedsize);
  }
  gt_fa_fclose(fp);

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x30, %rsp
movq %rdx, %r15
movq %rsi, %rax
movq %rdi, %r14
leaq 0x268b1f(%rip), %rsi    # 0x3935b5
leaq 0x24da99(%rip), %rdx    # 0x378536
movq %rax, %rdi
movl $0x3b3, %ecx            # imm = 0x3B3
movq %r15, %r8
callq 0xfcdbb
movq %rax, %rbx
testq %rax, %rax
je 0x12ab60
movq %r14, %rdi
callq 0x12aa39
movq 0xa8(%r14), %rax
addq 0xa0(%r14), %rax
addq 0xc8(%r14), %rax
addq 0xd0(%r14), %rax
leaq 0x50(,%rax,8), %r12
leaq 0x90(%rip), %rdi        # 0x12ab7c
movq %rbx, %rsi
movq %r14, %rdx
movq %r12, %rcx
movq %r15, %r8
callq 0x105023
movl %eax, %ebp
testl %eax, %eax
jne 0x12ab65
movl 0xd8(%r14), %esi
movl 0xdc(%r14), %ecx
movq 0xa0(%r14), %rdx
movq 0xa8(%r14), %r8
movl 0xe0(%r14), %r9d
movups 0xb0(%r14), %xmm0
movq 0xc0(%r14), %rax
movl 0xec(%r14), %edi
movq %r12, 0x20(%rsp)
movl %edi, 0x18(%rsp)
movq %rax, 0x10(%rsp)
movups %xmm0, (%rsp)
leaq 0x24db58(%rip), %rdi    # 0x3786ad
xorl %ebp, %ebp
xorl %eax, %eax
callq 0x103d72
jmp 0x12ab65
movl $0xffffffff, %ebp       # imm = 0xFFFFFFFF
movq %rbx, %rdi
callq 0xfd018
movl %ebp, %eax
addq $0x30, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/compressed_bitsequence.c
// Function: gt_compressed_bitsequence_data_setup_mapspec
static void gt_compressed_bitsequence_data_setup_mapspec(GtMapspec *mapspec,
                                                         void *data,
                                                         GT_UNUSED bool write)
{
  GtCompressedBitsequence *cbs = data;

  /* this makes writing easy, and solves the problem of knowing where the data
     starts within the file/mapped area */
  gt_compressed_bitsequence_header_setup_mapspec(mapspec, data, write);

  gt_mapspec_add_bitsequence(mapspec, cbs->c_offsets, cbs->c_offsets_size);
  gt_mapspec_add_bitsequence(mapspec, cbs->classes, cbs->classes_size);
  gt_mapspec_add_bitsequence(mapspec, cbs->superblockoffsets,
                             cbs->superblockoffsets_size);
  gt_mapspec_add_bitsequence(mapspec, cbs->superblockranks,
                             cbs->superblockranks_size);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
callq 0x12ae42
leaq 0x70(%rbx), %rsi
movq 0xa0(%rbx), %rdx
movq %r14, %rdi
callq 0x105660
leaq 0x78(%rbx), %rsi
movq 0xa8(%rbx), %rdx
movq %r14, %rdi
callq 0x105660
leaq 0x80(%rbx), %rsi
movq 0xc8(%rbx), %rdx
movq %r14, %rdi
callq 0x105660
movq 0xd0(%rbx), %rdx
addq $0x88, %rbx
movq %r14, %rdi
movq %rbx, %rsi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x105660
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/compressed_bitsequence.c
// Function: gt_compressed_bitsequence_delete
void gt_compressed_bitsequence_delete(GtCompressedBitsequence *cbs)
{
  if (cbs != NULL) {
    gt_popcount_tab_delete(cbs->popcount_tab);
    if (cbs->from_file) {
      gt_fa_xmunmap(cbs->mmapped);
    }
    else {
      gt_free(cbs->classes);
      gt_free(cbs->c_offsets);
      gt_free(cbs->superblockranks);
      gt_free(cbs->superblockoffsets);
    }
    gt_free(cbs->cbs_bi);
    gt_free(cbs);
  }
}

// Assembly:
testq %rdi, %rdi
je 0x12aff4
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq 0x68(%rdi), %rdi
callq 0x164222
cmpb $0x1, 0xf0(%rbx)
jne 0x12aff5
movq 0x98(%rbx), %rdi
callq 0xfdc54
jmp 0x12b046
retq
movq 0x78(%rbx), %rdi
leaq 0x24d536(%rip), %r14    # 0x378536
movq %r14, %rsi
movl $0x429, %edx            # imm = 0x429
callq 0x1045eb
movq 0x70(%rbx), %rdi
movq %r14, %rsi
movl $0x42a, %edx            # imm = 0x42A
callq 0x1045eb
movq 0x88(%rbx), %rdi
movq %r14, %rsi
movl $0x42b, %edx            # imm = 0x42B
callq 0x1045eb
movq 0x80(%rbx), %rdi
movq %r14, %rsi
movl $0x42c, %edx            # imm = 0x42C
callq 0x1045eb
movq 0x90(%rbx), %rdi
leaq 0x24d4e2(%rip), %r14    # 0x378536
movq %r14, %rsi
movl $0x42e, %edx            # imm = 0x42E
callq 0x1045eb
movq %rbx, %rdi
movq %r14, %rsi
movl $0x42f, %edx            # imm = 0x42F
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x1045eb
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/condenseq.c
// Function: gt_condenseq_seqstartpos
GtUword gt_condenseq_seqstartpos(const GtCondenseq *condenseq, GtUword seqnum)
{
  GtUword ret = 0;
  if (seqnum != 0)
    ret = gt_intset_get(condenseq->ssptab, seqnum - 1) + 1;
  return ret;
}

// Assembly:
testq %rsi, %rsi
je 0x12bb48
pushq %rax
movq 0x28(%rdi), %rdi
decq %rsi
callq 0x15673b
incq %rax
addq $0x8, %rsp
retq
xorl %eax, %eax
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/condenseq.c
// Function: gt_condenseq_description
const char *gt_condenseq_description(const GtCondenseq *condenseq,
                                     GtUword *desclen,
                                     GtUword seqnum)
{
  gt_assert(condenseq != NULL);
  gt_assert(condenseq->orig_num_seq != 0);
  gt_assert(seqnum < condenseq->orig_num_seq);
  if (condenseq->id_len == GT_UNDEF_UWORD) {
    GtUword this = gt_intset_get(condenseq->sdstab, seqnum), previous;
    if (seqnum == 0) {
      *desclen = this;
      return condenseq->orig_ids;
    }
    previous = gt_intset_get(condenseq->sdstab, seqnum - 1);
    *desclen =  this - previous;
    return condenseq->orig_ids + previous;
  }
  else {
    const char *id = condenseq->orig_ids + seqnum * condenseq->id_len;
    *desclen = condenseq->id_len;
    while (id[*desclen - 1] == '\0')
      (*desclen)--;
    return condenseq->orig_ids + seqnum * condenseq->id_len;
  }
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x12bc47
movq %rdi, %rbx
movq 0x80(%rdi), %rax
testq %rax, %rax
je 0x12bc4c
movq %rdx, %r15
cmpq %rdx, %rax
jbe 0x12bc51
movq %rsi, %r14
movq 0x58(%rbx), %rcx
cmpq $-0x1, %rcx
je 0x12bc05
movq 0x48(%rbx), %rax
leaq 0x1(%r15), %rdx
imulq %rcx, %rdx
addq %rax, %rdx
decq %rdx
movq %rcx, (%r14)
decq %rcx
cmpb $0x0, (%rdx)
leaq -0x1(%rdx), %rdx
je 0x12bbec
imulq 0x58(%rbx), %r15
addq %r15, %rax
jmp 0x12bc3b
movq 0x20(%rbx), %rdi
movq %r15, %rsi
callq 0x15673b
movq %rax, %r12
testq %r15, %r15
je 0x12bc34
movq 0x20(%rbx), %rdi
decq %r15
movq %r15, %rsi
callq 0x15673b
subq %rax, %r12
movq %r12, (%r14)
addq 0x48(%rbx), %rax
jmp 0x12bc3b
movq %r12, (%r14)
movq 0x48(%rbx), %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
callq 0x3cec7
callq 0x3ce8e
callq 0x3ce55
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/condenseq.c
// Function: gt_condenseq_total_link_len
GtUword gt_condenseq_total_link_len(const GtCondenseq *condenseq)
{
  GtUword total = 0,
          i;

  for (i = 0; i < condenseq->lds_nelems; i++) {
    total += condenseq->links[i].len;
  }

  return total;
}

// Assembly:
movq 0x70(%rdi), %rcx
testq %rcx, %rcx
je 0x12c0ff
movq 0x8(%rdi), %rdx
addq $0x10, %rdx
xorl %eax, %eax
movl (%rdx), %esi
addq %rsi, %rax
addq $0x20, %rdx
decq %rcx
jne 0x12c0f0
retq
xorl %eax, %eax
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/condenseq.c
// Function: gt_condenseq_add_unique_to_db
void gt_condenseq_add_unique_to_db(GtCondenseq *condenseq,
                                   GtUword orig_startpos,
                                   ces_unsigned len)
{
  gt_assert(len != 0);
  /* if previous unique and this one are not consecutive, add the new one */
  if (condenseq->uds_nelems == 0 ||
      condenseq->uniques[condenseq->uds_nelems - 1].orig_startpos +
      condenseq->uniques[condenseq->uds_nelems - 1].len != orig_startpos) {
    gt_assert(condenseq->uds_nelems == 0 ||
              condenseq->uniques[condenseq->uds_nelems - 1].orig_startpos +
              condenseq->uniques[condenseq->uds_nelems - 1].len <
              orig_startpos);
    gt_assert(condenseq->lds_nelems == 0 ||
              condenseq->links[condenseq->lds_nelems - 1].orig_startpos +
              condenseq->links[condenseq->lds_nelems - 1].len <=
              orig_startpos);
    condenseq_uds_resize(condenseq);
    condenseq->uniques[condenseq->uds_nelems].orig_startpos = orig_startpos;
    condenseq->uniques[condenseq->uds_nelems].len = len;
    condenseq->uniques[condenseq->uds_nelems].links.spaceuint32_t = NULL;
    condenseq->uds_nelems++;
  }
  else {
    condenseq->uniques[condenseq->uds_nelems - 1].len += len;
  }
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
testl %edx, %edx
je 0x12c299
movl %edx, %ebx
movq %rsi, %r15
movq %rdi, %r14
movq 0x98(%rdi), %rcx
testq %rcx, %rcx
je 0x12c1bb
movq 0x10(%r14), %rdx
leaq (%rcx,%rcx,4), %rsi
movl -0x8(%rdx,%rsi,8), %eax
movq -0x10(%rdx,%rsi,8), %rdi
addq %rax, %rdi
cmpq %r15, %rdi
jne 0x12c1b5
leaq (%rdx,%rsi,8), %rcx
addl %ebx, %eax
movl %eax, -0x8(%rcx)
jmp 0x12c293
jae 0x12c2a3
movq 0x70(%r14), %rax
testq %rax, %rax
je 0x12c1de
movq 0x8(%r14), %rdx
shlq $0x5, %rax
movl -0x10(%rdx,%rax), %esi
addq -0x18(%rdx,%rax), %rsi
cmpq %r15, %rsi
ja 0x12c29e
cmpq 0x90(%r14), %rcx
jne 0x12c270
movq %rcx, %xmm0
punpckldq 0x21b6e8(%rip), %xmm0 # xmm0 = xmm0[0],mem[0],xmm0[1],mem[1]
subpd 0x21b6f0(%rip), %xmm0   # 0x3478f0
movapd %xmm0, %xmm1
unpckhpd %xmm0, %xmm1            # xmm1 = xmm1[1],xmm0[1]
addsd %xmm0, %xmm1
mulsd 0x21bb04(%rip), %xmm1   # 0x347d18
cvttsd2si %xmm1, %rax
movq %rax, %rdx
sarq $0x3f, %rdx
subsd 0x21baf8(%rip), %xmm1   # 0x347d20
cvttsd2si %xmm1, %rsi
andq %rdx, %rsi
orq %rax, %rsi
testq %rcx, %rcx
movl $0x64, %eax
cmovneq %rsi, %rax
movq %rax, 0x90(%r14)
movq 0x10(%r14), %rdi
shlq $0x3, %rax
leaq (%rax,%rax,4), %rsi
leaq 0x24c9cd(%rip), %rdx    # 0x378c26
movl $0x13f, %ecx            # imm = 0x13F
callq 0x104461
movq %rax, 0x10(%r14)
movq 0x98(%r14), %rcx
jmp 0x12c274
movq 0x10(%r14), %rax
leaq (%rcx,%rcx,4), %rdx
movq %r15, 0x18(%rax,%rdx,8)
movl %ebx, 0x20(%rax,%rdx,8)
movq $0x0, (%rax,%rdx,8)
incq %rcx
movq %rcx, 0x98(%r14)
popq %rbx
popq %r14
popq %r15
retq
callq 0x3d01b
callq 0x3cfe2
callq 0x3cfa9