LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa-mmsearch.c
// Function: gt_mmsearch_extendright
static GtUword gt_mmsearch_extendright(const GtEncseq *dbencseq,
                                             GtEncseqReader *esr,
                                             GtReadmode readmode,
                                             GtUword totallength,
                                             GtUword dbend,
                                             const GtQuerysubstring
                                               *querysubstring,
                                             GtUword matchlength)
{
  GtUchar dbchar;
  GtUword dbpos, querypos;

  if (dbend < totallength)
  {
    gt_encseq_reader_reinit_with_readmode(esr,dbencseq,readmode,dbend);
  }
  for (dbpos = dbend, querypos = querysubstring->currentoffset + matchlength;
       dbpos < totallength &&
       querypos < querysubstring->queryrep->seqlen;
       dbpos++, querypos++)
  {
    dbchar = gt_encseq_reader_next_encoded_char(esr);
    if (GT_ISSPECIAL(dbchar) ||
        dbchar != gt_mmsearch_accessquery(querysubstring->queryrep,querypos))
    {
      break;
    }
  }
  return dbpos - dbend;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r8, %r13
cmpq %rcx, %r8
jae 0x1a4f92
movq %r9, %r14
movq %rcx, %r15
movq %rsi, %r12
movq %rdi, %rsi
movq 0x40(%rsp), %rbp
movq %r12, %rdi
movq %r8, %rcx
movq %r8, %r13
callq 0xe8eed
addq 0x8(%r14), %rbp
movq %r13, (%rsp)
movq (%r14), %rax
cmpq 0x20(%rax), %rbp
jae 0x1a4f8e
movq %r12, %rdi
callq 0xe8186
cmpb $-0x3, %al
ja 0x1a4f8e
movl %eax, %ebx
movq (%r14), %rdi
movq %rbp, %rsi
callq 0x1a4fa7
cmpb %al, %bl
jne 0x1a4f8e
incq %r13
incq %rbp
cmpq %r13, %r15
jne 0x1a4f5a
movq %r15, %r13
movq (%rsp), %r8
subq %r8, %r13
movq %r13, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa-mmsearch.c
// Function: gt_mmsearch_accessquery
static GtUchar gt_mmsearch_accessquery(const GtQueryrepresentation *queryrep,
                                       GtUword pos)
{
  GtUword abspos, cc;

  gt_assert(queryrep != NULL);
  gt_assert(pos < queryrep->seqlen);
  abspos = queryrep->startpos + (queryrep->readmode == GT_READMODE_FORWARD
                                  ? pos
                                  : GT_REVERSEPOS(queryrep->seqlen,pos));
  if (queryrep->sequence != NULL)
  {
    cc = queryrep->sequence[abspos];
  } else
  {
    gt_assert(queryrep->encseq != NULL);
    cc = gt_encseq_get_encoded_char(queryrep->encseq,abspos,
                                    GT_READMODE_FORWARD);
  }
  if (GT_ISDIRCOMPLEMENT(queryrep->readmode))
  {
    if (GT_ISSPECIAL(cc))
    {
      return cc;
    }
    return GT_COMPLEMENTBASE(cc);
  } else
  {
    return cc;
  }
}

// Assembly:
pushq %rbx
testq %rdi, %rdi
je 0x1a500e
movq %rsi, %rax
movq %rdi, %rbx
movq 0x20(%rdi), %rsi
cmpq %rax, %rsi
jbe 0x1a5013
movl 0x10(%rbx), %edx
movq %rax, %rcx
notq %rcx
addq %rcx, %rsi
testl %edx, %edx
cmoveq %rax, %rsi
addq 0x18(%rbx), %rsi
movq (%rbx), %rax
testq %rax, %rax
je 0x1a4fdf
movb (%rax,%rsi), %al
jmp 0x1a4ff2
movq 0x8(%rbx), %rdi
testq %rdi, %rdi
je 0x1a5018
xorl %edx, %edx
callq 0xe7bbc
movl 0x10(%rbx), %edx
andl $-0x2, %edx
movb $0x3, %cl
subb %al, %cl
cmpb $-0x2, %al
movzbl %cl, %ecx
movzbl %al, %eax
cmovael %eax, %ecx
cmpl $0x2, %edx
cmovnel %eax, %ecx
movl %ecx, %eax
popq %rbx
retq
callq 0x62483
callq 0x62415
callq 0x6244c
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa-seqread.c
// Function: gt_newSequentialsuffixarrayreaderfromfile
Sequentialsuffixarrayreader *gt_newSequentialsuffixarrayreaderfromfile(
                                        const char *indexname,
                                        unsigned int demand,
                                        bool scanfile,
                                        GtLogger *logger,
                                        GtError *err)
{
  Sequentialsuffixarrayreader *ssar;

  ssar = gt_malloc(sizeof *ssar);
  ssar->suffixarray = gt_malloc(sizeof *ssar->suffixarray);
  if ((scanfile ? streamsuffixarray : gt_mapsuffixarray)(ssar->suffixarray,
                                                         demand,
                                                         indexname,
                                                         logger,
                                                         err) != 0)
  {
    gt_free(ssar->suffixarray);
    gt_free(ssar);
    return NULL;
  }
  ssar->nextsuftabindex = 0;
  ssar->nextlcptabindex = 1UL;
  ssar->largelcpindex = 0;
  ssar->scanfile = scanfile;
  ssar->suftab = NULL;
  gt_assert(ssar->suffixarray != NULL);
  ssar->encseq = ssar->suffixarray->encseq;
  ssar->readmode = ssar->suffixarray->readmode;
  ssar->numberofsuffixes = gt_encseq_total_length(ssar->encseq) + 1;
  ssar->nonspecials = gt_encseq_total_length(ssar->encseq) -
                      gt_encseq_specialcharacters(ssar->encseq);
  ssar->extrainfo = NULL;
  return ssar;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r8, (%rsp)
movq %rcx, %r15
movl %edx, %ebp
movl %esi, %r13d
movq %rdi, %r12
leaq 0x1ff8e1(%rip), %r14    # 0x3a4e82
movl $0x58, %edi
movq %r14, %rsi
movl $0x23, %edx
callq 0x104226
movq %rax, %rbx
movl $0x100, %edi            # imm = 0x100
movq %r14, %rsi
movl $0x24, %edx
callq 0x104226
movq %rax, (%rbx)
testl %ebp, %ebp
je 0x1a55d8
leaq -0x3f60(%rip), %r9      # 0x1a1676
jmp 0x1a55df
leaq -0x3357(%rip), %r9      # 0x1a2288
movq %rax, %rdi
movl %r13d, %esi
movq %r12, %rdx
movq %r15, %rcx
movq (%rsp), %r8
callq *%r9
testl %eax, %eax
je 0x1a5621
movq (%rbx), %rdi
leaq 0x1ff882(%rip), %r14    # 0x3a4e82
movq %r14, %rsi
movl $0x2b, %edx
callq 0x1045eb
movq %rbx, %rdi
movq %r14, %rsi
movl $0x2c, %edx
callq 0x1045eb
xorl %ebx, %ebx
jmp 0x1a5681
movq $0x0, 0x18(%rbx)
movq $0x1, 0x20(%rbx)
xorps %xmm0, %xmm0
movups %xmm0, 0x28(%rbx)
movb %bpl, 0x40(%rbx)
movq (%rbx), %rax
testq %rax, %rax
je 0x1a5693
movq (%rax), %rdi
movq %rdi, 0x38(%rbx)
movl 0x48(%rax), %eax
movl %eax, 0x50(%rbx)
callq 0xe7b9c
incq %rax
movq %rax, 0x10(%rbx)
movq 0x38(%rbx), %rdi
callq 0xe7b9c
movq %rax, %r14
movq 0x38(%rbx), %rdi
callq 0xec58b
subq %rax, %r14
movq %r14, 0x8(%rbx)
movq $0x0, 0x48(%rbx)
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x6267c
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa-seqread.c
// Function: gt_freeSequentialsuffixarrayreader
void gt_freeSequentialsuffixarrayreader(Sequentialsuffixarrayreader **ssar)
{
  if ((*ssar)->suffixarray != NULL)
  {
    gt_freesuffixarray((*ssar)->suffixarray);
    gt_free((*ssar)->suffixarray);
  }
  gt_free(*ssar);
}

// Assembly:
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
movq (%rdi), %rax
testq %rax, %rax
je 0x1a56c9
movq %rax, %rdi
callq 0x1a1540
movq (%rbx), %rax
movq (%rax), %rdi
leaq 0x1ff7c6(%rip), %rsi    # 0x3a4e82
movl $0x43, %edx
callq 0x1045eb
movq (%rbx), %rdi
leaq 0x1ff7b2(%rip), %rsi    # 0x3a4e82
movl $0x45, %edx
popq %rbx
jmp 0x1045eb
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa-seqread.c
// Function: gt_nextSequentialsuftabvalue
int gt_nextSequentialsuftabvalue(GtUword *currentsuffix,
                                 Sequentialsuffixarrayreader *ssar)
{
  gt_assert(ssar != NULL);
  if (ssar->scanfile)
  {
#if defined (_LP64) || defined (_WIN64)
    if (ssar->suffixarray->suftabstream_GtUword.fp != NULL)
    {
      return gt_readnextfromstream_GtUword(currentsuffix,
                                 &ssar->suffixarray->suftabstream_GtUword);
    } else
    {
      uint32_t readvalue = 0;
      int ret = gt_readnextfromstream_uint32_t(
                                 &readvalue,
                                 &ssar->suffixarray->suftabstream_uint32_t);
      *currentsuffix = (GtUword) readvalue;
      return ret;
    }
#else
     return gt_readnextfromstream_GtUword(currentsuffix,
                                      &ssar->suffixarray->suftabstream_GtUword);
#endif
  }
  if (ssar->scanfile)
  {
    *currentsuffix = ESASUFFIXPTRGET(ssar->suftab,ssar->nextsuftabindex++);
  } else
  {
    *currentsuffix = ESASUFFIXPTRGET(ssar->suffixarray->suftab,
                                     ssar->nextsuftabindex++);
  }
  return 1;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
testq %rsi, %rsi
je 0x1a59e7
movq %rdi, %rbx
movq (%rsi), %r15
cmpb $0x1, 0x40(%rsi)
jne 0x1a5950
movq 0xb0(%r15), %rcx
testq %rcx, %rcx
je 0x1a5966
movl 0xa4(%r15), %eax
cmpl 0xa0(%r15), %eax
jb 0x1a5934
movq 0xa8(%r15), %rdi
movl $0x8, %esi
movl $0x1000, %edx           # imm = 0x1000
callq 0x17b40
movq %rax, %r14
movl %r14d, 0xa0(%r15)
movq 0xb0(%r15), %rdi
callq 0x17f00
testl %eax, %eax
jne 0x1a59ec
movl $0x0, 0xa4(%r15)
xorl %eax, %eax
testl %r14d, %r14d
je 0x1a59dd
movq 0xa8(%r15), %rcx
leal 0x1(%rax), %edx
movl %edx, 0xa4(%r15)
movl %eax, %eax
movq (%rcx,%rax,8), %rcx
jmp 0x1a59d5
movq 0x58(%r15), %rax
movq 0x18(%rsi), %rcx
leaq 0x1(%rcx), %rdx
movq %rdx, 0x18(%rsi)
movq (%rax,%rcx,8), %rcx
jmp 0x1a59d5
movl 0x8c(%r15), %eax
cmpl 0x88(%r15), %eax
jb 0x1a59bf
movq 0x90(%r15), %rdi
movq 0x98(%r15), %rcx
movl $0x4, %esi
movl $0x1000, %edx           # imm = 0x1000
callq 0x17b40
movq %rax, %r14
movl %r14d, 0x88(%r15)
movq 0x98(%r15), %rdi
callq 0x17f00
testl %eax, %eax
jne 0x1a59f1
movl $0x0, 0x8c(%r15)
xorl %eax, %eax
testl %r14d, %r14d
je 0x1a59e3
movq 0x90(%r15), %rcx
leal 0x1(%rax), %edx
movl %edx, 0x8c(%r15)
movl %eax, %eax
movl (%rcx,%rax,4), %ecx
movl $0x1, %eax
movq %rcx, (%rbx)
popq %rbx
popq %r14
popq %r15
retq
xorl %ecx, %ecx
jmp 0x1a59da
callq 0x627c1
callq 0x62771
callq 0x62799
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa-seqread.c
// Function: gt_suftabSequentialsuffixarrayreader
const ESASuffixptr *gt_suftabSequentialsuffixarrayreader(
                        const Sequentialsuffixarrayreader *ssar)
{
  gt_assert(ssar != NULL);
  if (ssar->scanfile)
  {
    return ssar->suftab;
  }
  return ssar->suffixarray->suftab;
}

// Assembly:
testq %rdi, %rdi
je 0x1a5a31
cmpb $0x1, 0x40(%rdi)
jne 0x1a5a26
addq $0x30, %rdi
jmp 0x1a5a2d
movq (%rdi), %rdi
addq $0x58, %rdi
movq (%rdi), %rax
retq
pushq %rax
callq 0x6286c
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa-shulen.c
// Function: gt_multiesa2shulengthdist_print
int gt_multiesa2shulengthdist_print(Sequentialsuffixarrayreader *ssar,
                                    const GtEncseq *encseq,
                                    GtError *err)
{
  GtBUstate_shulen *state;
  bool haserr = false;

  state = gt_malloc(sizeof (*state));
  state->numofdbfiles = gt_encseq_num_of_files(encseq);
  state->encseq = encseq;
#ifdef GENOMEDIFF_PAPER_IMPL
  state->leafdist = gt_malloc(sizeof (*state->leafdist) * state->numofdbfiles);
#endif
#ifdef SHUDEBUG
  state->nextid = 0;
#endif
  state->shulengthdist = shulengthdist_new(state->numofdbfiles);
  if (gt_esa_bottomup_shulen(ssar, state, err) != 0)
  {
    haserr = true;
  }
  if (!haserr)
  {
    shulengthdist_print(NULL,(const uint64_t * const*) state->shulengthdist,
                        state->numofdbfiles);
  }
  gt_array2dim_delete(state->shulengthdist);
#ifdef GENOMEDIFF_PAPER_IMPL
  gt_free(state->leafdist);
#endif
  gt_free(state);
  return haserr ? -1 : 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movq %rdx, %r14
movq %rsi, %r15
movq %rdi, %r12
leaq 0x1ff60f(%rip), %rsi    # 0x3a5167
movl $0x48, %edi
movl $0x17e, %edx            # imm = 0x17E
callq 0x104226
movq %rax, %rbx
movq %r15, %rdi
callq 0xefbc9
movq %rax, (%rbx)
movq %r15, 0x10(%rbx)
movq %rax, %rdi
callq 0x1a5bf2
movq %rax, 0x8(%rbx)
movq %r12, %rdi
movq %rbx, %rsi
movq %r14, %rdx
callq 0x1a5c85
movl %eax, %ebp
testl %eax, %eax
jne 0x1a5ba7
movq (%rbx), %rdx
movq 0x8(%rbx), %rsi
xorl %edi, %edi
callq 0x1a64f4
movq 0x8(%rbx), %rax
movq (%rax), %rdi
leaq 0x1ff5b2(%rip), %r14    # 0x3a5167
movq %r14, %rsi
movl $0x191, %edx            # imm = 0x191
callq 0x1045eb
movq 0x8(%rbx), %rdi
movq %r14, %rsi
movl $0x191, %edx            # imm = 0x191
callq 0x1045eb
movq %rbx, %rdi
movq %r14, %rsi
movl $0x195, %edx            # imm = 0x195
callq 0x1045eb
xorl %eax, %eax
negl %ebp
sbbl %eax, %eax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa-shulen.c
// Function: shulengthdist_new
static uint64_t **shulengthdist_new(GtUword numofdbfiles)
{
  GtUword idx1, idx2;
  uint64_t **shulengthdist;

  gt_array2dim_malloc(shulengthdist,numofdbfiles,numofdbfiles);
  for (idx1=0; idx1 < numofdbfiles; idx1++)
  {
    for (idx2=0; idx2 < numofdbfiles; idx2++)
    {
      shulengthdist[idx1][idx2] = 0;
    }
  }
  return shulengthdist;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rdi, %rbx
leaq (,%rdi,8), %r14
leaq 0x1ff55b(%rip), %r12    # 0x3a5167
movq %r14, %rdi
movq %r12, %rsi
movl $0x145, %edx            # imm = 0x145
callq 0x104226
movq %rax, %r15
movq %r14, %rdi
imulq %rbx, %rdi
movq %r12, %rsi
movl $0x145, %edx            # imm = 0x145
callq 0x104226
movq %rax, (%r15)
cmpq $0x2, %rbx
jb 0x1a5c58
movq (%r15), %rax
addq %r14, %rax
movl $0x1, %ecx
movq %rax, (%r15,%rcx,8)
incq %rcx
addq %r14, %rax
cmpq %rcx, %rbx
jne 0x1a5c47
jmp 0x1a5c5d
testq %rbx, %rbx
je 0x1a5c76
xorl %r12d, %r12d
movq (%r15,%r12,8), %rdi
xorl %esi, %esi
movq %r14, %rdx
callq 0x173a0
incq %r12
cmpq %r12, %rbx
jne 0x1a5c60
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/match/esa-shulen.c
// Function: shulengthdist_print
static void shulengthdist_print(const GtStrArray *file_names,
                                const uint64_t * const*shulengthdist,
                                GtUword numofdbfiles)
{
  GtUword idx1, idx2;

  /*shulengthdist[0][0] = 0; for testing */
  printf("# sum of shulen\n" GT_WU "\n",numofdbfiles);
  for (idx2=0; idx2 < numofdbfiles; idx2++)
  {
    if (file_names != NULL)
    {
      printf("%s\t",gt_str_array_get(file_names,idx2));
    } else
    {
      printf("" GT_WU "\t",idx2);
    }
    for (idx1=0; idx1 < numofdbfiles; idx1++)
    {
      if (idx1 != idx2)
      {
        printf(Formatuint64_t"\t",
               PRINTuint64_tcast(shulengthdist[idx1][idx2]));
      } else
      {
        printf("0.000000\t");
      }
    }
    printf("\n");
  }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rdx, %rbx
movq %rsi, %r14
movq %rdi, %r15
leaq 0x1fed8f(%rip), %rdi    # 0x3a529e
movq %rdx, %rsi
xorl %eax, %eax
callq 0x17070
testq %rbx, %rbx
je 0x1a65a3
leaq 0x20531f(%rip), %r12    # 0x3ab848
leaq 0x1fed83(%rip), %r13    # 0x3a52b3
xorl %ebp, %ebp
movq %r15, (%rsp)
testq %r15, %r15
je 0x1a6552
movq %r15, %rdi
movq %rbp, %rsi
callq 0x11bfb3
leaq 0x1af757(%rip), %rdi    # 0x355ca4
movq %rax, %rsi
jmp 0x1a6558
movq %r12, %rdi
movq %rbp, %rsi
xorl %eax, %eax
callq 0x17070
xorl %r15d, %r15d
cmpq %r15, %rbp
jne 0x1a6573
movq %r13, %rdi
xorl %eax, %eax
callq 0x17070
jmp 0x1a6585
movq (%r14,%r15,8), %rax
movq (%rax,%rbp,8), %rsi
movq %r12, %rdi
xorl %eax, %eax
callq 0x17070
incq %r15
cmpq %r15, %rbx
jne 0x1a6562
movl $0xa, %edi
callq 0x17a20
incq %rbp
cmpq %rbx, %rbp
movq (%rsp), %r15
jne 0x1a6536
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa-shulen.c
// Function: gt_multiesa2shulengthdist
int gt_multiesa2shulengthdist(Sequentialsuffixarrayreader *ssar,
                              const GtEncseq *encseq,
                              uint64_t **shulen,
                              const GtShuUnitFileInfo *unit_info,
                              GtError *err)
{
  GtBUstate_shulen *bustate;
  bool haserr = false;

  bustate = gt_malloc(sizeof (*bustate));
  bustate->numofdbfiles = unit_info->num_of_genomes;
  bustate->file_to_genome_map = unit_info->map_files;
  bustate->encseq = encseq;
#ifdef GENOMEDIFF_PAPER_IMPL
  bustate->leafdist
    = gt_malloc(sizeof (*bustate->leafdist) * bustate->numofdbfiles);
#endif
#ifdef SHUDEBUG
  bustate->nextid = 0;
#endif
  bustate->shulengthdist = shulen;
  if (gt_esa_bottomup_shulen(ssar, bustate, err) != 0)
  {
    haserr = true;
  }
#ifdef GENOMEDIFF_PAPER_IMPL
  gt_free(bustate->leafdist);
#endif
  gt_free(bustate);
  return haserr ? -1 : 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r8, %rbx
movq %rcx, %r14
movq %rdx, %r15
movq %rsi, %r12
movq %rdi, %r13
leaq 0x1fe973(%rip), %rsi    # 0x3a5167
movl $0x48, %edi
movl $0x21c, %edx            # imm = 0x21C
callq 0x104226
movq %rax, %rbp
movq (%r14), %rax
movq %rax, (%rbp)
movq 0x20(%r14), %rax
movq %rax, 0x18(%rbp)
movq %r12, 0x10(%rbp)
movq %r15, 0x8(%rbp)
movq %r13, %rdi
movq %rbp, %rsi
movq %rbx, %rdx
callq 0x1a5c85
movl %eax, %ebx
movq %rbp, %rdi
leaq 0x1fe930(%rip), %rsi    # 0x3a5167
movl $0x22f, %edx            # imm = 0x22F
callq 0x1045eb
xorl %eax, %eax
negl %ebx
sbbl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa-shulen.c
// Function: gt_sfx_multiesashulengthdist_new
GtBUstate_shulen *gt_sfx_multiesashulengthdist_new(const GtEncseq *encseq,
                                            GenomediffInfo *gd_info)
{
  GtBUstate_shulen *bustate;

  bustate = gt_malloc(sizeof (*bustate));
  bustate->encseq = encseq;
  bustate->previousbucketlastsuffix = ULONG_MAX;
  bustate->idxoffset = 0;
  bustate->firstedgefromroot = false;
#ifdef SHUDEBUG
  bustate->nextid = 0;
#endif
  if (gd_info == NULL)
    bustate->unit_info = gt_shu_unit_info_new(encseq);
  else
    bustate->unit_info = gd_info->unit_info;

  bustate->numofdbfiles = gt_encseq_num_of_files(encseq);
#ifdef GENOMEDIFF_PAPER_IMPL
  bustate->leafdist
    = gt_malloc(sizeof (*bustate->leafdist) * bustate->numofdbfiles);
#endif
  bustate->file_to_genome_map = bustate->unit_info->map_files;
  if (gd_info == NULL)
    bustate->shulengthdist = shulengthdist_new(bustate->numofdbfiles);
  else
    bustate->shulengthdist = gd_info->shulensums;

  bustate->stack = (void *) gt_GtArrayGtBUItvinfo_new_shulen();
  return bustate;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %rsi, %r14
movq %rdi, %r15
leaq 0x1fe8ff(%rip), %rsi    # 0x3a5167
movl $0x48, %edi
movl $0x238, %edx            # imm = 0x238
callq 0x104226
movq %rax, %rbx
movq %r15, 0x10(%rax)
movq $-0x1, 0x28(%rax)
movq $0x0, 0x20(%rax)
movb $0x0, 0x30(%rax)
testq %r14, %r14
je 0x1a689c
movq (%r14), %rax
jmp 0x1a68a4
movq %r15, %rdi
callq 0x1fe855
movq %rax, 0x38(%rbx)
movq %r15, %rdi
callq 0xefbc9
movq %rax, (%rbx)
movq 0x38(%rbx), %rcx
movq 0x20(%rcx), %rcx
movq %rcx, 0x18(%rbx)
testq %r14, %r14
je 0x1a68ca
movq 0x8(%r14), %rax
jmp 0x1a68d2
movq %rax, %rdi
callq 0x1a5bf2
movq %rax, 0x8(%rbx)
leaq 0x1fe868(%rip), %rsi    # 0x3a5145
movl $0x18, %edi
movl $0x5f, %edx
callq 0x104226
xorps %xmm0, %xmm0
movups %xmm0, (%rax)
movq $0x0, 0x10(%rax)
movq %rax, 0x40(%rbx)
movq %rbx, %rax
popq %rbx
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa-shulen.c
// Function: gt_sfx_multiesashulengthdist_delete
void gt_sfx_multiesashulengthdist_delete(GtBUstate_shulen *bustate,
                                         GenomediffInfo *gd_info)
{
  if (bustate == NULL)
  {
    return;
  }
  gt_assert(bustate->shulengthdist != NULL);
  if (gd_info == NULL) {
    shulengthdist_print(bustate->unit_info->file_names,
                        (const uint64_t * const*) bustate->shulengthdist,
                        bustate->numofdbfiles);
    gt_array2dim_delete(bustate->shulengthdist);
    gt_shu_unit_info_delete(bustate->unit_info);
  }
  gt_GtArrayGtBUItvinfo_delete_shulen(bustate->stack,bustate);
#ifdef GENOMEDIFF_PAPER_IMPL
  gt_free(bustate->leafdist);
#endif
  gt_free(bustate);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x1a6fad
movq %rsi, %rax
movq %rdi, %rbx
movq 0x8(%rdi), %rsi
testq %rsi, %rsi
je 0x1a6fb5
testq %rax, %rax
jne 0x1a6f89
movq (%rbx), %rdx
movq 0x38(%rbx), %rax
movq 0x18(%rax), %rdi
callq 0x1a64f4
movq 0x8(%rbx), %rax
movq (%rax), %rdi
leaq 0x1fe205(%rip), %r14    # 0x3a5167
movq %r14, %rsi
movl $0x295, %edx            # imm = 0x295
callq 0x1045eb
movq 0x8(%rbx), %rdi
movq %r14, %rsi
movl $0x295, %edx            # imm = 0x295
callq 0x1045eb
movq 0x38(%rbx), %rdi
callq 0x1fe810
movq 0x40(%rbx), %rdi
callq 0x1a5acb
leaq 0x1fe1ce(%rip), %rsi    # 0x3a5167
movq %rbx, %rdi
movl $0x29c, %edx            # imm = 0x29C
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x1045eb
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x62fd2
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa-shulen.c
// Function: processleafedge_shulen
static int processleafedge_shulen(bool firstsucc,
                                  GtUword fatherdepth,
                                  GtBUinfo_shulen *father,
                                  GtUword leafnumber,
                                  GtBUstate_shulen *state,
                                  GT_UNUSED GtError *err)
{
  GtUword gnum;

#ifdef SHUDEBUG
  printf("processleafedge " GT_WU " firstsucc=%s, "
         " depth(father)=" GT_WU ", path=",
         leafnumber,
         firstsucc ? "true" : "false",
         fatherdepth);
  if (fatherdepth > 0)
  {
    gt_encseq_showatstartposwithdepth(stdout,
                                      state->encseq,
                                      GT_READMODE_FORWARD,
                                      leafnumber,
                                      fatherdepth);
  }
  printf("\n");
#endif
  if (state->file_to_genome_map != NULL)
  {
    gnum = state->file_to_genome_map[gt_encseq_filenum(state->encseq,
                                                       leafnumber)];
  } else
  {
    gnum = gt_encseq_filenum(state->encseq,leafnumber);
  }
  if (firstsucc)
  {
    gt_assert(father != NULL);
    if (father->gnumdist == NULL)
    {
      father->gnumdist
        = gt_malloc(sizeof (*father->gnumdist) * state->numofdbfiles);
    }
    resetgnumdist_shulen(father,state->numofdbfiles);
#ifdef SHUDEBUG
    shownode(__LINE__,state,"father",father);
#endif
  } else
  {
#ifdef SHUDEBUG
    shownode(__LINE__,state,"father",father);
#endif
    shu_compute_leaf_edge_contrib(state,father->gnumdist,gnum,fatherdepth);
  }
  father->gnumdist[gnum]++;
#ifdef SHUDEBUG
  printf("gnumdist[id=" GT_WU ",filenum=" GT_WU "]=" GT_WU "\n",father->id,gnum,
                                              father->gnumdist[gnum]);
  state->lastleafnumber = leafnumber;
#endif
  return 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r8, %r14
movq %rdx, %r13
movq %rsi, %r12
movl %edi, %ebp
movq 0x10(%r8), %rdi
movq 0x18(%r8), %r15
movq %rcx, %rsi
callq 0xf6438
movq %rax, %rbx
testq %r15, %r15
je 0x1a70c6
movq (%r15,%rbx,8), %rbx
testb %bpl, %bpl
je 0x1a7114
testq %r13, %r13
je 0x1a716d
movq (%r13), %r15
testq %r15, %r15
jne 0x1a70fc
movq (%r14), %rdi
shlq $0x3, %rdi
leaq 0x1fe07c(%rip), %rsi    # 0x3a5167
movl $0xeb, %edx
callq 0x104226
movq %rax, %r15
movq %rax, (%r13)
movq (%r14), %rdx
testq %rdx, %rdx
je 0x1a715a
shlq $0x3, %rdx
movq %r15, %rdi
xorl %esi, %esi
callq 0x173a0
jmp 0x1a715a
movq (%r13), %r15
cmpq $0x0, (%r14)
je 0x1a715a
incq %r12
xorl %eax, %eax
cmpq %rax, %rbx
je 0x1a7152
cmpq $0x0, (%r15,%rax,8)
je 0x1a7152
movq 0x8(%r14), %rcx
movq (%rcx,%rax,8), %rdx
addq %r12, (%rdx,%rbx,8)
cmpq $0x0, (%r15,%rbx,8)
jne 0x1a7152
movq (%r15,%rax,8), %rdx
imulq %r12, %rdx
movq (%rcx,%rbx,8), %rcx
addq %rdx, (%rcx,%rax,8)
incq %rax
cmpq (%r14), %rax
jb 0x1a7123
incq (%r15,%rbx,8)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x63042
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa-shulen.c
// Function: cartproduct_shulen
static void cartproduct_shulen(GtBUstate_shulen *state,
                               GtUword depth,
                               const GtUword *refnumdist,
                               const GtUword *querynumdist)
{
  GtUword referidx, shulenidx;

  for (referidx=0; referidx < state->numofdbfiles; referidx++)
  {
    if (refnumdist[referidx] > 0 && querynumdist[referidx] == 0)
    {
      for (shulenidx=0; shulenidx < state->numofdbfiles; shulenidx++)
      {
        if (querynumdist[shulenidx] > 0)
        {
          gt_assert(referidx != shulenidx);
          contribute_shulen(__LINE__,
                            state->shulengthdist,
                            referidx,
                            shulenidx,
                            querynumdist[shulenidx],
                            depth + 1);
        }
      }
    }
  }
}

// Assembly:
pushq %rax
movq (%rdi), %r8
testq %r8, %r8
je 0x1a7277
incq %rsi
xorl %eax, %eax
cmpq $0x0, (%rdx,%rax,8)
je 0x1a726f
cmpq $0x0, (%rcx,%rax,8)
jne 0x1a726f
xorl %r9d, %r9d
movq (%rcx,%r9,8), %r10
testq %r10, %r10
je 0x1a7267
cmpq %r9, %rax
je 0x1a7279
movq 0x8(%rdi), %r8
imulq %rsi, %r10
movq (%r8,%rax,8), %r8
addq %r10, (%r8,%r9,8)
movq (%rdi), %r8
incq %r9
cmpq %r8, %r9
jb 0x1a7246
incq %rax
cmpq %r8, %rax
jb 0x1a7235
popq %rax
retq
callq 0x630b4
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa-splititv.c
// Function: gt_lcpintervalfindcharchildintv
bool gt_lcpintervalfindcharchildintv(const GtEncseq *encseq,
                                     GtReadmode readmode,
                                     GtUword totallength,
                                     const ESASuffixptr *suftab,
                                     Simplelcpinterval *itv,
                                     GtUchar cc,
                                     GtUword offset,
                                     GtUword left,
                                     GtUword right)
{
  GtUchar leftcc, rightcc;
  GtUword pos, rightbound, leftbound = left;

  pos = ESASUFFIXPTRGET(suftab,right) + offset;
  rightcc = SEQUENCE(encseq,pos);
  while (true)
  {
    pos = ESASUFFIXPTRGET(suftab,leftbound) + offset;
    leftcc = SEQUENCE(encseq,pos);
    if (leftcc == rightcc)
    {
      break;
    }
    rightbound = lcpintervalfindrightbound(encseq,readmode,
                                           totallength,suftab,leftcc,
                                           offset,leftbound,right);
    if (leftcc == cc)
    {
      itv->left = leftbound;
      itv->right = rightbound;
      return true;
    }
    if (leftcc > cc)
    {
      return false;
    }
    leftbound = rightbound+1;
  }
  if (leftcc == cc)
  {
    itv->left = leftbound;
    itv->right = right;
    return true;
  }
  return false;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movl %r9d, %ebp
movq %r8, 0x10(%rsp)
movq %rcx, %r14
movq %rdx, %r15
movl %esi, (%rsp)
movq %rdi, 0x8(%rsp)
movq 0x60(%rsp), %rax
movq (%rcx,%rax,8), %rsi
addq 0x50(%rsp), %rsi
movl $0xff, 0x4(%rsp)
cmpq %rdx, %rsi
je 0x1a72d3
movq 0x8(%rsp), %rdi
movl (%rsp), %edx
callq 0xe7bbc
movzbl %al, %eax
movl %eax, 0x4(%rsp)
movq 0x58(%rsp), %r13
movq (%r14,%r13,8), %rsi
addq 0x50(%rsp), %rsi
movb $-0x1, %bl
cmpq %r15, %rsi
je 0x1a72f7
movq 0x8(%rsp), %rdi
movl (%rsp), %edx
callq 0xe7bbc
movl %eax, %ebx
movzbl %bl, %r12d
cmpl %r12d, 0x4(%rsp)
je 0x1a7339
movq 0x8(%rsp), %rdi
movl (%rsp), %esi
movq %r15, %rdx
movq %r14, %rcx
movl %r12d, %r8d
movq 0x50(%rsp), %r9
pushq 0x60(%rsp)
pushq %r13
callq 0x1a7367
addq $0x10, %rsp
cmpb %bpl, %r12b
je 0x1a7347
cmpb %bpl, %bl
ja 0x1a7343
incq %rax
movq %rax, %r13
jmp 0x1a72d8
cmpb %bpl, %bl
movq 0x60(%rsp), %rcx
je 0x1a734a
xorl %eax, %eax
jmp 0x1a7358
movq %rax, %rcx
movq 0x10(%rsp), %rax
movq %r13, (%rax)
movq %rcx, 0x8(%rax)
movb $0x1, %al
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa-splititv.c
// Function: lcpintervalfindrightbound
static GtUword lcpintervalfindrightbound(const GtEncseq *encseq,
                                        GtReadmode readmode,
                                        GtUword totallength,
                                        const ESASuffixptr *suftab,
                                        GtUchar cc,
                                        GtUword offset,
                                        GtUword left,
                                        GtUword right)
{
  GtUword pos, mid;
  GtUchar midcc;

  while (right > left+1)
  {
    mid = GT_DIV2(left+right);
    pos = ESASUFFIXPTRGET(suftab,mid) + offset;
    midcc = SEQUENCE(encseq,pos);
    if (cc < midcc)
    {
      right = mid;
    } else
    {
      left = mid;
    }
  }
  return left;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movl %esi, 0xc(%rsp)
movq %rdi, 0x10(%rsp)
movq 0x58(%rsp), %rbp
movq 0x50(%rsp), %r12
leaq 0x1(%r12), %rax
cmpq %rbp, %rax
jae 0x1a73ea
movq %r9, %r14
movq %rcx, %r15
movq %rdx, %rbx
movzbl %r8b, %edi
movl %edi, 0x8(%rsp)
leaq (%r12,%rbp), %r13
shrq %r13
movq (%r15,%r13,8), %rsi
addq %r14, %rsi
movl $0xff, %eax
cmpq %rbx, %rsi
je 0x1a73d0
movq 0x10(%rsp), %rdi
movl 0xc(%rsp), %edx
callq 0xe7bbc
movl 0x8(%rsp), %edi
movzbl %al, %eax
cmpl %edi, %eax
ja 0x1a73d9
movq %r13, %r12
jmp 0x1a73df
movq %r13, %rbp
movq %r12, %r13
leaq 0x1(%r13), %rax
cmpq %rax, %rbp
ja 0x1a73a3
jmp 0x1a73ed
movq %r12, %r13
movq %r13, %rax
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa-splititv.c
// Function: gt_findmaximalprefixinESA
GtUword gt_findmaximalprefixinESA(const GtEncseq *encseq,
                                  GtReadmode readmode,
                                  GtUword totallength,
                                  const ESASuffixptr *suftab,
                                  const GtUchar *query,
                                  GtUword querylen)
{
  Simplelcpinterval current_itv;
  GtUword idx;

  current_itv.left = 0;
  current_itv.right = totallength;

  for (idx = 0; idx < querylen; idx++)
  {
    if (GT_ISSPECIAL(query[idx]))
    {
      gt_assert(query[idx] != GT_SEPARATOR);
      break;
    }
    if (!gt_lcpintervalfindcharchildintv(encseq,
                                         readmode,
                                         totallength,
                                         suftab,
                                         &current_itv,
                                         query[idx],
                                         idx,
                                         current_itv.left,
                                         current_itv.right))
    {
      break;
    }
  }
  return idx;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x38, %rsp
movq %rcx, 0x20(%rsp)
movq $0x0, 0x28(%rsp)
movq %rdx, 0x30(%rsp)
testq %r9, %r9
je 0x1a7477
movq %r9, %r14
movq %r8, %r15
movq %rdx, %r13
movl %esi, %ebp
movq %rdi, %r12
xorl %ebx, %ebx
movb (%r15,%rbx), %al
cmpb $-0x2, %al
jae 0x1a747b
movups 0x28(%rsp), %xmm0
movups %xmm0, 0x8(%rsp)
movq %rbx, (%rsp)
movzbl %al, %r9d
movq %r12, %rdi
movl %ebp, %esi
movq %r13, %rdx
movq 0x20(%rsp), %rcx
leaq 0x28(%rsp), %r8
callq 0x1a7280
testb %al, %al
je 0x1a747f
incq %rbx
cmpq %rbx, %r14
jne 0x1a7435
movq %r14, %rbx
jmp 0x1a747f
xorl %ebx, %ebx
jmp 0x1a747f
cmpb $-0x1, %al
je 0x1a7491
movq %rbx, %rax
addq $0x38, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x630ed
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa-splititv.c
// Function: gt_lcpintervalextendlcp
GtUchar gt_lcpintervalextendlcp(const GtEncseq *encseq,
                                GtReadmode readmode,
                                const ESASuffixptr *suftab,
                                GtUword totallength,
                                GtUchar alphasize,
                                GtUword parentoffset,
                                GtUword parentleft,
                                GtUword parentright)
{
  GtUchar ccl, ccr;

  ccl = SEQUENCE(encseq,ESASUFFIXPTRGET(suftab,parentleft) + parentoffset);
  ccr = SEQUENCE(encseq,ESASUFFIXPTRGET(suftab,parentright) + parentoffset);
  if (ccl != ccr || GT_ISSPECIAL(ccl))
  {
    return alphasize;
  }
  gt_assert(ccl < alphasize);
  return ccl;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r9, %r14
movl %r8d, 0x4(%rsp)
movq %rcx, %r13
movq %rdx, %rbx
movl %esi, %r15d
movq %rdi, %r12
movq 0x48(%rsp), %rcx
movq 0x40(%rsp), %rax
movq (%rdx,%rax,8), %rsi
addq %r9, %rsi
movb $-0x1, %bpl
cmpq %r13, %rsi
je 0x1a767f
movq %r12, %rdi
movl %r15d, %edx
movq %rcx, %rbp
callq 0xe7bbc
movq %rbp, %rcx
movl %eax, %ebp
addq (%rbx,%rcx,8), %r14
movl $0xff, %eax
cmpq %r13, %r14
je 0x1a769e
movq %r12, %rdi
movq %r14, %rsi
movl %r15d, %edx
callq 0xe7bbc
movzbl %al, %eax
cmpb $-0x3, %bpl
ja 0x1a76b8
movzbl %bpl, %ecx
cmpl %ecx, %eax
jne 0x1a76b8
cmpb 0x4(%rsp), %bpl
jb 0x1a76be
callq 0x63196
movl 0x4(%rsp), %eax
movl %eax, %ebp
movl %ebp, %eax
addq $0x8, %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/match/esa-spmitvs.c
// Function: gt_process_spmitv
int gt_process_spmitv(const char *inputindex, GtLogger *logger, GtError *err)
{
  bool haserr = false;
  Sequentialsuffixarrayreader *ssar;

  gt_error_check(err);
  ssar = gt_newSequentialsuffixarrayreaderfromfile(inputindex,
                                                   SARR_LCPTAB |
                                                   SARR_SUFTAB |
                                                   SARR_ESQTAB,
                                                   true,
                                                   logger,
                                                   err);
  if (ssar == NULL)
  {
    haserr = true;
  }
  if (!haserr)
  {
    GtESAVisitor *ev;
    GtUword nonspecials;

    nonspecials = gt_Sequentialsuffixarrayreader_nonspecials(ssar);
    ev = gt_esa_spmitvs_visitor_new(
                              gt_encseqSequentialsuffixarrayreader(ssar),
                              gt_readmodeSequentialsuffixarrayreader(ssar),
                              gt_Sequentialsuffixarrayreader_prefixlength(ssar),
                              err);

    if (gt_esa_bottomup(ssar, ev, err) != 0)
    {
      haserr = true;
    } else
    {
      gt_esa_spmitvs_visitor_print_results((GtESASpmitvsVisitor*) ev,
                                           nonspecials);
    }
    gt_esa_visitor_delete(ev);
  }
  if (ssar != NULL)
  {
    gt_freeSequentialsuffixarrayreader(&ssar);
  }
  return haserr ? -1 : 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x10, %rsp
movq %rdx, %rbx
movq %rsi, %r14
movq %rdi, %r15
testq %rdx, %rdx
je 0x1a76fa
movq %rbx, %rdi
callq 0xfcc32
testb %al, %al
jne 0x1a77a5
movq %r15, %rdi
movl $0x7, %esi
movl $0x1, %edx
movq %r14, %rcx
movq %rbx, %r8
callq 0x1a5580
movq %rax, 0x8(%rsp)
testq %rax, %rax
je 0x1a7791
movq %rax, %r15
movq %rax, %rdi
callq 0x1a5a46
movq %rax, %r14
movq %r15, %rdi
callq 0x1a59f6
movq %rax, %r12
movq %r15, %rdi
callq 0x1a5a06
movl %eax, %ebp
movq %r15, %rdi
callq 0x1a5a8c
movq %r12, %rdi
movl %ebp, %esi
movl %eax, %edx
movq %rbx, %rcx
callq 0x1a830d
movq %rax, %r12
movq %r15, %rdi
movq %rax, %rsi
movq %rbx, %rdx
callq 0x30fecb
movl $0xffffffff, %ebx       # imm = 0xFFFFFFFF
testl %eax, %eax
jne 0x1a777d
movq %r12, %rdi
movq %r14, %rsi
callq 0x1a83b6
xorl %ebx, %ebx
movq %r12, %rdi
callq 0x1a8790
leaq 0x8(%rsp), %rdi
callq 0x1a5698
jmp 0x1a7796
movl $0xffffffff, %ebx       # imm = 0xFFFFFFFF
movl %ebx, %eax
addq $0x10, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
callq 0x631cf
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa-spmsk.c
// Function: gt_spmsk_inl_new
GtBUstate_spmsk *gt_spmsk_inl_new(const GtEncseq *encseq,
                            GtReadmode readmode,
                            GtUword minmatchlength,
                            bool countspms,
                            bool outputspms,
                            GT_UNUSED const char *indexname)
{
  GtBUstate_spmsk *state = gt_malloc(sizeof (*state));

  state->encseq = encseq;
  state->readmode = readmode;
  state->totallength = gt_encseq_total_length(encseq);
  state->minmatchlength = minmatchlength;
  state->countspms = countspms;
  state->outputspms = outputspms;
  state->spmcounter = 0;
  state->stack = (void *) gt_GtArrayGtBUItvinfo_new();
  GT_INITARRAY(&state->Wset,GtUword);
  GT_INITARRAY(&state->Lset,GtUword);
  return state;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movl %r8d, %ebx
movl %ecx, %ebp
movq %rdx, %r14
movl %esi, %r15d
movq %rdi, %r12
leaq 0x1fdc4a(%rip), %rsi    # 0x3a5472
movl $0x70, %edi
movl $0x87, %edx
callq 0x104226
movq %rax, %r13
movq %r12, (%rax)
movl %r15d, 0x8(%rax)
movq %r12, %rdi
callq 0xe7b9c
movq %rax, 0x10(%r13)
movq %r14, 0x18(%r13)
movb %bpl, 0x30(%r13)
movb %bl, 0x31(%r13)
movq $0x0, 0x20(%r13)
callq 0x30fe38
movq %rax, 0x68(%r13)
xorps %xmm0, %xmm0
movups %xmm0, 0x38(%r13)
movups %xmm0, 0x48(%r13)
movups %xmm0, 0x58(%r13)
movq %r13, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa-spmsk.c
// Function: gt_spmsk_inl_delete
GtUword gt_spmsk_inl_delete(GtBUstate_spmsk *state)
{
  if (state != NULL)
  {
    GtUword tmpcount;

    GT_FREEARRAY(&state->Wset,GtUword);
    GT_FREEARRAY(&state->Lset,GtUword);
    gt_GtArrayGtBUItvinfo_delete_spmsk(
                 (GtArrayGtBUItvinfo_spmsk *) state->stack,state);
    tmpcount = state->spmcounter;
    gt_free(state);
    return tmpcount;
  }
  return 0;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0x1a793e
movq %rdi, %rbx
movq 0x38(%rdi), %rdi
testq %rdi, %rdi
je 0x1a78cc
leaq 0x38(%rbx), %r14
leaq 0x1fdbbf(%rip), %rsi    # 0x3a5472
movl $0x9c, %edx
callq 0x1045eb
xorps %xmm0, %xmm0
movups %xmm0, (%r14)
movq $0x0, 0x10(%r14)
movq 0x50(%rbx), %rdi
testq %rdi, %rdi
je 0x1a78f9
leaq 0x50(%rbx), %r14
leaq 0x1fdb92(%rip), %rsi    # 0x3a5472
movl $0x9d, %edx
callq 0x1045eb
xorps %xmm0, %xmm0
movups %xmm0, (%r14)
movq $0x0, 0x10(%r14)
movq 0x68(%rbx), %r14
movq (%r14), %rdi
leaq 0x1fdb4a(%rip), %r15    # 0x3a5451
movq %r15, %rsi
movl $0x6b, %edx
callq 0x1045eb
movq %r14, %rdi
movq %r15, %rsi
movl $0x6c, %edx
callq 0x1045eb
movq 0x20(%rbx), %r14
leaq 0x1fdb43(%rip), %rsi    # 0x3a5472
movq %rbx, %rdi
movl $0xa1, %edx
callq 0x1045eb
jmp 0x1a7941
xorl %r14d, %r14d
movq %r14, %rax
popq %rbx
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa-spmsk.c
// Function: processleafedge_spmsk
static int processleafedge_spmsk(bool firstedge,
                                 GtUword fd,
                                 GtBUinfo_spmsk *finfo,
                                 GtUword seqnum,
                                 GtUword relpos,
                                 GtBUstate_spmsk *state,
                                 GT_UNUSED GtError *err)

{
  if (fd >= state->minmatchlength)
  {
    if (firstedge)
    {
      gt_assert(finfo != NULL);
      ((GtBUinfo_spmsk *) finfo)->firstinW = state->Wset.nextfreeGtUword;
    }
    if (relpos == 0)
    {
      GT_STOREINARRAY(&state->Wset,GtUword,128,seqnum);
    }
    if (relpos + fd == gt_encseq_seqlength(state->encseq,seqnum))
    {
      GT_STOREINARRAY(&state->Lset,GtUword,128,seqnum);
    }
  }
  return 0;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
cmpq %rsi, 0x18(%r9)
ja 0x1a7f43
movq %r9, %rbx
movq %r8, %r15
movq %rcx, %r14
movq %rsi, %r12
testb %dil, %dil
je 0x1a7e85
testq %rdx, %rdx
je 0x1a7f4f
movq 0x48(%rbx), %rax
movq %rax, (%rdx)
testq %r15, %r15
jne 0x1a7edf
movq 0x40(%rbx), %rax
cmpq %rax, 0x48(%rbx)
jae 0x1a7e9a
movq 0x38(%rbx), %rax
jmp 0x1a7ec6
leaq 0x80(%rax), %rcx
movq %rcx, 0x40(%rbx)
movq 0x38(%rbx), %rdi
leaq 0x400(,%rax,8), %rsi
leaq 0x1fd5ba(%rip), %rdx    # 0x3a5472
movl $0x4d, %ecx
callq 0x104461
movq %rax, 0x38(%rbx)
testq %rax, %rax
je 0x1a7f59
movq 0x48(%rbx), %rcx
leaq 0x1(%rcx), %rdx
movq %rdx, 0x48(%rbx)
movq %r14, (%rax,%rcx,8)
addq %r12, %r15
movq (%rbx), %rdi
movq %r14, %rsi
callq 0xeb9d2
cmpq %rax, %r15
jne 0x1a7f43
movq 0x58(%rbx), %rax
cmpq %rax, 0x60(%rbx)
jae 0x1a7f02
movq 0x50(%rbx), %rax
jmp 0x1a7f2e
leaq 0x80(%rax), %rcx
movq %rcx, 0x58(%rbx)
movq 0x50(%rbx), %rdi
leaq 0x400(,%rax,8), %rsi
leaq 0x1fd552(%rip), %rdx    # 0x3a5472
movl $0x51, %ecx
callq 0x104461
movq %rax, 0x50(%rbx)
testq %rax, %rax
je 0x1a7f54
movq 0x60(%rbx), %rcx
leaq 0x1(%rcx), %rdx
movq %rdx, 0x60(%rbx)
movq %r14, (%rax,%rcx,8)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
callq 0x6351e
callq 0x634b0
callq 0x634e7
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa-spmsk.c
// Function: processlcpinterval_spmsk
static int processlcpinterval_spmsk(GtUword lcp,
                                    GtBUinfo_spmsk *info,
                                    GtBUstate_spmsk *state,
                                    GT_UNUSED GtError *err)
{
  if (lcp >= state->minmatchlength)
  {
    GtUword lidx, widx, firstpos;

    gt_assert(info != NULL);
    firstpos = ((GtBUinfo_spmsk *) info)->firstinW;
    for (lidx = 0; lidx < state->Lset.nextfreeGtUword; lidx++)
    {
      if (state->outputspms)
      {
        GtUword lpos = state->Lset.spaceGtUword[lidx];

        for (widx = firstpos; widx < state->Wset.nextfreeGtUword; widx++)
        {
          printf(GT_WU " " GT_WU " " GT_WU "\n",lpos,
                 state->Wset.spaceGtUword[widx],lcp);
        }
      } else
      {
        gt_assert(state->countspms);
        if (firstpos < state->Wset.nextfreeGtUword)
        {
          state->spmcounter += state->Wset.nextfreeGtUword - firstpos;
        }
      }
    }
    state->Lset.nextfreeGtUword = 0;
  } else
  {
    state->Wset.nextfreeGtUword = 0;
  }
  return 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %rdx, %rbx
cmpq %rdi, 0x18(%rdx)
jbe 0x1a7f81
addq $0x48, %rbx
movq %rbx, %rdx
jmp 0x1a8010
testq %rsi, %rsi
je 0x1a802b
leaq 0x60(%rbx), %rdx
movq 0x60(%rbx), %rax
testq %rax, %rax
je 0x1a8010
movq %rdi, %r14
movq (%rsi), %rbp
leaq 0x1fc662(%rip), %r15    # 0x3a4606
xorl %r13d, %r13d
movq %rdx, 0x10(%rsp)
movq %rbp, 0x8(%rsp)
cmpb $0x1, 0x31(%rbx)
jne 0x1a7ff5
cmpq 0x48(%rbx), %rbp
jae 0x1a8008
movq 0x50(%rbx), %rax
movq (%rax,%r13,8), %r12
movq 0x38(%rbx), %rax
movq (%rax,%rbp,8), %rdx
movq %r15, %rdi
movq %r12, %rsi
movq %r14, %rcx
xorl %eax, %eax
callq 0x17070
incq %rbp
cmpq 0x48(%rbx), %rbp
jb 0x1a7fc5
movq 0x10(%rsp), %rdx
movq (%rdx), %rax
movq 0x8(%rsp), %rbp
jmp 0x1a8008
cmpb $0x0, 0x30(%rbx)
je 0x1a8026
movq 0x48(%rbx), %rcx
subq %rbp, %rcx
jbe 0x1a8008
addq %rcx, 0x20(%rbx)
incq %r13
cmpq %rax, %r13
jb 0x1a7fb1
movq $0x0, (%rdx)
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x63555
callq 0x6358c
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa_spmitvs_visitor.c
// Function: gt_esa_spmitvs_visitor_delete
void gt_esa_spmitvs_visitor_delete(GtESAVisitor *ev)
{
  GtESASpmitvsVisitor *esv;
  gt_assert(ev);
  esv = gt_esa_spmitvs_visitor_cast(ev);
  gt_free(esv->wholeleafcount);
}

// Assembly:
pushq %rbx
testq %rdi, %rdi
je 0x1a80e7
movq %rdi, %rbx
callq 0x1a80ec
movq %rax, %rdi
movq %rbx, %rsi
callq 0x1a85ad
movq 0x40(%rax), %rdi
leaq 0x1fd4ca(%rip), %rsi    # 0x3a55a6
movl $0x9f, %edx
popq %rbx
jmp 0x1045eb
callq 0x635c3
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa_spmitvs_visitor.c
// Function: gt_esa_spmitvs_visitor_class
const GtESAVisitorClass* gt_esa_spmitvs_visitor_class()
{
  static const GtESAVisitorClass *esc = NULL;
  gt_class_alloc_lock_enter();
  if (!esc) {
    esc = gt_esa_visitor_class_new(sizeof (GtESASpmitvsVisitor),
                                   gt_esa_spmitvs_visitor_delete,
                                   gt_esa_spmitvs_visitor_processleafedge,
                                   gt_esa_spmitvs_visitor_processbranchingedge,
                                   gt_esa_spmitvs_visitor_processlcpinterval,
                                   NULL,
                                   NULL);
  }
  gt_class_alloc_lock_leave();
  return esc;
}

// Assembly:
pushq %rax
callq 0xe252f
cmpq $0x0, 0x31681e(%rip)    # 0x4be918
jne 0x1a8134
movq $0x0, (%rsp)
leaq -0x53(%rip), %rsi       # 0x1a80b8
leaq 0x30(%rip), %rdx        # 0x1a8142
leaq 0xae(%rip), %rcx        # 0x1a81c7
leaq 0x15a(%rip), %r8        # 0x1a827a
movl $0x58, %edi
xorl %r9d, %r9d
callq 0x1a851c
movq %rax, 0x3167e4(%rip)    # 0x4be918
callq 0xe2545
movq 0x3167d8(%rip), %rax    # 0x4be918
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/esa_spmitvs_visitor.c
// Function: gt_esa_spmitvs_visitor_processleafedge
static int gt_esa_spmitvs_visitor_processleafedge(GtESAVisitor *ev,
                                                  GT_UNUSED bool firstsucc,
                                                  GtUword fd,
                                                  GT_UNUSED GtUword flb,
                                                  GT_UNUSED
                                                         GtESAVisitorInfo *info,
                                                  GtUword leafnumber,
                                                  GT_UNUSED GtError *err)

{
  GtESASpmitvsVisitor *esv;
  gt_assert(ev);
  esv = gt_esa_spmitvs_visitor_cast(ev);

  if (gt_esa_spmitvs_visitor_iswholeleaf(esv->encseq,esv->readmode,leafnumber))
  {
    gt_assert(esv->currentleafindex != esv->totallength);
    esv->lastwholeleaf = esv->currentleafindex;
  } else
  {
    if (leafnumber + fd < esv->totallength &&
        !gt_encseq_position_is_separator(esv->encseq,
                                         leafnumber + fd,
                                         esv->readmode))
    {
      esv->unnecessaryleaves++;
    }
  }
  esv->currentleafindex++;
  return 0;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0x1a81bd
movq %r9, %r14
movq %rdx, %r15
movq %rdi, %rbx
callq 0x1a80ec
movq %rax, %rdi
movq %rbx, %rsi
callq 0x1a85ad
movq %rax, %rbx
testq %r14, %r14
je 0x1a8181
movl 0x50(%rbx), %edx
movq 0x48(%rbx), %rdi
leaq -0x1(%r14), %rsi
callq 0xe811c
testb %al, %al
je 0x1a819b
movq 0x20(%rbx), %rax
cmpq 0x18(%rbx), %rax
je 0x1a81c2
movq %rax, 0x28(%rbx)
incq 0x20(%rbx)
xorl %eax, %eax
popq %rbx
popq %r14
popq %r15
retq
addq %r15, %r14
cmpq 0x18(%rbx), %r14
jae 0x1a818f
movq 0x48(%rbx), %rdi
movl 0x50(%rbx), %edx
movq %r14, %rsi
callq 0xe811c
testb %al, %al
jne 0x1a818f
incq 0x10(%rbx)
jmp 0x1a818f
callq 0x63633
callq 0x635fc