LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/randomcodes-correct.c
// Function: gt_randomcodes_correct_process_bucket
int gt_randomcodes_correct_process_bucket(void *data,
    const GtUword *bucketofsuffixes, const GtSeqnumrelpos *snrp,
    const uint16_t *lcptab_bucket, GtUword numberofsuffixes,
    GT_UNUSED unsigned int sortingdepth, GT_UNUSED GtError *err)
{
  GtUword itvstart, next_itvstart;
  unsigned int lcpvalue;
  bool haserr = false;
  GtRandomcodesCorrectData *cdata = data;

  for (itvstart = 0, next_itvstart = 1UL; next_itvstart < numberofsuffixes;
      next_itvstart++)
  {
    lcpvalue = (unsigned int) lcptab_bucket[next_itvstart];
    if (lcpvalue < cdata->k)
    {
      gt_randomcodes_correct_process_kmer_itv(bucketofsuffixes + itvstart,
          next_itvstart - itvstart, data);
      itvstart = next_itvstart;
      if (lcpvalue < cdata->k - 1)
      {
        gt_randomcodes_correct_process_kmergroup_end(snrp, data);
      }
    }
  }
  gt_randomcodes_correct_process_kmer_itv(bucketofsuffixes + itvstart,
      numberofsuffixes - itvstart, data);
  gt_randomcodes_correct_process_kmergroup_end(snrp, data);
  return haserr ? -1 : 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r8, %r14
movq %rdx, %rbx
movq %rsi, %r12
movq %rdi, %r15
cmpq $0x2, %r8
jb 0x1c54bc
movq %rcx, %r13
movl $0x1, %ebp
xorl %eax, %eax
movdqa 0x1bb009(%rip), %xmm3   # 0x380410
movzwl (%r13,%rbp,2), %ecx
cmpl %ecx, 0x20(%r15)
jbe 0x1c54ae
movq %rbp, %rdx
subq %rax, %rdx
movl 0x24(%r15), %esi
movdqu 0x50(%r15), %xmm0
movq %rdx, %xmm1
movdqa %xmm3, %xmm2
punpcklqdq %xmm1, %xmm2    # xmm2 = xmm2[0],xmm1[0]
paddq %xmm0, %xmm2
movdqu %xmm2, 0x50(%r15)
movl %esi, %r8d
cmpq %rsi, %rdx
jae 0x1c544e
movb $0x0, 0x45(%r15)
movl %edx, %r8d
testl %r8d, %r8d
je 0x1c547c
leaq (%r12,%rax,8), %rax
movl 0x40(%r15), %edi
imull %esi, %edi
shlq $0x3, %rdi
addq 0x30(%r15), %rdi
movl %r8d, %esi
xorl %r8d, %r8d
movq (%rax,%r8,8), %r9
movq %r9, (%rdi,%r8,8)
incq %r8
cmpq %r8, %rsi
jne 0x1c546c
movq 0x28(%r15), %rax
movl 0x40(%r15), %esi
movl %edx, (%rax,%rsi,4)
incl 0x40(%r15)
movl 0x20(%r15), %edx
decl %edx
movq %rbp, %rax
cmpl %ecx, %edx
jbe 0x1c54ae
movq %rbx, %rdi
movq %r15, %rsi
callq 0x1c554c
movdqa 0x1baf65(%rip), %xmm3   # 0x380410
movq %rbp, %rax
incq %rbp
cmpq %r14, %rbp
jne 0x1c5407
jmp 0x1c54be
xorl %eax, %eax
subq %rax, %r14
movl 0x24(%r15), %ecx
movdqu 0x50(%r15), %xmm0
movq %r14, %xmm1
movdqa 0x1baf38(%rip), %xmm2   # 0x380410
punpcklqdq %xmm1, %xmm2    # xmm2 = xmm2[0],xmm1[0]
paddq %xmm0, %xmm2
movdqu %xmm2, 0x50(%r15)
movl %ecx, %esi
cmpq %rcx, %r14
jae 0x1c54f5
movb $0x0, 0x45(%r15)
movl %r14d, %esi
testl %esi, %esi
je 0x1c5520
leaq (%r12,%rax,8), %rax
movl 0x40(%r15), %edx
imull %ecx, %edx
shlq $0x3, %rdx
addq 0x30(%r15), %rdx
movl %esi, %ecx
xorl %esi, %esi
movq (%rax,%rsi,8), %rdi
movq %rdi, (%rdx,%rsi,8)
incq %rsi
cmpq %rsi, %rcx
jne 0x1c5510
movq 0x28(%r15), %rax
movl 0x40(%r15), %ecx
movl %r14d, (%rax,%rcx,4)
incl 0x40(%r15)
movq %rbx, %rdi
movq %r15, %rsi
callq 0x1c554c
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/randomcodes-correct.c
// Function: gt_randomcodes_correct_data_delete
void gt_randomcodes_correct_data_delete(GtRandomcodesCorrectData *cdata)
{
  if (cdata == NULL)
    return;
  if (cdata->outfile != NULL)
    gt_fa_fclose(cdata->outfile);
  gt_free(cdata->kpositions);
  gt_free(cdata->count);
  gt_free(cdata);
}

// Assembly:
testq %rdi, %rdi
je 0x1c593f
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq 0x38(%rdi), %rdi
testq %rdi, %rdi
je 0x1c58ff
callq 0x101e80
movq 0x30(%rbx), %rdi
leaq 0x1efb94(%rip), %r14    # 0x3b549e
movq %r14, %rsi
movl $0xe8, %edx
callq 0x109670
movq 0x28(%rbx), %rdi
movq %r14, %rsi
movl $0xe9, %edx
callq 0x109670
movq %rbx, %rdi
movq %r14, %rsi
movl $0xea, %edx
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/randomcodes-correct.c
// Function: gt_randomcodes_correct_data_collect_stats
void gt_randomcodes_correct_data_collect_stats(GtRandomcodesCorrectData *cdata,
    unsigned int threadnum, GtUword *nofkmergroups,
    GtUword *nofkmeritvs, GtUword *nofkmers,
    GtUword *nofcorrections)
{
  GT_RANDOMCODES_COLLECT_STAT(nofkmergroups);
  GT_RANDOMCODES_COLLECT_STAT(nofkmeritvs);
  GT_RANDOMCODES_COLLECT_STAT(nofkmers);
  GT_RANDOMCODES_COLLECT_STAT(nofcorrections);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r9, %rbx
movq %r8, %r15
movq %rcx, %r12
movq %rdx, %r13
movl %esi, %ebp
movq %rdi, %r14
movq 0x48(%rdi), %rdx
leaq 0x1efb77(%rip), %rdi    # 0x3b54de
xorl %eax, %eax
callq 0x108e02
testq %r13, %r13
je 0x1c597b
movq 0x48(%r14), %rax
addq %rax, (%r13)
movq 0x50(%r14), %rdx
leaq 0x1efb75(%rip), %rdi    # 0x3b54fb
movl %ebp, %esi
xorl %eax, %eax
callq 0x108e02
testq %r12, %r12
je 0x1c599c
movq 0x50(%r14), %rax
addq %rax, (%r12)
movq 0x58(%r14), %rdx
leaq 0x1efb6f(%rip), %rdi    # 0x3b5516
movl %ebp, %esi
xorl %eax, %eax
callq 0x108e02
testq %r15, %r15
je 0x1c59bc
movq 0x58(%r14), %rax
addq %rax, (%r15)
movq 0x60(%r14), %rdx
leaq 0x1efb67(%rip), %rdi    # 0x3b552e
movl %ebp, %esi
xorl %eax, %eax
callq 0x108e02
testq %rbx, %rbx
je 0x1c59dc
movq 0x60(%r14), %rax
addq %rax, (%rbx)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
nop
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/randomcodes-find-seldom.c
// Function: gt_randomcodes_find_seldom_process_bucket
int gt_randomcodes_find_seldom_process_bucket(void *data,
    const GtUword *bucketofsuffixes, const GtSeqnumrelpos *snrp,
    const uint16_t *lcptab_bucket, GtUword numberofsuffixes,
    GT_UNUSED unsigned int sortingdepth, GT_UNUSED GtError *err)
{
  GtUword itvstart, next_itvstart;
  unsigned int lcpvalue;
  GtRandomcodesFindSeldomData *sdata = data;

  for (itvstart = 0, next_itvstart = 1UL; next_itvstart < numberofsuffixes;
      next_itvstart++)
  {
    lcpvalue = (unsigned int) lcptab_bucket[next_itvstart];
    if (lcpvalue < (unsigned int)sdata->k)
    {
      gt_randomcodes_find_seldom_process_kmer_itv(snrp,
          bucketofsuffixes + itvstart, next_itvstart - itvstart, data);
      itvstart = next_itvstart;
    }
  }
  gt_randomcodes_find_seldom_process_kmer_itv(snrp,
      bucketofsuffixes + itvstart, next_itvstart - itvstart, data);
  return 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %rdx, (%rsp)
movq %rsi, %r15
movq %rdi, %r12
cmpq $0x2, %r8
jb 0x1c5ada
movl $0x1, %ebx
xorl %ebp, %ebp
movq %r8, 0x10(%rsp)
movq %rcx, 0x8(%rsp)
movq %rbp, %r14
movzwl (%rcx,%rbx,2), %eax
cmpl 0x20(%r12), %eax
jae 0x1c5ac4
movq %rbx, %rax
movq %rbx, %rbp
subq %r14, %rax
je 0x1c5ac7
movq %rbx, %rbp
cmpq %rax, 0x28(%r12)
jbe 0x1c5ac7
movq (%r15,%r14,8), %rsi
movq (%rsp), %rbp
movq %rbp, %rdi
callq 0x1ec4c8
movq %rax, %r13
movq (%r15,%r14,8), %rsi
movq %rbp, %rdi
callq 0x1ec4be
movq %rax, %rbp
cmpq 0x8(%r12), %rax
jb 0x1c5a7b
notq %rbp
addq 0x10(%r12), %rbp
movq (%r12), %rdi
movq %rbp, %rsi
callq 0xeffd3
subq %r13, %rax
cmpq 0x20(%r12), %rax
jb 0x1c5ab2
movabsq $-0x8000000000000000, %rax # imm = 0x8000000000000000
movl %ebp, %ecx
shrq %cl, %rax
movq 0x18(%r12), %rcx
shrq $0x6, %rbp
orq %rax, (%rcx,%rbp,8)
incq 0x30(%r12)
incq %r14
cmpq %r14, %rbx
jne 0x1c5a4a
movq %rbx, %rbp
movq 0x8(%rsp), %rcx
jmp 0x1c5ac7
movq %r14, %rbp
incq %rbx
movq 0x10(%rsp), %r14
cmpq %r14, %rbx
jne 0x1c5a1f
jmp 0x1c5ae2
movl $0x1, %r14d
xorl %ebp, %ebp
movq %r14, %rax
subq %rbp, %rax
je 0x1c5b62
cmpq %rax, 0x28(%r12)
jbe 0x1c5b62
movq (%r15,%rbp,8), %rsi
movq (%rsp), %r13
movq %r13, %rdi
callq 0x1ec4c8
movq %rax, %rbx
movq (%r15,%rbp,8), %rsi
movq %r13, %rdi
callq 0x1ec4be
movq %rax, %r13
cmpq 0x8(%r12), %rax
jb 0x1c5b22
notq %r13
addq 0x10(%r12), %r13
movq (%r12), %rdi
movq %r13, %rsi
callq 0xeffd3
subq %rbx, %rax
cmpq 0x20(%r12), %rax
jb 0x1c5b5a
movabsq $-0x8000000000000000, %rax # imm = 0x8000000000000000
movl %r13d, %ecx
shrq %cl, %rax
movq 0x18(%r12), %rcx
shrq $0x6, %r13
orq %rax, (%rcx,%r13,8)
incq 0x30(%r12)
incq %rbp
cmpq %rbp, %r14
jne 0x1c5af1
xorl %eax, %eax
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/randomcodes-find-seldom.c
// Function: gt_randomcodes_find_seldom_data_new
GtRandomcodesFindSeldomData *gt_randomcodes_find_seldom_data_new(
    GtEncseq *encseq, unsigned int k, unsigned int c,
    GtBitsequence *seldom_reads)
{
  GtRandomcodesFindSeldomData *sdata = gt_malloc(sizeof *sdata);
  sdata->k = (GtUword)k;
  sdata->c = (GtUword)c;
  sdata->encseq = encseq;
  sdata->mirror_nofseqs = gt_encseq_num_of_sequences(encseq);
  sdata->nofreads = sdata->mirror_nofseqs;
  sdata->seldom_reads = seldom_reads;
  if (gt_encseq_is_mirrored(sdata->encseq))
    sdata->nofreads >>= 1;
  sdata->nofseldomkmers = 0;
  return sdata;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movq %rcx, %r14
movl %edx, %ebp
movl %esi, %r15d
movq %rdi, %r12
leaq 0x1efa1c(%rip), %rsi    # 0x3b55a9
movl $0x38, %edi
movl $0x58, %edx
callq 0x1092b2
movq %rax, %rbx
movl %r15d, %eax
movq %rax, 0x20(%rbx)
movl %ebp, %eax
movq %rax, 0x28(%rbx)
movq %r12, (%rbx)
movq %r12, %rdi
callq 0xec1e8
movq %rax, 0x10(%rbx)
movq %rax, 0x8(%rbx)
movq %r14, 0x18(%rbx)
movq (%rbx), %rdi
callq 0xfac80
testb %al, %al
je 0x1c5bd3
shrq 0x8(%rbx)
movq $0x0, 0x30(%rbx)
movq %rbx, %rax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/randomcodes.c
// Function: gt_randomcodes_insertsuffixes_flush
static void gt_randomcodes_insertsuffixes_flush(void *data)
{
  GtRandomcodesinfo *fci = (GtRandomcodesinfo *) data;

  if (fci->buf.nextfree > 0)
  {
    const GtUword *ptr;

    gt_assert(fci->allrandomcodes != NULL);
    fci->codebuffer_total += fci->buf.nextfree;
    gt_radixsort_inplace_sort(fci->radixsort_codepos, fci->buf.nextfree);
    ptr = gt_randomcodes_find_insert(fci, fci->buf.spaceGtUwordPair[0].a);
    gt_assert(ptr != NULL);
    fci->total_inserted += gt_randomcodes_insertsuffixes_merge(fci,
        fci->buf.spaceGtUwordPair, ptr);
    gt_assert(fci->total_inserted == fci->codebuffer_total);
    fci->flushcount++;
    fci->buf.nextfree = 0;
  }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq 0xc0(%rdi), %rsi
testq %rsi, %rsi
je 0x1ca331
movq %rdi, %rbx
cmpq $0x0, 0xa0(%rdi)
je 0x1ca359
addq %rsi, 0x20(%rbx)
movq 0x80(%rbx), %rdi
callq 0x115413
movq 0xe8(%rbx), %r13
movq (%r13), %rsi
movq %rbx, %rdi
callq 0x1c5dbf
testq %rax, %rax
je 0x1ca35e
movq %rax, %r14
movq 0xc0(%rbx), %rax
shlq $0x4, %rax
leaq (%rax,%r13), %rcx
addq $-0x10, %rcx
xorl %esi, %esi
cmpq %r13, %rcx
jb 0x1ca315
movq 0x30(%rbx), %rdx
shlq $0x3, %rdx
addq 0xa0(%rbx), %rdx
cmpq %r14, %rdx
jb 0x1ca315
xorl %esi, %esi
movq %rcx, 0x8(%rsp)
movq %rdx, (%rsp)
movq (%r13), %rax
cmpq (%r14), %rax
jbe 0x1ca213
addq $0x8, %r14
jmp 0x1ca307
movq %r14, %rax
subq 0xa0(%rbx), %rax
sarq $0x3, %rax
movq 0x1a0(%rbx), %rcx
testq %rcx, %rcx
je 0x1ca24a
movq 0x190(%rbx), %rdx
xorl %r15d, %r15d
cmpq %rax, (%rdx,%r15,8)
jae 0x1ca24d
incq %r15
cmpq %r15, %rcx
jne 0x1ca237
movq %rcx, %r15
jmp 0x1ca24d
xorl %r15d, %r15d
cmpq %rax, 0x110(%rbx)
jbe 0x1ca34f
movq 0x150(%rbx), %rcx
movl (%rcx,%rax,4), %ebp
testl %ebp, %ebp
movq %rsi, 0x10(%rsp)
je 0x1ca271
decl %ebp
jmp 0x1ca28f
testq %r15, %r15
je 0x1ca354
movq 0x190(%rbx), %rdx
incq -0x8(%rdx,%r15,8)
decq %r15
movl 0x188(%rbx), %ebp
movl %ebp, (%rcx,%rax,4)
movb 0x18c(%rbx), %cl
shlq %cl, %r15
movq 0x88(%rbx), %r12
movq %r12, %rdi
callq 0x2083a2
testb %al, %al
je 0x1ca2c3
movq 0xf8(%rbx), %rdi
movq 0x8(%r13), %rsi
callq 0x1ec4a3
movq %rax, %rdx
jmp 0x1ca2c7
movq 0x8(%r13), %rdx
movl %ebp, %eax
addq %rax, %r15
subq (%r12), %r15
jb 0x1ca34a
cmpq 0x8(%r12), %r15
jae 0x1ca340
cmpq %rdx, 0x10(%r12)
jb 0x1ca340
movq 0x20(%r12), %rdi
testq %rdi, %rdi
je 0x1ca345
movq %r15, %rsi
callq 0xe8138
movq 0x10(%rsp), %rsi
incq %rsi
addq $0x10, %r13
movq 0x8(%rsp), %rcx
movq (%rsp), %rdx
cmpq %rcx, %r13
ja 0x1ca315
cmpq %rdx, %r14
jbe 0x1ca201
addq 0x8(%rbx), %rsi
movq %rsi, 0x8(%rbx)
cmpq 0x20(%rbx), %rsi
jne 0x1ca363
incl 0x70(%rbx)
movq $0x0, 0xc0(%rbx)
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x6a379
callq 0x6a342
callq 0x6a3b0
callq 0x6a30b
callq 0x6a3e7
callq 0x6a490
callq 0x6a457
callq 0x6a41e
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/randomcodes.c
// Function: gt_randomcodes_delete_before_end
static void gt_randomcodes_delete_before_end(GtRandomcodesinfo *fci)
{
  if (fci->binsearchcache.spaceGtIndexwithcodeRC != NULL)
  {
    GT_FCI_SUBTRACTWORKSPACE(fci->fcsl, "binsearchcache");
    GT_FREEARRAY(&fci->binsearchcache, GtIndexwithcodeRC);
  }
  if (fci->radixsort_codepos != NULL)
  {
    gt_radixsort_delete(fci->radixsort_codepos);
    GT_FCI_SUBTRACTWORKSPACE(fci->fcsl, "radixsort_codepos");
    fci->radixsort_codepos = NULL;
  }
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
cmpq $0x0, 0x48(%rdi)
je 0x1ca3ce
movq 0xa8(%rbx), %rdi
movq $0x0, (%rsp)
leaq 0x1eb311(%rip), %rdx    # 0x3b569d
leaq 0x1eb7ac(%rip), %r8     # 0x3b5b3f
movl $0x31f, %esi            # imm = 0x31F
xorl %ecx, %ecx
movl $0x1, %r9d
callq 0x320ca8
movq 0x48(%rbx), %rdi
testq %rdi, %rdi
je 0x1ca3ce
leaq 0x1eb2e8(%rip), %rsi    # 0x3b569d
movl $0x320, %edx            # imm = 0x320
callq 0x109670
movq $0x0, 0x48(%rbx)
xorps %xmm0, %xmm0
movups %xmm0, 0x58(%rbx)
movq 0x80(%rbx), %rdi
testq %rdi, %rdi
je 0x1ca414
callq 0x114bc7
movq 0xa8(%rbx), %rdi
xorl %r14d, %r14d
movq %r14, (%rsp)
leaq 0x1eb2a9(%rip), %rdx    # 0x3b569d
leaq 0x1e4d0b(%rip), %r8     # 0x3af106
movl $0x325, %esi            # imm = 0x325
xorl %ecx, %ecx
movl $0x1, %r9d
callq 0x320ca8
movq %r14, 0x80(%rbx)
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/randomcodes.c
// Function: gt_randomcodes_accumulatecounts_flush
static void gt_randomcodes_accumulatecounts_flush(void *data)
{
  GtRandomcodesinfo *fci = (GtRandomcodesinfo *) data;

  if (fci->buf.nextfree > 0)
  {
    GtUword foundindex;

    gt_assert(fci->allrandomcodes != NULL);
    fci->codebuffer_total += fci->buf.nextfree;
    gt_radixsort_inplace_sort(fci->radixsort_code, fci->buf.nextfree);
    foundindex = gt_randomcodes_find_accu(fci, fci->buf.spaceGtUword[0]);
    gt_assert(foundindex != ULONG_MAX);
    fci->total_count += gt_randomcodes_accumulatecounts_merge(fci,
        fci->buf.spaceGtUword, fci->allrandomcodes + foundindex);
    gt_assert(fci->total_count == fci->codebuffer_total);
    fci->flushcount++;
    fci->buf.nextfree = 0;
  }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq 0xc0(%rdi), %rsi
testq %rsi, %rsi
je 0x1ca7b2
movq %rdi, %rbx
cmpq $0x0, 0xa0(%rdi)
je 0x1ca7c6
addq %rsi, 0x20(%rbx)
movq 0x78(%rbx), %rdi
callq 0x115413
movq 0xf0(%rbx), %rax
movq (%rax), %rsi
movq %rbx, %rdi
callq 0x1c5c24
cmpq $-0x1, %rax
je 0x1ca7cb
movq 0xf0(%rbx), %r13
movq 0xc0(%rbx), %rcx
leaq -0x8(,%rcx,8), %rsi
addq %r13, %rsi
xorl %r12d, %r12d
cmpq %r13, %rsi
jb 0x1ca798
movq 0x38(%rbx), %rcx
movq 0xa0(%rbx), %rdx
leaq (%rdx,%rax,8), %rbp
leaq (%rdx,%rcx,8), %r14
addq $-0x8, %r14
cmpq %rbp, %r14
jb 0x1ca798
xorl %r12d, %r12d
movq %rsi, 0x8(%rsp)
movq (%r13), %rax
cmpq (%rbp), %rax
jbe 0x1ca66d
addq $0x8, %rbp
jmp 0x1ca78a
movq %rbp, %r15
subq 0xa0(%rbx), %r15
incq 0x140(%rbx)
sarq $0x3, %r15
movq 0x158(%rbx), %rax
movzbl (%rax,%r15), %ecx
cmpl $0xfe, %ecx
je 0x1ca6cf
cmpl $0xff, %ecx
jne 0x1ca72c
movq 0x180(%rbx), %rax
testq %rax, %rax
je 0x1ca734
cmpq %r15, 0x178(%rbx)
jne 0x1ca734
movl (%rax), %ecx
cmpl $-0x1, %ecx
je 0x1ca7d5
incl %ecx
movl %ecx, (%rax)
jmp 0x1ca77c
movb $-0x1, (%rax,%r15)
movq 0x160(%rbx), %rdi
movq %r15, 0x18(%rsp)
movl $0x1, 0x20(%rsp)
leaq 0x18(%rsp), %rsi
leaq 0x10(%rsp), %rdx
callq 0x106536
testl %eax, %eax
jne 0x1ca707
movq 0x10(%rsp), %rax
movl $0x1, 0x8(%rax)
movq 0x10(%rsp), %rax
addq $0x8, %rax
movq %rax, 0x180(%rbx)
movq %r15, 0x178(%rbx)
incq 0x128(%rbx)
movq 0x8(%rsp), %rsi
jmp 0x1ca783
incb %cl
movb %cl, (%rax,%r15)
jmp 0x1ca783
movq 0x160(%rbx), %rdi
movq %r15, 0x18(%rsp)
leaq 0x18(%rsp), %rsi
callq 0x10620e
incq 0x138(%rbx)
leaq 0x8(%rax), %rcx
testq %rax, %rax
cmoveq %rax, %rcx
je 0x1ca7c1
movl (%rcx), %eax
cmpl $-0x1, %eax
je 0x1ca7c1
incl %eax
movl %eax, (%rcx)
movq %r15, 0x178(%rbx)
movq %rcx, 0x180(%rbx)
movq 0x8(%rsp), %rsi
incq 0x130(%rbx)
incq %r12
addq $0x8, %r13
cmpq %rsi, %r13
ja 0x1ca798
cmpq %r14, %rbp
jbe 0x1ca65a
addq (%rbx), %r12
movq %r12, (%rbx)
cmpq 0x20(%rbx), %r12
jne 0x1ca7d0
incl 0x70(%rbx)
movq $0x0, 0xc0(%rbx)
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x6a537
callq 0x6a5e0
callq 0x6a5a7
callq 0x6a56e
callq 0x6a500
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/randomcodes.c
// Function: gt_randomcodes_thread_caller_sortremaining
static void *gt_randomcodes_thread_caller_sortremaining(void *data)
{
  GtRandomcodesSortRemainingThreadinfo *threadinfo =
    (GtRandomcodesSortRemainingThreadinfo *) data;

  if (gt_randomcodes_sortremaining(threadinfo->srsw,
                                  threadinfo->encseq,
                                  threadinfo->readmode,
                                  threadinfo->spmsuftab,
                                  threadinfo->snrp,
                                  threadinfo->rct,
                                  threadinfo->allrandomcodes,
                                  threadinfo->minindex,
                                  threadinfo->maxindex,
                                  threadinfo->sumofwidth,
                                  threadinfo->sortingdepth,
                                  threadinfo->bucketkeysize,
                                  threadinfo->itvprocess,
                                  threadinfo->itvprocess_end,
                                  threadinfo->itvprocessdata,
                                  threadinfo->withsuftabcheck,
                                  threadinfo->err) != 0)
  {
    gt_assert(false);
  }
  return NULL;
}

// Assembly:
pushq %rbp
pushq %rbx
subq $0x58, %rsp
movq (%rdi), %rax
movq 0x8(%rdi), %rsi
movl 0x10(%rdi), %edx
movq 0x18(%rdi), %rcx
movq 0x20(%rdi), %r8
movq 0x28(%rdi), %r9
movups 0x30(%rdi), %xmm0
movups 0x40(%rdi), %xmm1
movl 0x50(%rdi), %r10d
movl 0x54(%rdi), %r11d
movups 0x60(%rdi), %xmm2
movq 0x70(%rdi), %rbx
movzbl 0x58(%rdi), %ebp
movq 0x78(%rdi), %rdi
movq %rdi, 0x50(%rsp)
movl %ebp, 0x48(%rsp)
movq %rbx, 0x40(%rsp)
movups %xmm2, 0x30(%rsp)
movl %r11d, 0x28(%rsp)
movl %r10d, 0x20(%rsp)
movups %xmm1, 0x10(%rsp)
movups %xmm0, (%rsp)
movq %rax, %rdi
callq 0x1ca7da
testl %eax, %eax
jne 0x1cad55
xorl %eax, %eax
addq $0x58, %rsp
popq %rbx
popq %rbp
retq
callq 0x6a8fa
nop
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-cntlist.c
// Function: gt_cntlist_write_bin_header
void gt_cntlist_write_bin_header(GtUword nofreads, FILE *file)
{
  gt_assert(file != NULL);
  gt_xfputc(GT_CNTLIST_BIN_HEADER, file);
  gt_xfputc((char)sizeof(GtUword), file);
  gt_xfwrite(&(nofreads), sizeof (GtUword), (size_t)1, file);
}

// Assembly:
pushq %rbx
subq $0x10, %rsp
movq %rdi, 0x8(%rsp)
testq %rsi, %rsi
je 0x1cada2
movq %rsi, %rbx
movl $0x1, %edi
callq 0x1255d6
movl $0x8, %edi
movq %rbx, %rsi
callq 0x1255d6
leaq 0x8(%rsp), %rdi
movl $0x8, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x125658
addq $0x10, %rsp
popq %rbx
retq
callq 0x6a933
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-cntlist.c
// Function: gt_cntlist_show
int gt_cntlist_show(GtBitsequence *cntlist, GtUword nofreads,
    const char *path, bool binary, GtError *err)
{
  FILE *file;
  gt_assert(cntlist != NULL);
  if (path == NULL)
    file = stdout;
  else
  {
    file = gt_fa_fopen(path, binary ? "wb" : "w", err);
    if (file == NULL)
      return -1;
  }
  gt_assert(file != NULL);
  (binary ? gt_cntlist_show_bit : gt_cntlist_show_ascii)
    (cntlist, nofreads, file);
  if (path != NULL)
    gt_fa_fclose(file);
  return 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
testq %rdi, %rdi
je 0x1cae49
movl %ecx, %ebp
movq %rdx, %rbx
movq %rsi, %r14
movq %rdi, %r15
testq %rdx, %rdx
je 0x1cae00
leaq 0x193d3e(%rip), %rax    # 0x35eb0d
leaq 0x1d1c5b(%rip), %rsi    # 0x39ca31
testb %bpl, %bpl
cmovneq %rax, %rsi
leaq 0x1eb28d(%rip), %rdx    # 0x3b6071
movq %rbx, %rdi
movl $0x45, %ecx
callq 0x101c23
movq %rax, %r12
testq %rax, %rax
jne 0x1cae0a
movl $0xffffffff, %ebp       # imm = 0xFFFFFFFF
jmp 0x1cae3e
movq 0x2f90e1(%rip), %rax    # 0x4c3ee8
movq (%rax), %r12
testq %r12, %r12
je 0x1cae4e
leaq 0x3d(%rip), %rax        # 0x1cae53
leaq 0xb9(%rip), %rcx        # 0x1caed6
testb %bpl, %bpl
cmovneq %rax, %rcx
movq %r15, %rdi
movq %r14, %rsi
movq %r12, %rdx
callq *%rcx
xorl %ebp, %ebp
testq %rbx, %rbx
je 0x1cae3e
movq %r12, %rdi
callq 0x101e80
movl %ebp, %eax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
callq 0x6a9a1
callq 0x6a96a
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-cntlist.c
// Function: gt_cntlist_show_bit
static inline void gt_cntlist_show_bit(GtBitsequence *cntlist,
    GtUword nofreads, FILE *file)
{
  gt_assert(file != NULL);
  gt_xfputc(GT_CNTLIST_BIT_HEADER, file);
  gt_xfputc((char)sizeof(GtUword), file);
  gt_xfwrite(&(nofreads), sizeof (GtUword), (size_t)1, file);
  gt_xfwrite(cntlist, sizeof (GtBitsequence), GT_NUMOFINTSFORBITS(nofreads),
      file);
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, (%rsp)
testq %rdx, %rdx
je 0x1caed1
movq %rdx, %rbx
movq %rdi, %r14
xorl %edi, %edi
movq %rdx, %rsi
callq 0x1255d6
movl $0x8, %edi
movq %rbx, %rsi
callq 0x1255d6
movq %rsp, %r15
movl $0x1, %r12d
movl $0x8, %esi
movl $0x1, %edx
movq %r15, %rdi
movq %rbx, %rcx
callq 0x125658
movq (%r15), %rax
leaq -0x1(%rax), %rdx
shrq $0x6, %rdx
incq %rdx
cmpq $0x40, %rax
cmovbq %r12, %rdx
movl $0x8, %esi
movq %r14, %rdi
movq %rbx, %rcx
callq 0x125658
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
callq 0x6a9d8
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-cntlist.c
// Function: gt_cntlist_show_ascii
static inline void gt_cntlist_show_ascii(GtBitsequence *cntlist,
    GtUword nofreads, FILE *file)
{
  GtUword i;
  gt_assert(file != NULL);
  fprintf(file, "[n: "GT_WU"]\n", nofreads);
  for (i = 0; i < nofreads; i++)
    if (GT_ISIBITSET(cntlist, i))
      fprintf(file, ""GT_WU"\n", i);
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
testq %rdx, %rdx
je 0x1caf49
movq %rdx, %rbx
movq %rsi, %r14
movq %rdi, %r15
leaq 0x1eb371(%rip), %rsi    # 0x3b6265
movq %rdx, %rdi
movq %r14, %rdx
xorl %eax, %eax
callq 0x17ab0
testq %r14, %r14
je 0x1caf3f
leaq 0x18eb56(%rip), %r12    # 0x359a63
xorl %r13d, %r13d
movq %r13, %rax
shrq $0x6, %rax
movq (%r15,%rax,8), %rax
movl %r13d, %ecx
shlq %cl, %rax
shrq $0x3f, %rax
je 0x1caf37
movq %rbx, %rdi
movq %r12, %rsi
movq %r13, %rdx
xorl %eax, %eax
callq 0x17ab0
incq %r13
cmpq %r13, %r14
jne 0x1caf10
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
callq 0x6aa0f
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-cntlist.c
// Function: gt_cntlist_count
GtUword gt_cntlist_count(const GtBitsequence *cntlist,
    GtUword nofreads)
{
  GtUword i, counter = 0;

  for (i = 0; i < nofreads; i++)
    if ((bool)GT_ISIBITSET(cntlist, i))
      counter++;
  return counter;
}

// Assembly:
xorl %eax, %eax
testq %rsi, %rsi
je 0x1cb3d4
xorl %ecx, %ecx
movq %rcx, %rdx
shrq $0x6, %rdx
movq (%rdi,%rdx,8), %rdx
shlq %cl, %rdx
shrq $0x3f, %rdx
addq %rdx, %rax
incq %rcx
cmpq %rcx, %rsi
jne 0x1cb3b7
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-cntlist.c
// Function: gt_cntlist_xload
GtUword gt_cntlist_xload(const char *filename, GtBitsequence **cntlist,
    GtUword expected_nofreads)
{
  int retval;
  GtUword found_nofreads;
  GtError *err;

  if (!gt_file_exists(filename))
  {
    fprintf(stderr, "FATAL: error by loading contained reads list: "
        "file %s does not exist\n", filename);
    exit(EXIT_FAILURE);
  }

  err = gt_error_new();
  retval = gt_cntlist_parse(filename, true, cntlist, &found_nofreads, err);
  if (retval != 0)
  {
    fprintf(stderr, "FATAL: error by parsing contained reads list: %s\n",
        gt_error_get(err));
    exit(EXIT_FAILURE);
  }
  gt_error_delete(err);

  if (found_nofreads != expected_nofreads)
  {
    fprintf(stderr, "FATAL: error by parsing contained reads list: "
        "file specifies a wrong number of reads\nexpected "GT_WU", found "
        GT_WU"\n", expected_nofreads, found_nofreads);
    exit(EXIT_FAILURE);
  }

  return gt_cntlist_count(*cntlist, found_nofreads);
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rdx, %r14
movq %rsi, %rbx
movq %rdi, %r12
callq 0x10415c
testb %al, %al
je 0x1cb45b
callq 0x1019b4
movq %rax, %r15
movq %rsp, %rcx
movq %r12, %rdi
movl $0x1, %esi
movq %rbx, %rdx
movq %rax, %r8
callq 0x1caf4e
movq %r15, %rdi
testl %eax, %eax
jne 0x1cb463
callq 0x101b35
movq (%rsp), %rsi
cmpq %r14, %rsi
jne 0x1cb468
testq %rsi, %rsi
je 0x1cb44d
movq (%rbx), %rdx
xorl %eax, %eax
xorl %ecx, %ecx
movq %rcx, %rdi
shrq $0x6, %rdi
movq (%rdx,%rdi,8), %rdi
shlq %cl, %rdi
shrq $0x3f, %rdi
addq %rdi, %rax
incq %rcx
cmpq %rcx, %rsi
jne 0x1cb42e
jmp 0x1cb44f
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
movq %r12, %rdi
callq 0x6ab28
callq 0x6ab4c
movq %r14, %rdi
callq 0x6ab78
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-cntlist.c
// Function: gt_cntlist_parse_bin_or_bit_header
static int gt_cntlist_parse_bin_or_bit_header(FILE *infp,
    GtUword *nofreads, GtError *err)
{
  int c;
  size_t n;

  gt_assert(infp != NULL && nofreads != NULL);
  gt_error_check(err);
  c = gt_xfgetc(infp);
  if (c == EOF)
  {
    gt_error_set(err, "contained reads list: unexpected end of file");
    return -1;
  }
  else if (c != (char)sizeof(GtUword))
  {
    gt_error_set(err, "contained reads list: %dbit version "
        "of GenomeTools required to use this list", c * CHAR_BIT);
    return -1;
  }
  n = fread(nofreads, sizeof (GtUword), (size_t)1, infp);
  if (n != (size_t)1 || *nofreads == 0)
  {
    gt_error_set(err, "contained reads list: unrecognized format");
    return -1;
  }
  return 0;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
testq %rsi, %rsi
je 0x1cb50a
movq %rdx, %rbx
movq %rsi, %r14
movq %rdi, %r15
testq %rdx, %rdx
je 0x1cb498
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0x1cb50f
movq %r15, %rdi
callq 0x12554f
cmpl $0x8, %eax
je 0x1cb4b3
cmpl $-0x1, %eax
jne 0x1cb4e9
leaq 0x1eae41(%rip), %rsi    # 0x3b62f2
jmp 0x1cb4dd
movl $0x8, %esi
movl $0x1, %edx
movq %r14, %rdi
movq %r15, %rcx
callq 0x17b40
cmpq $0x1, %rax
jne 0x1cb4d6
xorl %eax, %eax
cmpq $0x0, (%r14)
jne 0x1cb504
leaq 0x1eae8f(%rip), %rsi    # 0x3b636c
movq %rbx, %rdi
xorl %eax, %eax
callq 0x1019cf
jmp 0x1cb4ff
shll $0x3, %eax
leaq 0x1eae2c(%rip), %rsi    # 0x3b631f
movq %rbx, %rdi
movl %eax, %edx
xorl %eax, %eax
callq 0x1019cf
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
popq %rbx
popq %r14
popq %r15
retq
callq 0x6abd6
callq 0x6ab9f
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-contfinder.c
// Function: gt_contfinder_write_seqnums
int gt_contfinder_write_seqnums(GtContfinder *contfinder, bool sorted,
    GtFile *outfp, GT_UNUSED GtError *err)
{
  int had_err = 0;
  gt_contfinder_seqnum_t i;
  if (sorted)
  {
    for (i = 0; i < contfinder->logicalnofseqs; i++)
      if (!GT_ISIBITSET(contfinder->contained,
            GT_READJOINER_CONTFINDER_GET_SEQNUM(contfinder->seqnums, i)))
        gt_file_xprintf(outfp, ""GT_WU"\n", (GtUword)
            GT_READJOINER_CONTFINDER_GET_SEQNUM(contfinder->seqnums, i));
  }
  else
  {
    for (i = 0; i < contfinder->nofseqs; i++)
      if (!GT_ISIBITSET(contfinder->contained, i))
        gt_file_xprintf(outfp, ""GT_WU"\n", (GtUword)i);
  }
  return had_err;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
movq %rdx, %rbx
movq %rdi, %r14
testl %esi, %esi
je 0x1ccf11
cmpl $0x0, 0x8(%r14)
je 0x1ccf61
movabsq $-0x8000000000000000, %r12 # imm = 0x8000000000000000
leaq 0x18cb90(%rip), %r15    # 0x359a63
xorl %r13d, %r13d
movq 0x10(%r14), %rax
movq 0x48(%r14), %rcx
movl (%rcx,%r13,4), %ecx
movq %r12, %rdx
shrq %cl, %rdx
movl %ecx, %esi
shrl $0x6, %esi
testq %rdx, (%rax,%rsi,8)
jne 0x1ccf03
movq %rbx, %rdi
movq %r15, %rsi
movq %rcx, %rdx
xorl %eax, %eax
callq 0x103d21
incq %r13
movl 0x8(%r14), %eax
cmpq %rax, %r13
jb 0x1cced6
jmp 0x1ccf61
cmpl $0x0, 0xc(%r14)
je 0x1ccf61
movabsq $-0x8000000000000000, %r13 # imm = 0x8000000000000000
leaq 0x18cb3a(%rip), %r15    # 0x359a63
xorl %r12d, %r12d
movq 0x10(%r14), %rax
movq %r13, %rdx
movl %r12d, %ecx
shrq %cl, %rdx
movl %r12d, %ecx
shrl $0x6, %ecx
testq %rdx, (%rax,%rcx,8)
jne 0x1ccf55
movq %rbx, %rdi
movq %r15, %rsi
movq %r12, %rdx
xorl %eax, %eax
callq 0x103d21
incq %r12
movl 0xc(%r14), %eax
cmpq %rax, %r12
jb 0x1ccf2c
xorl %eax, %eax
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-contfinder.c
// Function: gt_contfinder_write_sorted_seqnums
int gt_contfinder_write_sorted_seqnums(GtContfinder *contfinder, char* path,
    GtError *err)
{
  int had_err = 0;
  GtFile *file;
  file = gt_file_new(path, "wb", err);
  if (file == NULL)
    had_err = -1;
  if (!had_err)
  {
    had_err = gt_contfinder_write_seqnums(contfinder, true, file, err);
  }
  gt_file_delete(file);
  return had_err;
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
movq %rsi, %rax
movq %rdi, %r14
leaq 0x191b8f(%rip), %rsi    # 0x35eb0d
movq %rax, %rdi
callq 0x103957
movq %rax, %rbx
testq %rax, %rax
je 0x1ccfa2
movq %r14, %rdi
movl $0x1, %esi
movq %rbx, %rdx
callq 0x1ccea4
xorl %ebp, %ebp
jmp 0x1ccfa7
movl $0xffffffff, %ebp       # imm = 0xFFFFFFFF
movq %rbx, %rdi
callq 0x1040fc
movl %ebp, %eax
popq %rbx
popq %r14
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-contfinder.c
// Function: gt_contfinder_write_copynum
int gt_contfinder_write_copynum(GtContfinder *contfinder, char* path,
    GtError *err)
{
  int had_err = 0;
  gt_contfinder_seqnum_t i;
  FILE *file;
  file = gt_fa_fopen(path, "wb", err);
  if (file == NULL)
    had_err = -1;
  else
  {
#ifndef NDEBUG
    gt_contfinder_seqnum_t n_noncontained = 0;
    GtUword cnsum = 0;
    bool had_overflow = false;
#endif
    gt_contfinder_copynum_t cn;
    for (i = 0; i < contfinder->nofseqs; i++)
    {
      cn = contfinder->copynum[i];
      if (cn > 0)
      {
        gt_xfwrite(contfinder->copynum + i, sizeof (*contfinder->copynum),
            (size_t)1, file);
#ifndef NDEBUG
        n_noncontained++;
        if (cn == GT_CONTFINDER_COPYNUM_MAX)
        {
          had_overflow = true;
        }
        cnsum += cn;
#endif
      }
    }
    gt_assert(n_noncontained == contfinder->nofseqs -
        gt_contfinder_nofcontained(contfinder));
    gt_assert(had_overflow || (cnsum == (GtUword)contfinder->nofseqs));
    gt_fa_fclose(file);
  }
  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rdx, %r8
movq %rsi, %rax
movq %rdi, %r14
leaq 0x191b22(%rip), %rsi    # 0x35eb0d
leaq 0x1e9593(%rip), %rdx    # 0x3b6585
movq %rax, %rdi
movl $0x32c, %ecx            # imm = 0x32C
callq 0x101c23
movq %rax, (%rsp)
testq %rax, %rax
je 0x1cd069
movl 0xc(%r14), %eax
xorl %r15d, %r15d
testl %eax, %eax
je 0x1cd070
xorl %ebp, %ebp
xorl %r12d, %r12d
xorl %r13d, %r13d
movq 0x40(%r14), %rdi
movzbl (%rdi,%rbp), %ebx
testq %rbx, %rbx
je 0x1cd058
addq %rbp, %rdi
movl $0x1, %esi
movl $0x1, %edx
movq (%rsp), %rcx
callq 0x125658
incl %r15d
cmpq $0xff, %rbx
movzbl %r12b, %r12d
movl $0x1, %eax
cmovel %eax, %r12d
addq %rbx, %r13
incq %rbp
movl 0xc(%r14), %eax
cmpq %rax, %rbp
jb 0x1cd01b
movl %r15d, %r15d
jmp 0x1cd076
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
jmp 0x1cd0a5
xorl %r13d, %r13d
xorl %r12d, %r12d
movl %eax, %ebx
movq %r14, %rdi
callq 0x1cd0be
movq %rbx, %rcx
subq %rax, %rcx
cmpq %r15, %rcx
jne 0x1cd0b4
cmpq %rbx, %r13
sete %al
orb %al, %r12b
testb $0x1, %r12b
je 0x1cd0b9
movq (%rsp), %rdi
callq 0x101e80
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x6b2ce
callq 0x6b307
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-contfinder.c
// Function: gt_contfinder_nofcontained
GtUword gt_contfinder_nofcontained(GtContfinder *contfinder)
{
  size_t i;
  GtBitsequence v;
  GtUword nofcontained;
  const size_t tabsize = GT_NUMOFINTSFORBITS(contfinder->nofseqs);
  if (contfinder->contained == NULL)
    return 0;
  nofcontained = 0;
  for (i = 0; i < tabsize; i++)
  {
    v = contfinder->contained[i];
    for (/**/; v; nofcontained++)
      v &= v - 1;
  }
  return nofcontained;
}

// Assembly:
movq 0x10(%rdi), %rcx
testq %rcx, %rcx
je 0x1cd0ff
movl 0xc(%rdi), %eax
leal -0x1(%rax), %esi
shrl $0x6, %esi
incl %esi
cmpl $0x40, %eax
movl $0x1, %edx
cmovael %esi, %edx
xorl %eax, %eax
xorl %esi, %esi
movq (%rcx,%rsi,8), %rdi
testq %rdi, %rdi
je 0x1cd0f6
leaq -0x1(%rdi), %r8
incq %rax
andq %r8, %rdi
jne 0x1cd0ea
incq %rsi
cmpq %rdx, %rsi
jne 0x1cd0e1
retq
xorl %eax, %eax
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-contfinder.c
// Function: gt_contfinder_delete
void gt_contfinder_delete(GtContfinder *contfinder)
{
  if (contfinder != NULL)
  {
    GT_READJOINER_CONTFINDER_FREE_SEQNUMS(contfinder->seqnums);
    gt_free(contfinder->contained);
    gt_free(contfinder->copynum);
    gt_free(contfinder);
  }
}

// Assembly:
testq %rdi, %rdi
je 0x1ce33a
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq 0x48(%rdi), %rdi
leaq 0x1e8291(%rip), %r14    # 0x3b6585
movq %r14, %rsi
movl $0x387, %edx            # imm = 0x387
callq 0x109670
movq 0x10(%rbx), %rdi
movq %r14, %rsi
movl $0x388, %edx            # imm = 0x388
callq 0x109670
movq 0x40(%rbx), %rdi
movq %r14, %rsi
movl $0x389, %edx            # imm = 0x389
callq 0x109670
movq %rbx, %rdi
movq %r14, %rsi
movl $0x38a, %edx            # imm = 0x38A
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-contfinder.c
// Function: gt_contfinder_new
GtContfinder* gt_contfinder_new(GtReads2Twobit *r2t)
{
  GtContfinder *contfinder;
  contfinder = gt_malloc(sizeof (*contfinder));
  contfinder->contained = NULL;
  contfinder->copynum = NULL;
  contfinder->seqnums = NULL;
  contfinder->twobitencoding = gt_reads2twobit_export_twobitencoding(r2t);
  contfinder->seppos = (size_t*)gt_reads2twobit_export_seppos(r2t);
  contfinder->nofseqs = (gt_contfinder_seqnum_t)gt_reads2twobit_nofseqs(r2t);
  contfinder->logicalnofseqs = contfinder->nofseqs;
  contfinder->len = (size_t)gt_reads2twobit_seqlen_eqlen(r2t);
  return contfinder;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
leaq 0x1e823c(%rip), %rsi    # 0x3b6585
movl $0x50, %edi
movl $0x3a3, %edx            # imm = 0x3A3
callq 0x1092b2
movq %rax, %r14
movq $0x0, 0x10(%rax)
xorps %xmm0, %xmm0
movups %xmm0, 0x40(%rax)
movq %rbx, %rdi
callq 0x1e7940
movq %rax, (%r14)
movq %rbx, %rdi
callq 0x1e7950
movq %rax, 0x20(%r14)
movq %rbx, %rdi
callq 0x1e7980
movl %eax, 0xc(%r14)
movl %eax, 0x8(%r14)
movq %rbx, %rdi
callq 0x1e7990
movq %rax, 0x18(%r14)
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-contfinder.c
// Function: gt_contfinder_radixsort_str_eqlen_tester
void gt_contfinder_radixsort_str_eqlen_tester(GtContfinder *contfinder,
    bool mirrored, GtUword depth,
    GtUword maxdepth, bool print)
{
  GtUword *suffixes, totallength, width, i;
  GtRadixsortstringinfo *rsi;

  totallength = (GtUword) contfinder->nofseqs * contfinder->len - 1;
  width = mirrored ? GT_MULT2(totallength + 1) : (totallength + 1);
  rsi = gt_radixsort_str_new(contfinder->twobitencoding,
                             totallength,
                             (GtUword) contfinder->len,
                             GT_MULT2(width));
  suffixes = gt_malloc(sizeof (GtUword) * width);
  for (i = 0; i < width; i++)
  {
    suffixes[i] = i;
  }
  gt_radixsort_str_eqlen(rsi, suffixes, NULL, 0, depth, maxdepth, width);
  if (print)
  {
    for (i = 0; i < width; i++)
    {
      printf(""GT_WU"\n", suffixes[i]);
    }
  }
  gt_free(suffixes);
  gt_radixsort_str_delete(rsi);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rcx, %r14
movl %esi, %ecx
movl 0xc(%rdi), %r13d
movq 0x18(%rdi), %rax
imulq %rax, %r13
leaq -0x1(%r13), %rsi
shlq %cl, %r13
movl %r8d, %ebp
movq %rdx, %r12
movq (%rdi), %rdi
leaq (,%r13,2), %rcx
movq %rax, %rdx
callq 0x32aa38
movq %rax, %rbx
leaq (,%r13,8), %rdi
leaq 0x1e818f(%rip), %rsi    # 0x3b6585
movl $0x3c0, %edx            # imm = 0x3C0
callq 0x1092b2
movq %rax, %r15
testq %r13, %r13
je 0x1ce49d
leaq 0x1(%r13), %rax
andq $-0x2, %rax
leaq -0x1(%r13), %rcx
movq %rcx, %xmm0
pshufd $0x44, %xmm0, %xmm0     # xmm0 = xmm0[0,1,0,1]
movdqa 0x193646(%rip), %xmm1   # 0x361a70
xorl %ecx, %ecx
movdqa 0x19364c(%rip), %xmm2   # 0x361a80
pxor %xmm2, %xmm0
pcmpeqd %xmm3, %xmm3
movdqa 0x19364c(%rip), %xmm4   # 0x361a90
movdqa %xmm1, %xmm5
pxor %xmm2, %xmm5
movdqa %xmm5, %xmm6
pcmpgtd %xmm0, %xmm6
pcmpeqd %xmm0, %xmm5
pshufd $0xf5, %xmm5, %xmm7     # xmm7 = xmm5[1,1,3,3]
pand %xmm6, %xmm7
pshufd $0xf5, %xmm6, %xmm5     # xmm5 = xmm6[1,1,3,3]
por %xmm7, %xmm5
movd %xmm5, %edx
notl %edx
testb $0x1, %dl
je 0x1ce479
movq %rcx, (%r15,%rcx,8)
pxor %xmm3, %xmm5
pextrw $0x4, %xmm5, %edx
testb $0x1, %dl
je 0x1ce490
leaq 0x1(%rcx), %rdx
movq %rdx, 0x8(%r15,%rcx,8)
addq $0x2, %rcx
paddq %xmm4, %xmm1
cmpq %rcx, %rax
jne 0x1ce444
movq %r13, (%rsp)
movq %rbx, %rdi
movq %r15, %rsi
xorl %edx, %edx
xorl %ecx, %ecx
movq %r12, %r8
movq %r14, %r9
callq 0x32ac49
testq %r13, %r13
sete %al
xorb $0x1, %bpl
orb %al, %bpl
jne 0x1ce4e5
leaq 0x18b597(%rip), %r14    # 0x359a63
xorl %r12d, %r12d
movq (%r15,%r12,8), %rsi
movq %r14, %rdi
xorl %eax, %eax
callq 0x17070
incq %r12
cmpq %r12, %r13
jne 0x1ce4cf
leaq 0x1e8099(%rip), %rsi    # 0x3b6585
movq %r15, %rdi
movl $0x3cd, %edx            # imm = 0x3CD
callq 0x109670
movq %rbx, %rdi
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x32ab9a
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-contfinder.c
// Function: gt_contfinder_mark_as_contained
static inline void gt_contfinder_mark_as_contained(
    GtContfinder contfinder, GtContfinderBucketInfo bucket,
    bool except_lowest_seqnum)
{
  size_t i, from = 0, to = bucket.nofseqs;
  gt_contfinder_seqnum_t container = 0;
  gt_assert(bucket.nofseqs > 0);
  if (except_lowest_seqnum)
  {
    gt_contfinder_seqnum_t first, last;
    if (bucket.nofseqs == (gt_contfinder_seqnum_t)1)
      return;
    first = GT_READJOINER_CONTFINDER_GET_SEQNUM(bucket.seqnums, 0 +
        bucket.seqnums_offset);
    last = GT_READJOINER_CONTFINDER_GET_SEQNUM(bucket.seqnums, bucket.nofseqs
        - 1 + bucket.seqnums_offset);
    from = (size_t)1;
    if (last >= contfinder.nofseqs)
      last = (contfinder.nofseqs << 1) - last - 1;
    if (first >= contfinder.nofseqs || last < first)
    {
      from--;
      to--;
      container = last;
    }
    else
    {
      container = first;
      if (first == last) /* palindromic */
        to--;
    }
  }
  for (i = from; i < to; i++)
  {
    gt_contfinder_seqnum_t corrected =
      GT_READJOINER_CONTFINDER_GET_SEQNUM(bucket.seqnums,
          i + bucket.seqnums_offset);
    if (corrected >= contfinder.nofseqs)
      corrected = (contfinder.nofseqs << 1) - corrected - 1;
    GT_CONTFINDER_CONTAINS(&contfinder, container, corrected);
  }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movl 0xa0(%rsp), %eax
testq %rax, %rax
je 0x1ce856
leaq 0x90(%rsp), %r8
leaq 0x40(%rsp), %rsi
testb %dil, %dil
je 0x1ce751
cmpl $0x1, %eax
jne 0x1ce757
xorl %edx, %edx
movq %rax, %r9
xorl %ecx, %ecx
jmp 0x1ce7a0
xorl %edx, %edx
xorl %ecx, %ecx
jmp 0x1ce7ac
movq (%r8), %rcx
movq 0x8(%r8), %rdx
leaq (%rcx,%rdx,4), %rcx
movl (%rcx), %edi
leal -0x1(%rax), %edx
movl (%rcx,%rdx,4), %edx
movl 0xc(%rsi), %r9d
cmpl %r9d, %edx
movl %edx, %ecx
notl %ecx
leal (%rcx,%r9,2), %ecx
cmovbl %edx, %ecx
cmpl %r9d, %edi
jae 0x1ce79a
cmpl %edi, %ecx
jb 0x1ce79a
sete %cl
movzbl %cl, %ecx
movq %rax, %r9
subq %rcx, %r9
movl $0x1, %edx
movl %edi, %ecx
jmp 0x1ce7a0
leaq -0x1(%rax), %r9
xorl %edx, %edx
cmpl $0x1, %eax
movq %r9, %rax
je 0x1ce842
cmpq %rax, %rdx
jae 0x1ce842
movabsq $-0x8000000000000000, %rdi # imm = 0x8000000000000000
movq 0x8(%r8), %r9
shlq $0x2, %r9
addq (%r8), %r9
movl 0xc(%rsi), %r8d
leal (%r8,%r8), %r10d
movq 0x10(%rsi), %r11
movq 0x40(%rsi), %rsi
movl %ecx, %ebx
shrl $0x6, %ebx
movq %rdi, %r14
shrq %cl, %r14
movl %ecx, %r15d
movl (%r9,%rdx,4), %ebp
movl %ebp, %ecx
notl %ecx
addl %r10d, %ecx
cmpl %r8d, %ebp
cmovbl %ebp, %ecx
movq %rdi, %r12
shrq %cl, %r12
movl %ecx, %r13d
shrl $0x6, %r13d
orq %r12, (%r11,%r13,8)
testq %rsi, %rsi
je 0x1ce83a
testq %r14, (%r11,%rbx,8)
jne 0x1ce851
movzbl (%rsi,%r15), %ebp
movl %ecx, %ecx
movzbl (%rsi,%rcx), %r12d
movl $0x100, %r13d           # imm = 0x100
subl %r12d, %r13d
cmpl %ebp, %r13d
jbe 0x1ce836
addb %bpl, %r12b
movb %r12b, (%rsi,%r15)
movb $0x0, (%rsi,%rcx)
incq %rdx
cmpq %rdx, %rax
jne 0x1ce7e8
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x6b424
callq 0x6b45d
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-contigpaths.c
// Function: gt_contigpaths_get_file
static GtFile* gt_contigpaths_get_file(const char *indexname,
    const char *suffix, const char* mode, GtError *err)
{
  GtStr *path;
  GtFile *file;

  path = gt_str_new_cstr(indexname);
  gt_str_append_cstr(path, suffix);
  file = gt_file_new(gt_str_get(path), mode, err);
  gt_str_delete(path);
  return file;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rcx, %rbx
movq %rdx, %r14
movq %rsi, %r15
callq 0x120955
movq %rax, %r12
movq %rax, %rdi
movq %r15, %rsi
callq 0x12097f
movq %r12, %rdi
callq 0x120d23
movq %rax, %rdi
movq %r14, %rsi
movq %rbx, %rdx
callq 0x103957
movq %rax, %rbx
movq %r12, %rdi
callq 0x121b03
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
nop
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-contigs-graph.c
// Function: gt_contigs_graph_delete
void gt_contigs_graph_delete(GtContigsGraph *cg)
{
  if (cg != NULL)
  {
    gt_free(cg->v_spm[0]);
    gt_free(cg->v_spm[1]);
    gt_free(cg->v_scf);
    gt_free(cg->v_d);
    gt_free(cg->v_m);
    gt_free(cg->e_spm[0]);
    gt_free(cg->e_spm[1]);
    gt_free(cg->e_scf);
    gt_free(cg->v_cmp);
    gt_free(cg->units);
    gt_reads_libraries_table_delete(cg->rlt);
    gt_free(cg);
  }
}

// Assembly:
testq %rdi, %rdi
je 0x1cff33
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq 0x18(%rdi), %rdi
leaq 0x1e69e0(%rip), %r14    # 0x3b6841
movq %r14, %rsi
movl $0x4c3, %edx            # imm = 0x4C3
callq 0x109670
movq 0x20(%rbx), %rdi
movq %r14, %rsi
movl $0x4c4, %edx            # imm = 0x4C4
callq 0x109670
movq 0x28(%rbx), %rdi
movq %r14, %rsi
movl $0x4c5, %edx            # imm = 0x4C5
callq 0x109670
movq 0x30(%rbx), %rdi
movq %r14, %rsi
movl $0x4c6, %edx            # imm = 0x4C6
callq 0x109670
movq 0x38(%rbx), %rdi
movq %r14, %rsi
movl $0x4c7, %edx            # imm = 0x4C7
callq 0x109670
movq 0x80(%rbx), %rdi
movq %r14, %rsi
movl $0x4c8, %edx            # imm = 0x4C8
callq 0x109670
movq 0x88(%rbx), %rdi
movq %r14, %rsi
movl $0x4c9, %edx            # imm = 0x4C9
callq 0x109670
movq 0x98(%rbx), %rdi
movq %r14, %rsi
movl $0x4ca, %edx            # imm = 0x4CA
callq 0x109670
movq 0x40(%rbx), %rdi
movq %r14, %rsi
movl $0x4cb, %edx            # imm = 0x4CB
callq 0x109670
movq 0x58(%rbx), %rdi
movq %r14, %rsi
movl $0x4cc, %edx            # imm = 0x4CC
callq 0x109670
movq 0xa0(%rbx), %rdi
callq 0x1e8c73
movq %rbx, %rdi
movq %r14, %rsi
movl $0x4ce, %edx            # imm = 0x4CE
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-contigs-graph.c
// Function: gt_contigs_graph_rm_vertex
void gt_contigs_graph_rm_vertex(GtContigsGraph *cg, GtUword cnum)
{
  GtContigsGraphSpmEdge *edge;
  unsigned int incoming;
  gt_log_log("rm vertex "GT_WU"", cnum);
  for (incoming = 0; incoming < 2U; incoming++)
  {
    for (GT_CONTIGS_GRAPH_EACH_SPM_EDGE(cg, cnum, incoming, edge))
    {
      if (edge->deleted)
        continue;
      gt_contigs_graph_rm_spm_edge(cg, cnum, incoming, edge);
    }
  }
  cg->v_m[cnum].deleted = true;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
leaq 0x1e67cb(%rip), %rdi    # 0x3b6b6c
xorl %r15d, %r15d
xorl %eax, %eax
callq 0x108e02
movq 0x18(%r14,%r15,8), %rax
movq 0x80(%r14,%r15,8), %rcx
movq (%rax,%rbx,8), %rdx
movq 0x8(%rax,%rbx,8), %rax
shrq $0x10, %rdx
leaq (%rcx,%rdx,8), %r12
shrq $0x10, %rax
leaq (%rcx,%rax,8), %rax
cmpq %rax, %r12
jae 0x1d040f
testb $0x40, 0x7(%r12)
jne 0x1d03ef
movq %r14, %rdi
movq %rbx, %rsi
movl %r15d, %edx
movq %r12, %rcx
callq 0x1d0296
addq $0x8, %r12
movq 0x18(%r14,%r15,8), %rax
movq 0x8(%rax,%rbx,8), %rax
shrq $0xd, %rax
andq $-0x8, %rax
addq 0x80(%r14,%r15,8), %rax
jmp 0x1d03d1
leaq 0x1(%r15), %rax
testq %r15, %r15
movq %rax, %r15
je 0x1d03ab
movq 0x38(%r14), %rax
orb $0x1, (%rax,%rbx)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-contigs-graph.c
// Function: gt_contigs_graph_nof_optional_neighbours
uint64_t gt_contigs_graph_nof_optional_neighbours(GtContigsGraph *cg,
    GtUword cnum, unsigned int incoming)
{
  uint64_t n = 0;
  GtContigsGraphSpmEdge *edge;
  for (GT_CONTIGS_GRAPH_EACH_SPM_EDGE(cg, cnum, incoming, edge))
  {
    if (edge->deleted)
      continue;
    if (GT_CONTIGS_GRAPH_IS_OPTIONAL(cg, edge->dest))
      n++;
  }
  return n;
}

// Assembly:
movl %edx, %eax
movq 0x18(%rdi,%rax,8), %rcx
movq (%rcx,%rsi,8), %rdx
movq 0x8(%rcx,%rsi,8), %rcx
shrq $0x10, %rdx
shrq $0x10, %rcx
cmpq %rcx, %rdx
jae 0x1d0482
movq 0x80(%rdi,%rax,8), %rax
leaq (%rax,%rcx,8), %rcx
leaq (%rax,%rdx,8), %rdx
xorl %eax, %eax
testb $0x40, 0x7(%rdx)
jne 0x1d0478
movq 0x38(%rdi), %rsi
movl (%rdx), %r8d
movzbl (%rsi,%r8), %esi
btl $0x1, %esi
adcq $0x0, %rax
addq $0x8, %rdx
cmpq %rcx, %rdx
jb 0x1d045e
retq
xorl %eax, %eax
retq