LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/gff3_out_stream.c
// Function: gt_gff3_out_stream_new
GtNodeStream* gt_gff3_out_stream_new(GtNodeStream *in_stream, GtFile *outfp)
{
  GtNodeStream *ns = gt_node_stream_create(gt_gff3_out_stream_class(),
                                           gt_node_stream_is_sorted(in_stream));
  GtGFF3OutStream *gff3_out_stream = gff3_out_stream_cast(ns);
  gff3_out_stream->in_stream = gt_node_stream_ref(in_stream);
  gff3_out_stream->gff3_visitor = gt_gff3_visitor_new(outfp);
  return ns;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
callq 0xdbc58
movq %rax, %r15
movq %r14, %rdi
callq 0x48ef8
movzbl %al, %esi
movq %r15, %rdi
callq 0x48c80
movq %rax, %r15
callq 0xdbc58
movq %rax, %rdi
movq %r15, %rsi
callq 0x48f0b
movq %rax, %r12
movq %r14, %rdi
callq 0x48cec
movq %rax, 0x10(%r12)
movq %rbx, %rdi
callq 0x47917
movq %rax, 0x18(%r12)
movq %r15, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/splicedseq.c
// Function: gt_splicedseq_new
Splicedseq* gt_splicedseq_new(void)
{
  Splicedseq *ss = gt_malloc(sizeof (Splicedseq));
  ss->splicedseq = gt_str_new();
  ss->positionmapping = gt_array_new(sizeof (GtUword));
  ss->forward = true;
  return ss;
}

// Assembly:
pushq %rbx
leaq 0x2fde8(%rip), %rsi     # 0x10bbac
movl $0x18, %edi
movl $0x22, %edx
callq 0x35862
movq %rax, %rbx
callq 0x3b728
movq %rax, (%rbx)
movl $0x8, %edi
callq 0x6ef7c
movq %rax, 0x8(%rbx)
movb $0x1, 0x10(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/splicedseq.c
// Function: gt_splicedseq_add
void gt_splicedseq_add(Splicedseq *ss, GtUword start, GtUword end,
                       const char *original_sequence)
{
  GtUword i;
  gt_assert(ss && start <= end && original_sequence);
  gt_str_append_cstr_nt(ss->splicedseq, original_sequence,
                        end - start + 1);
  /* make sure elements are added in ascending order */
  gt_assert(!gt_array_size(ss->positionmapping) ||
            start > *(GtUword*) gt_array_get_last(ss->positionmapping));
  for (i = start; i <= end; i++)
    gt_array_add(ss->positionmapping, i);
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xdbe73
movq %rdx, %rbx
movq %rsi, %r15
subq %rsi, %rdx
jb 0xdbe73
testq %rcx, %rcx
je 0xdbe73
movq %rdi, %r14
movq (%rdi), %rdi
incq %rdx
movq %rcx, %rsi
callq 0x3b8d7
movq 0x8(%r14), %rdi
callq 0x6f310
testq %rax, %rax
je 0xdbe3f
movq 0x8(%r14), %rdi
callq 0x6f05b
cmpq %r15, (%rax)
jae 0xdbe78
movq %rsp, %r12
movq %r15, (%r12)
movq 0x8(%r14), %rdi
movl $0x8, %edx
movq %r12, %rsi
callq 0x6f240
movq (%rsp), %rax
incq %rax
movq %rax, (%rsp)
cmpq %rbx, %rax
jbe 0xdbe46
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
callq 0x339bb
callq 0x33984
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/splicedseq.c
// Function: gt_splicedseq_pos_is_border
bool gt_splicedseq_pos_is_border(const Splicedseq *ss, GtUword pos)
{
  gt_assert(ss &&
         gt_str_length(ss->splicedseq) == gt_array_size(ss->positionmapping));
  gt_assert(pos < gt_str_length(ss->splicedseq)); /* legal position */
  if (ss->forward && pos + 1 < gt_array_size(ss->positionmapping) &&
      *(GtUword*) gt_array_get(ss->positionmapping, pos) + 1 !=
      *(GtUword*) gt_array_get(ss->positionmapping, pos+1)) {
    return true;
  }
  if (!ss->forward && pos &&
      *(GtUword*) gt_array_get(ss->positionmapping, pos-1) - 1 !=
      *(GtUword*) gt_array_get(ss->positionmapping, pos)) {
    return true;
  }
  return false;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xdbf4e
movq %rsi, %rbx
movq %rdi, %r14
movq (%rdi), %rdi
callq 0x3bb86
movq %rax, %r15
movq 0x8(%r14), %rdi
callq 0x6f310
cmpq %rax, %r15
jne 0xdbf4e
movq (%r14), %rdi
callq 0x3bb86
cmpq %rbx, %rax
jbe 0xdbf53
cmpb $0x1, 0x10(%r14)
jne 0xdbf0b
leaq 0x1(%rbx), %r15
movq 0x8(%r14), %rdi
callq 0x6f310
cmpq %rax, %r15
jae 0xdbf0b
movq 0x8(%r14), %rdi
movq %rbx, %rsi
callq 0x6f037
movq (%rax), %r12
incq %r12
movq 0x8(%r14), %rdi
movq %r15, %rsi
callq 0x6f037
movq %rax, %rcx
movb $0x1, %al
cmpq (%rcx), %r12
jne 0xdbf42
testq %rbx, %rbx
je 0xdbf40
cmpb $0x0, 0x10(%r14)
jne 0xdbf40
movq 0x8(%r14), %rdi
leaq -0x1(%rbx), %rsi
callq 0x6f037
movq (%rax), %r15
decq %r15
movq 0x8(%r14), %rdi
movq %rbx, %rsi
callq 0x6f037
movq %rax, %rcx
movb $0x1, %al
cmpq (%rcx), %r15
jne 0xdbf42
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
callq 0x33a29
callq 0x339f2
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/splicedseq.c
// Function: gt_splicedseq_map
GtUword gt_splicedseq_map(const Splicedseq *ss, GtUword pos)
{
  gt_assert(ss &&
         gt_str_length(ss->splicedseq) == gt_array_size(ss->positionmapping));
  gt_assert(pos < gt_str_length(ss->splicedseq)); /* legal position */
  return *(GtUword*) gt_array_get(ss->positionmapping, pos);
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0xdbfa3
movq %rsi, %rbx
movq %rdi, %r14
movq (%rdi), %rdi
callq 0x3bb86
movq %rax, %r15
movq 0x8(%r14), %rdi
callq 0x6f310
cmpq %rax, %r15
jne 0xdbfa3
movq (%r14), %rdi
callq 0x3bb86
cmpq %rbx, %rax
jbe 0xdbfa8
movq 0x8(%r14), %rdi
movq %rbx, %rsi
callq 0x6f037
movq (%rax), %rax
popq %rbx
popq %r14
popq %r15
retq
callq 0x33a97
callq 0x33a60
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/splicedseq.c
// Function: gt_splicedseq_reverse
int gt_splicedseq_reverse(Splicedseq *ss, GtError *err)
{
  int had_err;
  gt_error_check(err);
  gt_assert(ss);
  had_err = gt_reverse_complement(gt_str_get(ss->splicedseq),
                               gt_str_length(ss->splicedseq), err);
  if (!had_err) {
    gt_array_reverse(ss->positionmapping);
    ss->forward = !ss->forward;
  }
  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %r14
movq %rdi, %rbx
testq %rsi, %rsi
je 0xdbfde
movq %r14, %rdi
callq 0x34fea
testb %al, %al
jne 0xdc029
testq %rbx, %rbx
je 0xdc024
movq (%rbx), %rdi
callq 0x3bb5d
movq %rax, %r15
movq (%rbx), %rdi
callq 0x3bb86
movq %r15, %rdi
movq %rax, %rsi
movq %r14, %rdx
callq 0xa8efc
movl %eax, %ebp
testl %eax, %eax
jne 0xdc017
movq 0x8(%rbx), %rdi
callq 0x6f179
xorb $0x1, 0x10(%rbx)
movl %ebp, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
callq 0x33b3c
callq 0x33b05
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/splicedseq.c
// Function: gt_splicedseq_reset
void gt_splicedseq_reset(Splicedseq *ss)
{
  gt_assert(ss);
  gt_str_reset(ss->splicedseq);
  gt_array_reset(ss->positionmapping);
  ss->forward = true;
}

// Assembly:
pushq %rbx
testq %rdi, %rdi
je 0xdc04e
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x3bbee
movq 0x8(%rbx), %rdi
callq 0x6f349
movb $0x1, 0x10(%rbx)
popq %rbx
retq
callq 0x33b73
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/splicedseq.c
// Function: gt_splicedseq_unit_test
int gt_splicedseq_unit_test(GtError *err)
{
  Splicedseq *ss;
  int had_err = 0;
  gt_error_check(err);
  ss = gt_splicedseq_new();
  had_err = check_splicedseq(ss, err);
  if (!had_err) {
    gt_splicedseq_reset(ss);
    had_err = check_splicedseq(ss, err);
  }
  gt_splicedseq_delete(ss);
  return had_err;
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
movq %rdi, %rbx
testq %rdi, %rdi
je 0xdc07b
movq %rbx, %rdi
callq 0x34fea
testb %al, %al
jne 0xdc0ba
callq 0xdbdbc
movq %rax, %r14
movq %rax, %rdi
movq %rbx, %rsi
jmp 0xdc088
callq 0xdbdbc
movq %rax, %r14
movq %rax, %rdi
xorl %esi, %esi
callq 0xdc0bf
movl $0xffffffff, %ebp       # imm = 0xFFFFFFFF
testl %eax, %eax
jne 0xdc0ab
movq %r14, %rdi
callq 0xdc02e
movq %r14, %rdi
movq %rbx, %rsi
callq 0xdc0bf
movl %eax, %ebp
movq %r14, %rdi
callq 0xdc288
movl %ebp, %eax
popq %rbx
popq %r14
popq %rbp
retq
callq 0x33baa
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/splicedseq.c
// Function: check_splicedseq
static int check_splicedseq(Splicedseq *ss, GtError *err)
{                       /*0123456789*/
  static char *origseq = "aaccaagtga", *splicedseq = "ccgtg";
  int had_err = 0;
  gt_error_check(err);
  gt_splicedseq_add(ss, 2, 3, origseq + 2);
  gt_splicedseq_add(ss, 6, 8, origseq + 6);
  gt_ensure(strcmp(gt_splicedseq_get(ss), splicedseq) == 0);
  gt_ensure(!gt_splicedseq_pos_is_border(ss, 0));
  gt_ensure(gt_splicedseq_pos_is_border(ss, 1));
  gt_ensure(!gt_splicedseq_pos_is_border(ss, 2));
  gt_ensure(!gt_splicedseq_pos_is_border(ss, 3));
  gt_ensure(!gt_splicedseq_pos_is_border(ss, 4));
  return had_err;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
testq %rsi, %rsi
je 0xdc0de
movq %rbx, %rdi
callq 0x34fea
testb %al, %al
jne 0xdc283
leaq 0x2fc72(%rip), %rcx     # 0x10bd57
movl $0x2, %esi
movl $0x3, %edx
movq %r14, %rdi
callq 0xdbdf5
leaq 0x2fc5d(%rip), %rcx     # 0x10bd5b
movl $0x6, %esi
movl $0x8, %edx
movq %r14, %rdi
callq 0xdbdf5
movq (%r14), %rdi
callq 0x3bb5d
leaq 0x2fc41(%rip), %rsi     # 0x10bd60
movq %rax, %rdi
callq 0xb890
testl %eax, %eax
je 0xdc155
leaq 0x7027(%rip), %rsi      # 0xe3159
leaq 0x2fc3e(%rip), %rdx     # 0x10bd77
leaq 0x2fc26(%rip), %rcx     # 0x10bd66
leaq 0x2fa65(%rip), %r8      # 0x10bbac
movq %rbx, %rdi
movl $0x79, %r9d
jmp 0xdc1f8
movq %r14, %rdi
xorl %esi, %esi
callq 0xdbe85
testb %al, %al
je 0xdc18a
leaq 0x6fef(%rip), %rsi      # 0xe3159
leaq 0x2fc35(%rip), %rdx     # 0x10bda6
leaq 0x2fbee(%rip), %rcx     # 0x10bd66
leaq 0x2fa2d(%rip), %r8      # 0x10bbac
movq %rbx, %rdi
movl $0x7a, %r9d
jmp 0xdc1f8
movl $0x1, %esi
movq %r14, %rdi
callq 0xdbe85
testb %al, %al
je 0xdc1d3
movl $0x2, %esi
movq %r14, %rdi
callq 0xdbe85
testb %al, %al
je 0xdc20c
leaq 0x6fa6(%rip), %rsi      # 0xe3159
leaq 0x2fc33(%rip), %rdx     # 0x10bded
leaq 0x2fba5(%rip), %rcx     # 0x10bd66
leaq 0x2f9e4(%rip), %r8      # 0x10bbac
movq %rbx, %rdi
movl $0x7c, %r9d
jmp 0xdc1f8
leaq 0x6f7f(%rip), %rsi      # 0xe3159
leaq 0x2fbe9(%rip), %rdx     # 0x10bdca
leaq 0x2fb7e(%rip), %rcx     # 0x10bd66
leaq 0x2f9bd(%rip), %r8      # 0x10bbac
movq %rbx, %rdi
movl $0x7b, %r9d
xorl %eax, %eax
callq 0x34f1f
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
addq $0x8, %rsp
popq %rbx
popq %r14
retq
movl $0x3, %esi
movq %r14, %rdi
callq 0xdbe85
testb %al, %al
je 0xdc244
leaq 0x6f35(%rip), %rsi      # 0xe3159
leaq 0x2fbe6(%rip), %rdx     # 0x10be11
leaq 0x2fb34(%rip), %rcx     # 0x10bd66
leaq 0x2f973(%rip), %r8      # 0x10bbac
movq %rbx, %rdi
movl $0x7d, %r9d
jmp 0xdc1f8
movl $0x4, %esi
movq %r14, %rdi
callq 0xdbe85
movl %eax, %ecx
xorl %eax, %eax
testb %cl, %cl
je 0xdc204
leaq 0x6ef9(%rip), %rsi      # 0xe3159
leaq 0x2fbce(%rip), %rdx     # 0x10be35
leaq 0x2faf8(%rip), %rcx     # 0x10bd66
leaq 0x2f937(%rip), %r8      # 0x10bbac
movq %rbx, %rdi
movl $0x7e, %r9d
jmp 0xdc1f8
callq 0x33be3
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/splicedseq.c
// Function: gt_splicedseq_delete
void gt_splicedseq_delete(Splicedseq *ss)
{
  if (!ss) return;
  gt_str_delete(ss->splicedseq);
  gt_array_delete(ss->positionmapping);
  gt_free(ss);
}

// Assembly:
testq %rdi, %rdi
je 0xdc2b7
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x3c87b
movq 0x8(%rbx), %rdi
callq 0x6f768
leaq 0x2f903(%rip), %rsi     # 0x10bbac
movq %rbx, %rdi
movl $0x96, %edx
popq %rbx
jmp 0x35c27
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/external/bzip2-1.0.6/huffman.c
// Function: BZ2_hbAssignCodes
void BZ2_hbAssignCodes ( Int32 *code,
                         UChar *length,
                         Int32 minLen,
                         Int32 maxLen,
                         Int32 alphaSize )
{
   Int32 n, vec, i;

   vec = 0;
   for (n = minLen; n <= maxLen; n++) {
      for (i = 0; i < alphaSize; i++)
         if (length[i] == n) { code[i] = vec; vec++; };
      vec <<= 1;
   }
}

// Assembly:
cmpl %ecx, %edx
jg 0xde0bb
movl %r8d, %eax
xorl %r9d, %r9d
testl %r8d, %r8d
jle 0xde0ad
xorl %r10d, %r10d
movzbl (%rsi,%r10), %r11d
cmpl %r11d, %edx
jne 0xde0a5
movl %r9d, (%rdi,%r10,4)
incl %r9d
incq %r10
cmpq %r10, %rax
jne 0xde094
addl %r9d, %r9d
leal 0x1(%rdx), %r10d
cmpl %ecx, %edx
movl %r10d, %edx
jne 0xde08c
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/external/bzip2-1.0.6/huffman.c
// Function: BZ2_hbCreateDecodeTables
void BZ2_hbCreateDecodeTables ( Int32 *limit,
                                Int32 *base,
                                Int32 *perm,
                                UChar *length,
                                Int32 minLen,
                                Int32 maxLen,
                                Int32 alphaSize )
{
   Int32 pp, i, j, vec;

   pp = 0;
   for (i = minLen; i <= maxLen; i++)
      for (j = 0; j < alphaSize; j++)
         if (length[j] == i) { perm[pp] = j; pp++; };

   for (i = 0; i < BZ_MAX_CODE_LEN; i++) base[i] = 0;
   for (i = 0; i < alphaSize; i++) base[length[i]+1]++;

   for (i = 1; i < BZ_MAX_CODE_LEN; i++) base[i] += base[i-1];

   for (i = 0; i < BZ_MAX_CODE_LEN; i++) limit[i] = 0;
   vec = 0;

   for (i = minLen; i <= maxLen; i++) {
      vec += (base[i+1] - base[i]);
      limit[i] = vec-1;
      vec <<= 1;
   }
   for (i = minLen + 1; i <= maxLen; i++)
      base[i] = ((limit[i-1] + 1) << 1) - base[i];
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
movl 0x20(%rsp), %r10d
movl %r10d, %eax
cmpl %r9d, %r8d
jg 0xde100
xorl %r11d, %r11d
movl %r8d, %ebx
testl %r10d, %r10d
jle 0xde0f6
xorl %r14d, %r14d
movzbl (%rcx,%r14), %ebp
cmpl %ebp, %ebx
jne 0xde0ee
movslq %r11d, %r11
movl %r14d, (%rdx,%r11,4)
incl %r11d
incq %r14
cmpq %r14, %rax
jne 0xde0db
leal 0x1(%rbx), %ebp
cmpl %r9d, %ebx
movl %ebp, %ebx
jne 0xde0d3
xorps %xmm0, %xmm0
movups %xmm0, 0x4c(%rsi)
movups %xmm0, 0x40(%rsi)
movups %xmm0, 0x30(%rsi)
movups %xmm0, 0x20(%rsi)
movups %xmm0, 0x10(%rsi)
movups %xmm0, (%rsi)
testl %r10d, %r10d
jle 0xde133
xorl %edx, %edx
movzbl (%rcx,%rdx), %r10d
incl 0x4(%rsi,%r10,4)
incq %rdx
cmpq %rdx, %rax
jne 0xde121
movl (%rsi), %eax
movl $0x1, %ecx
addl (%rsi,%rcx,4), %eax
movl %eax, (%rsi,%rcx,4)
incq %rcx
cmpq $0x17, %rcx
jne 0xde13a
xorps %xmm0, %xmm0
movups %xmm0, 0x4c(%rdi)
movups %xmm0, 0x40(%rdi)
movups %xmm0, 0x30(%rdi)
movups %xmm0, 0x20(%rdi)
movups %xmm0, 0x10(%rdi)
movups %xmm0, (%rdi)
cmpl %r9d, %r8d
jg 0xde1a6
movslq %r8d, %rcx
leaq (%rsi,%rcx,4), %rax
addq $0x4, %rax
leaq (%rdi,%rcx,4), %rcx
movl %r9d, %edx
subl %r8d, %edx
incl %edx
xorl %r10d, %r10d
xorl %r11d, %r11d
movl (%rax,%r10,4), %ebx
subl -0x4(%rax,%r10,4), %ebx
leal (%rbx,%r11), %ebp
decl %ebp
addl %ebx, %r11d
movl %ebp, (%rcx,%r10,4)
addl %r11d, %r11d
incq %r10
cmpl %r10d, %edx
jne 0xde185
cmpl %r9d, %r8d
jge 0xde1cd
movslq %r8d, %rcx
movslq %r9d, %rax
movl (%rdi,%rcx,4), %edx
addl %edx, %edx
subl 0x4(%rsi,%rcx,4), %edx
addl $0x2, %edx
movl %edx, 0x4(%rsi,%rcx,4)
leaq 0x1(%rcx), %rdx
movq %rdx, %rcx
cmpq %rdx, %rax
jne 0xde1b1
popq %rbx
popq %r14
popq %rbp
retq
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/core/bitpackstringop32.c
// Function: gt_bsGetUInt32
uint32_t
gt_bsGetUInt32(constBitString str, BitOffset offset, unsigned numBits)
{
  GtUword accum = 0;
  unsigned bitsLeft = numBits, bitTop = offset%bitElemBits;
  size_t elemStart = offset/bitElemBits;
  const BitElem *p = str + elemStart;
  gt_assert(str);
#ifndef NDEBUG
  if (numBits > sizeof (accum)*CHAR_BIT)
    fprintf(stderr, "numBits = %u\n", numBits);
#endif
  gt_assert(numBits <= sizeof (accum)*CHAR_BIT);
  if (bitTop)
  {
    GtUword mask;
    unsigned bits2Read = GT_MIN(bitElemBits - bitTop, bitsLeft);
    unsigned unreadRightBits = (bitElemBits - bitTop - bits2Read);
    mask = (~((~(GtUword)0) << bits2Read)) << unreadRightBits;
    accum = ((*p++) & mask) >> unreadRightBits;
    bitsLeft -= bits2Read;
  }
  /* get bits from intervening elems */
  while (bitsLeft >= bitElemBits)
  {
    accum = accum << bitElemBits | (*p++);
    bitsLeft -= bitElemBits;
  }
  /* get bits from last elem */
  if (bitsLeft)
  {
    accum = accum << bitsLeft |
      (((*p) & ((~(GtUword)0)<<(bitElemBits - bitsLeft)))
       >>(bitElemBits - bitsLeft));
  }
  return accum;
}

// Assembly:
pushq %rax
testq %rdi, %rdi
je 0xde278
cmpl $0x41, %edx
jae 0xde27d
movl %esi, %eax
andl $0x7, %eax
shrq $0x3, %rsi
addq %rsi, %rdi
testl %eax, %eax
je 0xde22d
movl $0x8, %esi
subl %eax, %esi
cmpl %edx, %esi
movl %edx, %r8d
cmovbl %esi, %r8d
subl %r8d, %esi
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
movl %r8d, %ecx
shll %cl, %eax
notl %eax
movl %esi, %ecx
shlq %cl, %rax
movzbl (%rdi), %ecx
incq %rdi
andl %ecx, %eax
movl %esi, %ecx
shrq %cl, %rax
subl %r8d, %edx
jmp 0xde22f
xorl %eax, %eax
cmpl $0x8, %edx
jb 0xde25a
leal -0x8(%rdx), %ecx
shrl $0x3, %ecx
incl %ecx
movq %rdi, %rsi
movq %rax, %r8
shlq $0x8, %r8
movzbl (%rsi), %eax
incq %rsi
orq %r8, %rax
addl $-0x8, %edx
cmpl $0x7, %edx
ja 0xde23f
addq %rcx, %rdi
testl %edx, %edx
je 0xde276
movl %edx, %ecx
shlq %cl, %rax
movzbl (%rdi), %esi
movb $0x8, %cl
subb %dl, %cl
shrq %cl, %rsi
shlq %cl, %rsi
shrq %cl, %rsi
orq %rsi, %rax
popq %rcx
retq
callq 0x33cf0
movl %edx, %edi
callq 0x33ca6
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/core/bitpackstringop32.c
// Function: gt_bsStoreUInt32
void
gt_bsStoreUInt32(BitString str, BitOffset offset,
                 unsigned numBits, uint32_t val)
{
  unsigned bitsLeft = numBits,
    bitTop = offset%bitElemBits;
  size_t elemStart = offset/bitElemBits;
  BitElem *p = str + elemStart;
  gt_assert(str);
  gt_assert(numBits <= sizeof (val)*CHAR_BIT);
  /* set bits of first element, accounting for bits to be preserved */
  if (bitTop)
  {
    GtUword mask = ~(GtUword)0;
    if (bitElemBits < (sizeof (GtUword)*CHAR_BIT))
    {
      mask <<= bitElemBits;
    }
    else
    {
      mask = 0;
    }
    mask = (~mask) >> bitTop;
    if (numBits < bitElemBits - bitTop)
    {
      unsigned backShift = bitElemBits - numBits - bitTop;
      mask &= ~(GtUword)0 << backShift;
      *p = (*p & ~mask) | ((val << backShift) & mask);
      /* TODO: try wether  r = a ^ ((a ^ b) & mask) is faster, see below */
      return;
    }
    else
    {
      bitsLeft -= bitElemBits - bitTop;
      *p = (*p & ~mask) | ((val >> bitsLeft) & mask);
      ++p;
    }
  }
  /* set bits for intervening elems */
  while (bitsLeft >= bitElemBits)
  {
    bitsLeft -= bitElemBits;
    *p++ = val >> bitsLeft;
  }
  /* set bits for last elem */
  if (bitsLeft)
  {
    GtUword mask =
      ((~(GtUword)0)<<(bitElemBits - bitsLeft));
    if (bitElemBits < (sizeof (GtUword)*CHAR_BIT))
      mask &= (~(~(GtUword)0<<bitElemBits));
    *p = (*p & ~mask) | ((val << (bitElemBits - bitsLeft)) & mask);
  }
}

// Assembly:
pushq %rax
testq %rdi, %rdi
je 0xde34e
cmpl $0x21, %edx
jae 0xde353
movl %ecx, %eax
movq %rsi, %rcx
movl %ecx, %r9d
andl $0x7, %r9d
shrq $0x3, %rsi
addq %rsi, %rdi
testl %r9d, %r9d
je 0xde2ee
andl $0x7, %ecx
movl $0xff, %r8d
shrq %cl, %r8
movl $0x8, %r10d
subl %r9d, %r10d
movl %edx, %esi
subl %r10d, %esi
jae 0xde2f2
addl %edx, %r9d
movb $0x8, %cl
subb %r9b, %cl
movq $-0x1, %rdx
shlq %cl, %rdx
andl %edx, %r8d
movzbl (%rdi), %edx
shll %cl, %eax
xorl %edx, %eax
andl %r8d, %eax
xorl %edx, %eax
jmp 0xde34a
movl %edx, %esi
jmp 0xde315
movq $-0x100, %rdx
sarq %cl, %rdx
movzbl (%rdi), %ecx
andl %ecx, %edx
movl %eax, %r9d
movl %esi, %ecx
shrl %cl, %r9d
andl %r9d, %r8d
orl %edx, %r8d
movb %r8b, (%rdi)
incq %rdi
cmpl $0x8, %esi
jb 0xde32d
addl $-0x8, %esi
movl %eax, %edx
movl %esi, %ecx
shrl %cl, %edx
movb %dl, (%rdi)
incq %rdi
cmpl $0x7, %esi
ja 0xde31a
testl %esi, %esi
je 0xde34c
movb $0x8, %cl
subb %sil, %cl
movl $0xfe, %edx
shrl %cl, %edx
shll %cl, %edx
movzbl (%rdi), %esi
shll %cl, %eax
xorl %esi, %eax
andl %edx, %eax
xorl %esi, %eax
movb %al, (%rdi)
popq %rax
retq
callq 0x33d5e
callq 0x33d27
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/core/md5_fingerprint.c
// Function: gt_md5_fingerprint
char* gt_md5_fingerprint(const char *sequence, GtUword seqlen)
{
  unsigned char output[16];
  char buf[64];
  char *fingerprint;
  GtMD5Encoder *enc;
  GtUword i, pos = 0;

  enc = gt_md5_encoder_new();
  for (i = 0; i < seqlen; i++) {
    if (pos == 64) {
      gt_md5_encoder_add_block(enc, buf, 64);
      pos = 0;
    }
    buf[pos++] = toupper(sequence[i]);
  }
  gt_md5_encoder_add_block(enc, buf, pos);
  fingerprint = gt_calloc(33, sizeof (char));
  gt_md5_encoder_finish(enc, output, fingerprint);

  gt_md5_encoder_delete(enc);
  return fingerprint;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x58, %rsp
movq %rsi, %r14
movq %rdi, %r15
callq 0xd728c
movq %rax, %rbx
testq %r14, %r14
je 0xdf38e
xorl %ebp, %ebp
leaq 0x10(%rsp), %r12
xorl %r13d, %r13d
cmpq $0x40, %r13
jne 0xdf36c
movl $0x40, %edx
movq %rbx, %rdi
movq %r12, %rsi
callq 0xd72fb
xorl %r13d, %r13d
callq 0xb0b0
movq (%rax), %rax
movsbq (%r15,%rbp), %rcx
movb (%rax,%rcx,4), %al
movb %al, 0x10(%rsp,%r13)
incq %r13
incq %rbp
cmpq %rbp, %r14
jne 0xdf353
jmp 0xdf391
xorl %r13d, %r13d
leaq 0x10(%rsp), %rsi
movq %rbx, %rdi
movq %r13, %rdx
callq 0xd72fb
leaq 0x2ce6a(%rip), %rdx     # 0x10c212
movl $0x21, %edi
movl $0x1, %esi
movl $0x2b, %ecx
callq 0x359a6
movq %rax, %r14
movq %rsp, %rsi
movq %rbx, %rdi
movq %rax, %rdx
callq 0xd76c5
movq %rbx, %rdi
callq 0xd7876
movq %r14, %rax
addq $0x58, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/csa_gene.c
// Function: gt_csa_gene_new
GtCSAGene* gt_csa_gene_new(GtCSASpliceForm *splice_form)
{
  GtCSAGene *gene;
  gt_assert(splice_form);
  gene = gt_malloc(sizeof *gene);
  gene->splice_forms = gt_array_new(sizeof (GtCSASpliceForm*));
  gt_array_add(gene->splice_forms, splice_form);
  return gene;
}

// Assembly:
pushq %rbx
subq $0x10, %rsp
movq %rdi, 0x8(%rsp)
testq %rdi, %rdi
je 0xdf5cc
leaq 0x2ccf4(%rip), %rsi     # 0x10c286
movl $0x8, %edi
movl $0x1d, %edx
callq 0x35862
movq %rax, %rbx
movl $0x8, %edi
callq 0x6ef7c
movq %rax, (%rbx)
leaq 0x8(%rsp), %rsi
movl $0x8, %edx
movq %rax, %rdi
callq 0x6f240
movq %rbx, %rax
addq $0x10, %rsp
popq %rbx
retq
callq 0x342b2
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/csa_gene.c
// Function: gt_csa_gene_delete
void gt_csa_gene_delete(GtCSAGene *gene)
{
  GtUword i;
  if (!gene) return;
  for (i = 0; i < gt_array_size(gene->splice_forms); i++) {
    gt_csa_splice_form_delete(*(GtCSASpliceForm**)
                              gt_array_get(gene->splice_forms, i));
  }
  gt_array_delete(gene->splice_forms);
  gt_free(gene);
}

// Assembly:
testq %rdi, %rdi
je 0xdf633
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x6f310
testq %rax, %rax
je 0xdf610
xorl %r14d, %r14d
movq (%rbx), %rdi
movq %r14, %rsi
callq 0x6f037
movq (%rax), %rdi
callq 0xdf7e0
incq %r14
movq (%rbx), %rdi
callq 0x6f310
cmpq %rax, %r14
jb 0xdf5ed
movq (%rbx), %rdi
callq 0x6f768
leaq 0x2cc67(%rip), %rsi     # 0x10c286
movq %rbx, %rdi
movl $0x2c, %edx
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x35c27
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/csa_gene.c
// Function: gt_csa_gene_add_splice_form
void gt_csa_gene_add_splice_form(GtCSAGene *gene, GtCSASpliceForm *splice_form)
{
  gt_assert(gene && splice_form);
  gt_assert(gt_csa_splice_form_strand(*(GtCSASpliceForm**)
                                gt_array_get(gene->splice_forms, 0)) ==
         gt_csa_splice_form_strand(splice_form));
  gt_array_add(gene->splice_forms, splice_form);
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
subq $0x10, %rsp
movq %rsi, 0x8(%rsp)
testq %rdi, %rdi
je 0xdf68c
movq %rsi, %r14
testq %rsi, %rsi
je 0xdf68c
movq %rdi, %rbx
movq (%rdi), %rdi
xorl %esi, %esi
callq 0x6f037
movq (%rax), %rdi
callq 0xdf889
movl %eax, %ebp
movq %r14, %rdi
callq 0xdf889
cmpl %eax, %ebp
jne 0xdf691
movq (%rbx), %rdi
leaq 0x8(%rsp), %rsi
movl $0x8, %edx
callq 0x6f240
addq $0x10, %rsp
popq %rbx
popq %r14
popq %rbp
retq
callq 0x342e9
callq 0x34320
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/csa_gene.c
// Function: gt_csa_gene_genomic_range
GtRange gt_csa_gene_genomic_range(const GtCSAGene *gene)
{
  GtRange gene_range, tmp_range;
  GtUword i;
  gt_assert(gene);
  gene_range.start = ~0UL;
  gene_range.end = 0UL;
  for (i = 0; i < gt_array_size(gene->splice_forms); i++) {
    tmp_range = gt_csa_splice_form_genomic_range(*(GtCSASpliceForm**)
                                              gt_array_get(gene->splice_forms,
                                                           i));
    if (tmp_range.start < gene_range.start)
      gene_range.start = tmp_range.start;
    if (tmp_range.end > gene_range.end)
      gene_range.end = tmp_range.end;
  }
  return gene_range;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xdf72e
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x6f310
movq $-0x1, %r14
xorl %r15d, %r15d
testq %rax, %rax
je 0xdf71c
xorl %r12d, %r12d
movq (%rbx), %rdi
movq %r12, %rsi
callq 0x6f037
movq (%rax), %rdi
callq 0xdf8d9
cmpq %r14, %rax
cmovbq %rax, %r14
cmpq %r15, %rdx
cmovaq %rdx, %r15
incq %r12
movq (%rbx), %rdi
callq 0x6f310
cmpq %rax, %r12
jb 0xdf6eb
movq %r14, %rax
movq %r15, %rdx
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
callq 0x343c5
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/csa_gene.c
// Function: gt_csa_gene_get_representative
void* gt_csa_gene_get_representative(const GtCSAGene *gene)
{
  gt_assert(gene);
  return gt_csa_splice_form_get_representative(*(GtCSASpliceForm**)
                                            gt_array_get(gene->splice_forms,
                                                         0));
}

// Assembly:
pushq %rax
testq %rdi, %rdi
je 0xdf76a
movq (%rdi), %rdi
xorl %esi, %esi
callq 0x6f037
movq (%rax), %rdi
popq %rax
jmp 0xdf94c
callq 0x34433
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/csa_splice_form.c
// Function: gt_csa_splice_form_new
GtCSASpliceForm* gt_csa_splice_form_new(void *spliced_alignment,
                                   GtGetGenomicRangeFunc get_genomic_range,
                                   GtGetStrandFunc get_strand)
{
  GtCSASpliceForm *splice_form;
  gt_assert(spliced_alignment && get_strand);
  splice_form = gt_malloc(sizeof (*splice_form));
  splice_form->spliced_alignments = gt_array_new(sizeof (void*));
  gt_array_add(splice_form->spliced_alignments, spliced_alignment);
  splice_form->get_genomic_range = get_genomic_range;
  splice_form->get_strand = get_strand;
  return splice_form;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
subq $0x10, %rsp
movq %rdi, 0x8(%rsp)
testq %rdi, %rdi
je 0xdf7db
movq %rdx, %rbx
testq %rdx, %rdx
je 0xdf7db
movq %rsi, %r14
leaq 0x2cc76(%rip), %rsi     # 0x10c40b
movl $0x18, %edi
movl $0x22, %edx
callq 0x35862
movq %rax, %r15
movl $0x8, %edi
callq 0x6ef7c
movq %rax, (%r15)
leaq 0x8(%rsp), %rsi
movl $0x8, %edx
movq %rax, %rdi
callq 0x6f240
movq %r14, 0x8(%r15)
movq %rbx, 0x10(%r15)
movq %r15, %rax
addq $0x10, %rsp
popq %rbx
popq %r14
popq %r15
retq
callq 0x3446a
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/csa_splice_form.c
// Function: gt_csa_splice_form_add_sa
void gt_csa_splice_form_add_sa(GtCSASpliceForm *splice_form,
                               void *spliced_alignment)
{
  gt_assert(splice_form);
  gt_assert(csa_splice_form_start(splice_form) <=
         splice_form->get_genomic_range(spliced_alignment).start);
  gt_assert(gt_csa_splice_form_strand(splice_form) ==
         splice_form->get_strand(spliced_alignment));
  gt_array_add(splice_form->spliced_alignments, spliced_alignment);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, (%rsp)
testq %rdi, %rdi
je 0xdf87a
movq %rsi, %r14
movq %rdi, %rbx
movq (%rdi), %rdi
movq 0x8(%rbx), %r15
xorl %esi, %esi
callq 0x6f037
movq (%rax), %rdi
callq *%r15
movq %rax, %r15
movq %r14, %rdi
callq *0x8(%rbx)
cmpq %rax, %r15
ja 0xdf87f
movq (%rbx), %rdi
movq 0x10(%rbx), %r15
xorl %esi, %esi
callq 0x6f037
movq (%rax), %rdi
callq *%r15
movl %eax, %ebp
movq %r14, %rdi
callq *0x10(%rbx)
cmpl %eax, %ebp
jne 0xdf884
movq (%rbx), %rdi
movq %rsp, %rsi
movl $0x8, %edx
callq 0x6f240
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
callq 0x3450f
callq 0x344d8
callq 0x344a1
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/csa_splice_form.c
// Function: gt_csa_splice_form_strand
GtStrand gt_csa_splice_form_strand(const GtCSASpliceForm *splice_form)
{
  gt_assert(splice_form);
  return splice_form->get_strand(*(void**)
                                 gt_array_get(splice_form->spliced_alignments,
                                              0));
}

// Assembly:
pushq %rbx
testq %rdi, %rdi
je 0xdf8a9
movq (%rdi), %rax
movq 0x10(%rdi), %rbx
movq %rax, %rdi
xorl %esi, %esi
callq 0x6f037
movq (%rax), %rdi
movq %rbx, %rax
popq %rbx
jmpq *%rax
callq 0x34546
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/csa_splice_form.c
// Function: gt_csa_splice_form_genomic_range
GtRange gt_csa_splice_form_genomic_range(const GtCSASpliceForm *splice_form)
{
  GtRange splice_form_range, tmp_range;
  GtUword i;
  gt_assert(splice_form);
  splice_form_range.start = ~0UL;
  splice_form_range.end = 0UL;
  for (i = 0; i < gt_array_size(splice_form->spliced_alignments); i++) {
    tmp_range = splice_form->get_genomic_range(*(void**)
                                               gt_array_get(splice_form
                                                         ->spliced_alignments,
                                                         i));
    if (tmp_range.start < splice_form_range.start)
      splice_form_range.start = tmp_range.start;
    if (tmp_range.end > splice_form_range.end)
      splice_form_range.end = tmp_range.end;
  }
  return splice_form_range;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
testq %rdi, %rdi
je 0xdf947
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x6f310
movq $-0x1, %r14
xorl %r15d, %r15d
testq %rax, %rax
je 0xdf937
xorl %r12d, %r12d
movq (%rbx), %rdi
movq 0x8(%rbx), %r13
movq %r12, %rsi
callq 0x6f037
movq (%rax), %rdi
callq *%r13
cmpq %r14, %rax
cmovbq %rax, %r14
cmpq %r15, %rdx
cmovaq %rdx, %r15
incq %r12
movq (%rbx), %rdi
callq 0x6f310
cmpq %rax, %r12
jb 0xdf904
movq %r14, %rax
movq %r15, %rdx
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
callq 0x345eb
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/csa_variable_strands.c
// Function: store_splice_form
static void store_splice_form(GtArray *spliced_alignments_in_form,
                              const void *set_of_sas,
                              GT_UNUSED GtUword number_of_sas,
                              size_t size_of_sa, void *data)
{
  StoreSpliceFormInfo *info = data;
  GtCSASpliceForm *splice_form;
  GtUword i, sa;
  gt_assert(info);
  gt_assert(spliced_alignments_in_form &&
         gt_array_size(spliced_alignments_in_form));
  sa = *(GtUword*) gt_array_get(spliced_alignments_in_form, 0);
  splice_form = gt_csa_splice_form_new((char*) set_of_sas + sa * size_of_sa,
                                    info->get_genomic_range, info->get_strand);
  for (i = 1; i < gt_array_size(spliced_alignments_in_form); i++) {
    sa = *(GtUword*) gt_array_get(spliced_alignments_in_form, i);
    gt_csa_splice_form_add_sa(splice_form,
                              (char*) set_of_sas + sa * size_of_sa);
  }
  gt_array_add(info->splice_forms, splice_form);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
testq %r8, %r8
je 0xdfc55
movq %rdi, %r12
testq %rdi, %rdi
je 0xdfc50
movq %r8, %rbx
movq %rcx, %r14
movq %rsi, %r15
movq %r12, %rdi
callq 0x6f310
testq %rax, %rax
je 0xdfc50
movq %r12, %rdi
xorl %esi, %esi
callq 0x6f037
movq (%rax), %rdi
imulq %r14, %rdi
addq %r15, %rdi
movq 0x8(%rbx), %rsi
movq 0x10(%rbx), %rdx
callq 0xdf770
movq %rax, %r13
movq %rax, (%rsp)
movq %r12, %rdi
callq 0x6f310
cmpq $0x2, %rax
jb 0xdfc31
movl $0x1, %ebp
movq %r12, %rdi
movq %rbp, %rsi
callq 0x6f037
movq (%rax), %rsi
imulq %r14, %rsi
addq %r15, %rsi
movq %r13, %rdi
callq 0xdf807
incq %rbp
movq %r12, %rdi
callq 0x6f310
cmpq %rax, %rbp
jb 0xdfc04
movq (%rbx), %rdi
movq %rsp, %rsi
movl $0x8, %edx
callq 0x6f240
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x3476c
callq 0x347a3
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/consensus_sa.c
// Function: extract_strand
static GtStrand extract_strand(const ConsensusSA *csa, GtUword sa)
{
  GtStrand strand;
  gt_assert(csa && csa->set_of_sas && sa < csa->number_of_sas);
  strand = csa->get_strand((char*) csa->set_of_sas + csa->size_of_sa * sa);
  /* XXX */
  gt_assert(strand == GT_STRAND_FORWARD || strand == GT_STRAND_REVERSE);
  return strand;
}

// Assembly:
pushq %rax
movq %rdi, %rax
movq (%rdi), %rdi
testq %rdi, %rdi
je 0xe07d1
cmpq %rsi, 0x8(%rax)
jbe 0xe07d1
imulq 0x10(%rax), %rsi
addq %rsi, %rdi
callq *0x20(%rax)
cmpl $0x2, %eax
jae 0xe07d6
popq %rcx
retq
callq 0x34a15
callq 0x349de
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/consensus_sa.c
// Function: extract_exons
static void extract_exons(const ConsensusSA *csa, GtArray *exon_ranges,
                          GtUword sa)
{
  gt_assert(csa && exon_ranges && csa->set_of_sas && sa < csa->number_of_sas);
  csa->get_exons(exon_ranges, (char*) csa->set_of_sas + csa->size_of_sa * sa);
  gt_assert(gt_array_size(exon_ranges));
  gt_assert(gt_ranges_are_sorted_and_do_not_overlap(exon_ranges));
}

// Assembly:
pushq %rbx
testq %rsi, %rsi
je 0xe081e
movq %rsi, %rbx
movq %rdi, %rax
movq (%rdi), %rsi
testq %rsi, %rsi
je 0xe081e
cmpq %rdx, 0x8(%rax)
jbe 0xe081e
imulq 0x10(%rax), %rdx
addq %rdx, %rsi
movq %rbx, %rdi
callq *0x28(%rax)
movq %rbx, %rdi
callq 0x6f310
testq %rax, %rax
je 0xe0823
movq %rbx, %rdi
callq 0x7eb8d
testb %al, %al
je 0xe0828
popq %rbx
retq
callq 0x34aba
callq 0x34a83
callq 0x34a4c
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/consensus_sa.c
// Function: compute_left_or_right
static void compute_left_or_right(GtBittab **left_or_right,
                                  const ConsensusSA *csa,
                                  bool (*cmp_func) (const ConsensusSA *csa,
                                                    GtUword sa_1,
                                                    GtUword sa_2))
{
  GtUword sa, sa_1;
  gt_assert(csa && left_or_right && *left_or_right);
  for (sa = 0; sa < csa->number_of_sas; sa++) {
    for (sa_1 = 0; sa_1 < csa->number_of_sas; sa_1++) {
      if (cmp_func(csa, sa, sa_1) && compatible(csa, sa, sa_1))
        gt_bittab_set_bit(left_or_right[sa], sa_1);
    }
  }
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
testq %rdi, %rdi
je 0xe08ef
movq %rdi, %r15
cmpq $0x0, (%rdi)
je 0xe08ef
movq %rsi, %r14
cmpq $0x0, 0x8(%rsi)
je 0xe08e5
movq %rdx, %rbx
xorl %r12d, %r12d
xorl %r13d, %r13d
movq %r14, %rdi
movq %r12, %rsi
movq %r13, %rdx
callq *%rbx
testb %al, %al
je 0xe08d1
movq %r14, %rdi
movq %r12, %rsi
movq %r13, %rdx
callq 0xe04b4
testb %al, %al
je 0xe08d1
movq (%r15,%r12,8), %rdi
movq %r13, %rsi
callq 0x70d40
incq %r13
movq 0x8(%r14), %rax
cmpq %rax, %r13
jb 0xe08a4
incq %r12
cmpq %rax, %r12
jb 0xe08a1
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
callq 0x34b5f
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/extended/consensus_sa.c
// Function: is_right_of
static bool is_right_of(const ConsensusSA *csa,
                        GtUword sa_1, GtUword sa_2)
{
  GtRange range_sa_1, range_sa_2;
  gt_assert(csa);
  range_sa_1 = extract_genomic_range(csa, sa_1);
  range_sa_2 = extract_genomic_range(csa, sa_2);
  if (range_sa_1.start  > range_sa_2.start && range_sa_1.end > range_sa_2.end)
    return true;
  return false;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xe0937
movq %rdx, %rbx
movq %rdi, %r14
callq 0xe0492
movq %rax, %r15
movq %rdx, %r12
movq %r14, %rdi
movq %rbx, %rsi
callq 0xe0492
cmpq %rax, %r15
seta %cl
cmpq %rdx, %r12
seta %al
andb %cl, %al
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
callq 0x34b98
// File: /workspace/github_c_makefile_star2_O3/samtools[P]htslib/test/test-regidx.c
// Function: main.cold.1
static void usage(void)
{
    fprintf(stderr, "Usage: test-regidx [OPTIONS]\n");
    fprintf(stderr, "Options:\n");
    fprintf(stderr, "   -h, --help          this help message\n");
    fprintf(stderr, "   -s, --seed <int>    random seed\n");
    fprintf(stderr, "   -v, --verbose       increase verbosity by giving multiple times\n");

    exit(1);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq 0xaf5ed(%rip), %r14     # 0xb3fd8
movq (%r14), %rcx
leaq 0x8dc81(%rip), %rdi     # 0x92676
pushq $0x1d
popq %rsi
pushq $0x1
popq %rbx
movq %rbx, %rdx
callq 0x49b0
movq (%r14), %rcx
leaq 0x8dc87(%rip), %rdi     # 0x92694
pushq $0x9
popq %rsi
movq %rbx, %rdx
callq 0x49b0
movq (%r14), %rcx
leaq 0x8dc7c(%rip), %rdi     # 0x9269e
pushq $0x29
popq %rsi
movq %rbx, %rdx
callq 0x49b0
movq (%r14), %rcx
leaq 0x8dc91(%rip), %rdi     # 0x926c8
pushq $0x23
popq %rsi
movq %rbx, %rdx
callq 0x49b0
movq (%r14), %rcx
leaq 0x8dca0(%rip), %rdi     # 0x926ec
pushq $0x43
popq %rsi
movq %rbx, %rdx
callq 0x49b0
pushq $0x1
popq %rdi
callq 0x45f0
// File: /workspace/github_c_makefile_star2_O3/samtools[P]htslib/test/test-regidx.c
// Function: custom_parse
int custom_parse(const char *line, char **chr_beg, char **chr_end, hts_pos_t *beg, hts_pos_t *end, void *payload, void *usr)
{
    // Use the standard parser for CHROM,FROM,TO
    int i, ret = regidx_parse_tab(line,chr_beg,chr_end,beg,end,NULL,NULL);
    if ( ret!=0 ) return ret;

    // Skip the fields that were parsed above
    char *ss = (char*) line;
    while ( *ss && isspace_c(*ss) ) ss++;
    for (i=0; i<3; i++)
    {
        while ( *ss && !isspace_c(*ss) ) ss++;
        if ( !*ss ) return -2;  // wrong number of fields
        while ( *ss && isspace_c(*ss) ) ss++;
    }
    if ( !*ss ) return -2;

    // Parse the payload
    char *se = ss;
    while ( *se && !isspace_c(*se) ) se++;
    char **dat = (char**) payload;
    *dat = (char*) malloc(se-ss+1);
    memcpy(*dat,ss,se-ss+1);
    (*dat)[se-ss] = 0;
    return 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r9, %rbx
movq %rdi, %r14
movq $0x0, (%rsp)
xorl %r9d, %r9d
callq 0x9018
movl %eax, %ebp
testl %eax, %eax
je 0x5ea4
movl %ebp, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movb (%r14), %r15b
testb %r15b, %r15b
je 0x5ecb
callq 0x4520
movq (%rax), %rax
movzbl %r15b, %ecx
testb $0x20, 0x1(%rax,%rcx,2)
je 0x5ece
movb 0x1(%r14), %r15b
incq %r14
testb %r15b, %r15b
jne 0x5eb4
xorl %r15d, %r15d
movl $0xfffffffe, %ebp       # imm = 0xFFFFFFFE
testb %r15b, %r15b
je 0x5e93
callq 0x4520
movq (%rax), %rax
xorl %edx, %edx
movl %r15d, %ecx
movzbl %r15b, %esi
testb $0x20, 0x1(%rax,%rsi,2)
jne 0x5f07
movzbl 0x1(%r14), %ecx
testq %rcx, %rcx
je 0x5e93
incq %r14
testb $0x20, 0x1(%rax,%rcx,2)
je 0x5ef0
movl %ecx, %r15d
movzbl %r15b, %esi
testb $0x20, 0x1(%rax,%rsi,2)
je 0x5f2e
incq %r14
movzbl (%r14), %ecx
testq %rcx, %rcx
je 0x5f37
incq %r14
testb $0x20, 0x1(%rax,%rcx,2)
jne 0x5f15
decq %r14
movl %ecx, %r15d
incl %edx
cmpl $0x3, %edx
jne 0x5f47
jmp 0x5f51
incl %edx
cmpl $0x3, %edx
je 0x5e93
xorl %ecx, %ecx
xorl %r15d, %r15d
testb %r15b, %r15b
jne 0x5ee5
jmp 0x5e93
testb %cl, %cl
je 0x5e93
movq %r14, %r13
movzbl %cl, %ecx
testb $0x20, 0x1(%rax,%rcx,2)
jne 0x5f71
movb 0x1(%r13), %cl
incq %r13
testb %cl, %cl
jne 0x5f5c
subq %r14, %r13
leaq 0x1(%r13), %r15
movq %r15, %rdi
callq 0x4690
movq %rax, %r12
movq %rax, (%rbx)
movq %rax, %rdi
movq %r14, %rsi
movq %r15, %rdx
callq 0x43c0
movb $0x0, (%r12,%r13)
xorl %ebp, %ebp
jmp 0x5e93
// File: /workspace/github_c_makefile_star2_O3/pahihu[P]mixal/asm.c
// Function: asm_store_field
void asm_store_field(Address address, unsigned L, unsigned R, Cell cell)
{
    // assert(address < memory_size);
    if (VERBOSE) {
        char temp[16];
        unparse_cell(temp, cell, false);
        printf("%s(%u,%u): %s\n", address_to_string(address), L, R, temp);
    }
    memory_store(address, set_field(cell, make_field_spec(L, R), memory_fetch(address)));
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x10, %rsp
movq %rcx, %r14
movl %edx, %ebp
movl %esi, %r15d
movl %edi, %ebx
leaq 0xd6a6(%rip), %rax      # 0x10ce0
cmpl $0x0, (%rax)
je 0x366f
movq %rsp, %r12
movq %r12, %rdi
movq %r14, %rsi
xorl %edx, %edx
callq 0x3a4f
movl %ebx, %edi
callq 0x3fa3
leaq 0x59fd(%rip), %rdi      # 0x905a
movq %rax, %rsi
movl %r15d, %edx
movl %ebp, %ecx
movq %r12, %r8
xorl %eax, %eax
callq 0x3120
movl %r15d, %edi
movl %ebp, %esi
callq 0x382a
movl %eax, %ebp
movl %ebx, %edi
callq 0x6cad
movq %r14, %rdi
movl %ebp, %esi
movq %rax, %rdx
callq 0x38b6
movl %ebx, %edi
movq %rax, %rsi
callq 0x6d25
addq $0x10, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O3/pahihu[P]mixal/asm.c
// Function: assemble
void assemble(Cell cell)
{
    if (VERBOSE) {
        char temp[16];
        unparse_cell(temp, cell, true);
        printf("%s: %s  %s\n", address_to_string(here), temp, current_line);
    }
    // if (here < memory_size)
    //	memory[here] = cell;
    // else
	//  error("Address out of range");
	memory_store(here, cell);
    ++here;
}

// Assembly:
pushq %r14
pushq %rbx
subq $0x18, %rsp
movq %rdi, %rbx
leaq 0xd629(%rip), %rax      # 0x10ce0
cmpl $0x0, (%rax)
je 0x36f5
movq %rsp, %r14
movq %r14, %rdi
movq %rbx, %rsi
movl $0x1, %edx
callq 0x3a4f
movl 0xc05f(%rip), %edi      # 0xf734
callq 0x3fa3
leaq 0x5988(%rip), %rdi      # 0x9069
leaq 0xc488(%rip), %rcx      # 0xfb70
movq %rax, %rsi
movq %r14, %rdx
xorl %eax, %eax
callq 0x3120
movl 0xc039(%rip), %edi      # 0xf734
movq %rbx, %rsi
callq 0x6d25
incl 0xc02b(%rip)            # 0xf734
addq $0x18, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_c_makefile_star2_O3/pahihu[P]mixal/cell.c
// Function: field
Cell field(Byte F, Cell cell)
{
    if (bad_field[F])
        error("Bad field spec: %02o", F);
    if (F < 8)      /* if F is of the form (0:R), retain the sign of -cell- */
        return ((cell & mask[F]) >> shift[F]) | sign_bit(cell);
    else
        return (cell & mask[F]) >> shift[F];
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
movq %rsi, %rbx
movl %edi, %ebp
movl %edi, %r14d
leaq 0xbf60(%rip), %rax      # 0xf740
cmpl $0x0, (%rax,%r14,4)
je 0x37f7
leaq 0x5930(%rip), %rdi      # 0x911e
movl %ebp, %esi
xorl %eax, %eax
callq 0x5bec
leaq 0xc042(%rip), %rax      # 0xf840
movq (%rax,%r14,8), %rdx
andq %rbx, %rdx
leaq 0xc234(%rip), %rax      # 0xfa40
movb (%rax,%r14,4), %cl
sarq %cl, %rdx
andl $0x40000000, %ebx       # imm = 0x40000000
xorl %eax, %eax
cmpl $0x8, %ebp
cmovbq %rbx, %rax
orq %rdx, %rax
popq %rbx
popq %r14
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O3/pahihu[P]mixal/cell.c
// Function: set_field
Cell set_field(Cell value, Byte F, Cell into)
{
    long m = mask[F];
    if (bad_field[F])
        error("Bad field spec: %02o", F);
    if (F < 8)      /* if F is of the form (0:R), use the sign of -value- */
        return (into & ~m & ~the_sign_bit) | ((value << shift[F]) & m) | sign_bit(value);
    else
        return (into & ~m) | ((value << shift[F]) & m);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movq %rdx, %r14
movl %esi, %ebp
movq %rdi, %rbx
movl %esi, %r12d
leaq 0xbf70(%rip), %rax      # 0xf840
movq (%rax,%r12,8), %r15
leaq 0xbe65(%rip), %rax      # 0xf740
cmpl $0x0, (%rax,%r12,4)
je 0x38f2
leaq 0x5835(%rip), %rdi      # 0x911e
movl %ebp, %esi
xorl %eax, %eax
callq 0x5bec
movq %r15, %rax
notq %rax
cmpl $0x7, %ebp
ja 0x3926
andq %rax, %r14
andq $-0x40000001, %r14      # imm = 0xBFFFFFFF
leaq 0xc132(%rip), %rax      # 0xfa40
movb (%rax,%r12,4), %cl
movq %rbx, %rax
shlq %cl, %rax
andq %r15, %rax
andl $0x40000000, %ebx       # imm = 0x40000000
orq %r14, %rbx
jmp 0x393a
leaq 0xc113(%rip), %rcx      # 0xfa40
movb (%rcx,%r12,4), %cl
shlq %cl, %rbx
andq %r14, %rax
andq %r15, %rbx
orq %rax, %rbx
movq %rbx, %rax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O3/pahihu[P]mixal/cell.c
// Function: precompute_field_data
void precompute_field_data(void)
{
    unsigned L, R;
    for (L = 0; L < 8; ++L)
        for (R = 0; R < 8; ++R) {
            unsigned F = 8 * L + R;
            bad_field[F] = R < L || 5 < R;
            if (bad_field[F])
                shift[F] = 0, mask[F] = 0;
            else {
                unsigned width = R - (L == 0 ? 1 : L) + 1;
                shift[F] = 6 * (5 - R);
                mask[F] = ((1L << (6 * width)) - 1) << shift[F];
            } 
        }
}

// Assembly:
leaq 0xc0f0(%rip), %rsi      # 0xfa40
leaq 0xbee9(%rip), %rdi      # 0xf840
leaq 0xbde2(%rip), %r8       # 0xf740
xorl %r9d, %r9d
cmpq $0x1, %r9
movq %r9, %rax
adcq $0x0, %rax
addq %rax, %rax
leaq (%rax,%rax,2), %rcx
movl $0x6, %eax
subq %rcx, %rax
movl $0x1e, %edx
xorl %r10d, %r10d
cmpq %r9, %r10
setb %cl
cmpq $0x6, %r10
setae %r11b
orb %cl, %r11b
movzbl %r11b, %ecx
movl %ecx, (%r8,%r10,4)
testb %cl, %cl
je 0x39a7
xorl %ecx, %ecx
xorl %r11d, %r11d
jmp 0x39bd
movq $-0x1, %r11
movl %eax, %ecx
shlq %cl, %r11
notq %r11
movl %edx, %ecx
shlq %cl, %r11
movl %edx, %ecx
movl %ecx, (%rsi,%r10,4)
movq %r11, (%rdi,%r10,8)
incq %r10
addq $-0x6, %rdx
addq $0x6, %rax
cmpq $0x8, %r10
jne 0x3983
incq %r9
addq $0x20, %rsi
addq $0x40, %rdi
addq $0x20, %r8
cmpq $0x8, %r9
jne 0x3961
retq
// File: /workspace/github_c_makefile_star2_O3/pahihu[P]mixal/cell.c
// Function: assert_valid_field
void assert_valid_field(Cell field_spec)
{
    if (is_negative(field_spec) 
        || 64 <= magnitude(field_spec)
        || bad_field[(unsigned)magnitude(field_spec)])
    {
        char buffer[16];
        unparse_cell(buffer, field_spec, false);
        error("Invalid field specifier: %s", buffer);
    }
}

// Assembly:
movl %edi, %ecx
andl $0x3fffffff, %ecx       # imm = 0x3FFFFFFF
btl $0x1e, %edi
jb 0x3a18
leaq 0x57c7(%rip), %rdx      # 0x91cc
cmpl $0x3f, %ecx
ja 0x3a1f
leaq 0xbd2f(%rip), %rax      # 0xf740
cmpl $0x0, (%rax,%rcx,4)
jne 0x3a1f
retq
leaq 0x5932(%rip), %rdx      # 0x9351
pushq %rbx
subq $0x10, %rsp
leaq 0x57a3(%rip), %rsi      # 0x91ce
movq %rsp, %rbx
movq %rbx, %rdi
xorl %eax, %eax
callq 0x3280
leaq 0x5733(%rip), %rdi      # 0x9172
movq %rbx, %rsi
xorl %eax, %eax
callq 0x5bec
addq $0x10, %rsp
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O3/pahihu[P]mixal/cell.c
// Function: unparse_cell
void unparse_cell(char *buffer, Cell cell, Flag disasm)
{
    Byte I, F, C;
    Cell A;

    if (disasm) {
        destructure_cell (cell, A, I, F, C);
        sprintf(buffer, "%s%04lo %02o %02o %02o",
                is_negative (A) ? "-" : "+", magnitude (A),
                I, F, C);
    } else
        sprintf(buffer, "%s%010lo",
                is_negative (cell) ? "-" : "+", magnitude (cell));
}

// Assembly:
movq %rsi, %rax
testl %edx, %edx
je 0x3aa6
pushq %rax
movl %eax, %esi
andl $0x3f, %esi
movl %eax, %r9d
shrl $0x6, %r9d
andl $0x3f, %r9d
movl %eax, %r8d
shrl $0xc, %r8d
andl $0x3f, %r8d
movl %eax, %ecx
shrl $0x12, %ecx
andl $0xfff, %ecx            # imm = 0xFFF
btl $0x1e, %eax
leaq 0x5744(%rip), %rax      # 0x91cc
leaq 0x58c2(%rip), %rdx      # 0x9351
cmovaeq %rax, %rdx
movl %esi, (%rsp)
leaq 0x5718(%rip), %rsi      # 0x91b5
xorl %eax, %eax
callq 0x3280
popq %rax
retq
btl $0x1e, %eax
leaq 0x571b(%rip), %rcx      # 0x91cc
leaq 0x5899(%rip), %rdx      # 0x9351
cmovaeq %rcx, %rdx
andl $0x3fffffff, %eax       # imm = 0x3FFFFFFF
leaq 0x5706(%rip), %rsi      # 0x91ce
movq %rax, %rcx
xorl %eax, %eax
jmp 0x3280