LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/esa-minunique.c
// Function: gt_suffixarrayfindmums
GtUword gt_suffixarrayfindmums (const void *genericindex,
                                      GtUword offset,
                                      GtUword left,
                                      GtUword right,
                                      GtUword *witnessposition,
                                      const GtUchar *qstart,
                                      const GtUchar *qend)
{
  const Suffixarray *suffixarray = (const Suffixarray *) genericindex;
  Simplelcpinterval itv;
  const GtUchar *qptr;
  GtUword totallength;

  itv.left = left;
  itv.right = right;
  totallength = gt_encseq_total_length(suffixarray->encseq);
  *witnessposition = ULONG_MAX;
  for (qptr = qstart; /* Nothing */; qptr++, offset++)
  {
    gt_assert(itv.left <= itv.right);
    if (qptr >= qend || GT_ISSPECIAL(*qptr) ||
        !gt_lcpintervalfindcharchildintv(suffixarray->encseq,
                                         suffixarray->readmode,
                                         totallength,
                                         suffixarray->suftab,
                                         &itv,
                                         *qptr,
                                         offset,
                                         itv.left,
                                         itv.right))
    {
      if (itv.left == itv.right)
      {
        *witnessposition = ESASUFFIXPTRGET(suffixarray->suftab,itv.left);
      }
      break;
    }
  }
  return offset;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %r9, %r12
movq %r8, %rbx
movq %rsi, %r14
movq %rdi, %r15
movq %rdx, (%rsp)
movq %rcx, 0x8(%rsp)
movq (%rdi), %rdi
callq 0xec1d8
movq %rax, %r13
movq %rbx, 0x10(%rsp)
movq $-0x1, (%rbx)
movq (%rsp), %rax
movq 0x8(%rsp), %r10
cmpq %r10, %rax
ja 0x1ac71b
movq 0x50(%rsp), %rbx
movq %rsp, %rbp
cmpq %rbx, %r12
jae 0x1ac720
movb (%r12), %dl
cmpb $-0x3, %dl
ja 0x1ac720
movq (%r15), %rdi
movl 0x48(%r15), %esi
movq 0x58(%r15), %rcx
subq $0x8, %rsp
movzbl %dl, %r9d
movq %r13, %rdx
movq %rbp, %r8
pushq %r10
pushq %rax
pushq %r14
callq 0x1afe94
addq $0x20, %rsp
testb %al, %al
je 0x1ac720
incq %r12
incq %r14
movq (%rsp), %rax
movq 0x8(%rsp), %r10
cmpq %r10, %rax
jbe 0x1ac6ce
callq 0x63610
movq (%rsp), %rax
cmpq 0x8(%rsp), %rax
jne 0x1ac73b
movq 0x58(%r15), %rcx
movq (%rcx,%rax,8), %rax
movq 0x10(%rsp), %rcx
movq %rax, (%rcx)
movq %r14, %rax
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/esa-minunique.c
// Function: gt_suffixarrayfindinterval
GtRange gt_suffixarrayfindinterval (const void *genericindex,
                                    GtUword offset,
                                    GtUword left,
                                    GtUword right,
                                    GtUword *matchlength,
                                    const GtUchar *qstart,
                                    const GtUchar *qend)
{
  const Suffixarray *suffixarray = (const Suffixarray *) genericindex;
  const GtUchar *qptr;
  GtUword totallength = gt_encseq_total_length(suffixarray->encseq);
  GtRange result;

  gt_assert(qstart < qend);
  for (qptr = qstart; /* Nothing */; qptr++, offset++)
  {
    Simplelcpinterval itv;

    if (qptr >= qend || GT_ISSPECIAL(*qptr) ||
        !gt_lcpintervalfindcharchildintv(suffixarray->encseq,
                                         suffixarray->readmode,
                                         totallength,
                                         suffixarray->suftab,
                                         &itv,
                                         *qptr,
                                         offset,
                                         left,
                                         right))
    {
      break;
    }
    gt_assert(itv.left <= itv.right);
    left = itv.left;
    right = itv.right;
  }
  *matchlength = (GtUword) (qptr - qstart);
  result.start = left;
  result.end = right;
  return result;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq %r9, %r14
movq %r8, (%rsp)
movq %rcx, %r15
movq %rdx, %r12
movq %rsi, 0x10(%rsp)
movq %rdi, %rbp
movq 0x60(%rsp), %r13
movq (%rdi), %rdi
callq 0xec1d8
movq %rax, 0x8(%rsp)
cmpq %r13, %r14
jae 0x1ac814
xorl %ebx, %ebx
leaq (%r14,%rbx), %rax
cmpq %r13, %rax
jae 0x1ac7e8
movb (%rax), %al
cmpb $-0x3, %al
ja 0x1ac7e8
movq 0x10(%rsp), %rcx
leaq (%rcx,%rbx), %r10
movq (%rbp), %rdi
movl 0x48(%rbp), %esi
movq 0x58(%rbp), %rcx
subq $0x8, %rsp
movzbl %al, %r9d
movq 0x10(%rsp), %rdx
leaq 0x20(%rsp), %r8
pushq %r15
pushq %r12
pushq %r10
callq 0x1afe94
addq $0x20, %rsp
testb %al, %al
je 0x1ac7e8
movq 0x18(%rsp), %r12
movq 0x20(%rsp), %r15
movb $0x1, %al
cmpq %r15, %r12
jbe 0x1ac7ea
jmp 0x1ac80f
xorl %eax, %eax
testb %al, %al
je 0x1ac7f3
incq %rbx
jmp 0x1ac78d
movq (%rsp), %rax
movq %rbx, (%rax)
movq %r12, %rax
movq %r15, %rdx
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x63680
callq 0x63647
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/esa-mmsearch.c
// Function: gt_mmsearchiterator_new_complete_plain
GtMMsearchiterator *gt_mmsearchiterator_new_complete_plain(
                                   const GtEncseq *dbencseq,
                                   const void *voidsuftab, /* XXX */
                                   GtUword leftbound,
                                   GtUword rightbound,
                                   GtUword itvoffset,
                                   GtReadmode readmode,
                                   const GtUchar *pattern,
                                   GtUword patternlength)
{
  GtQueryrepresentation queryrep;
  GtQuerysubstring querysubstring;
  const ESASuffixptr *suftab = (const ESASuffixptr *) voidsuftab; /* XXX */

  queryrep.sequence = pattern;
  queryrep.encseq = NULL;
  queryrep.readmode = GT_READMODE_FORWARD;
  queryrep.startpos = 0;
  queryrep.seqlen = patternlength;
  querysubstring.queryrep = &queryrep;
  querysubstring.currentoffset = 0;
  return gt_mmsearchiterator_new(dbencseq,
                                 suftab,
                                 leftbound,
                                 rightbound,
                                 itvoffset,
                                 readmode,
                                 &querysubstring,
                                 patternlength);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x58, %rsp
movq %r9, 0x18(%rsp)
movq %r8, 0x10(%rsp)
movq %rcx, 0x8(%rsp)
movq %rdx, %r12
movq %rsi, %r13
movq %rdi, %rbp
movq 0x98(%rsp), %rdx
movq 0x90(%rsp), %rax
leaq 0x30(%rsp), %rcx
movq %rax, (%rcx)
xorl %r14d, %r14d
movq %r14, 0x8(%rcx)
movl $0x0, 0x10(%rcx)
movq %r14, 0x18(%rcx)
movq %rdx, 0x20(%rcx)
leaq 0x20(%rsp), %r15
movq %rcx, (%r15)
movq %r14, 0x8(%r15)
leaq 0x2015c1(%rip), %rsi    # 0x3ade44
movl $0x30, %edi
movl $0xf3, %edx
callq 0x1092b2
movq %rax, %rbx
movq %r14, 0x28(%rax)
subq $0x8, %rsp
movq %rax, %rdi
movq %rbp, %rsi
movq %r13, %rdx
movq %r12, %rcx
movq 0x10(%rsp), %r8
movq 0x18(%rsp), %r9
pushq 0xa0(%rsp)
pushq %r15
pushq 0x30(%rsp)
callq 0x1ad417
addq $0x20, %rsp
movq %rbx, %rax
addq $0x58, %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/esa-mmsearch.c
// Function: gt_mmsearchiterator_next
bool gt_mmsearchiterator_next(GtUword *dbstart,GtMMsearchiterator *mmsi)
{
  gt_assert(mmsi != NULL);
  if (mmsi->sufindex <= mmsi->lcpitv.right)
  {
    *dbstart = ESASUFFIXPTRGET(mmsi->suftab,mmsi->sufindex++);
    return true;
  }
  return false;
}

// Assembly:
testq %rsi, %rsi
je 0x1ac925
movq 0x10(%rsi), %rax
movq 0x18(%rsi), %rcx
cmpq %rax, %rcx
ja 0x1ac91e
movq 0x20(%rsi), %rdx
leaq 0x1(%rcx), %r8
movq %r8, 0x18(%rsi)
movq (%rdx,%rcx,8), %rdx
movq %rdx, (%rdi)
cmpq %rax, %rcx
setbe %al
retq
pushq %rax
callq 0x636f2
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/esa-mmsearch.c
// Function: gt_querysubstringmatchiterator_delete
void gt_querysubstringmatchiterator_delete(GtQuerysubstringmatchiterator *qsmi)
{
  if (qsmi != NULL)
  {
    gt_mmsearchiterator_delete(qsmi->mmsi);
    gt_seq_iterator_delete(qsmi->seqit);
    gt_free(qsmi);
  }
}

// Assembly:
testq %rdi, %rdi
je 0x1ad13f
pushq %rbx
movq %rdi, %rbx
movq 0x30(%rdi), %rdi
callq 0x1ac968
movq 0x80(%rbx), %rdi
callq 0x119a53
leaq 0x200d13(%rip), %rsi    # 0x3ade44
movq %rbx, %rdi
movl $0x31b, %edx            # imm = 0x31B
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/esa-mmsearch.c
// Function: gt_mmsearch_isleftmaximal
static bool gt_mmsearch_isleftmaximal(const GtEncseq *dbencseq,
                                      GtReadmode readmode,
                                      GtUword dbstart,
                                      const GtQuerysubstring *querysubstring)
{
  GtUchar dbleftchar;

  if (dbstart == 0 || querysubstring->currentoffset == 0)
  {
    return true;
  }
  dbleftchar = gt_encseq_get_encoded_char(dbencseq, /* Random access */
                                          dbstart-1,
                                          readmode);
  if (GT_ISSPECIAL(dbleftchar) ||
      dbleftchar != gt_mmsearch_accessquery(querysubstring->queryrep,
                                            querysubstring->currentoffset-1))
  {
    return true;
  }
  return false;
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
movb $0x1, %bl
testq %rdx, %rdx
je 0x1ad9f6
movq %rcx, %r14
cmpq $0x0, 0x8(%rcx)
je 0x1ad9f6
movl %esi, %eax
decq %rdx
movq %rdx, %rsi
movl %eax, %edx
callq 0xec1f8
cmpb $-0x3, %al
ja 0x1ad9f6
movl %eax, %ebp
movq (%r14), %rdi
movq 0x8(%r14), %rsi
decq %rsi
callq 0x1ada8f
cmpb %al, %bpl
setne %bl
movl %ebx, %eax
popq %rbx
popq %r14
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O1/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 %r9, %r14
movq %rcx, %r15
movq %rsi, %r12
cmpq %rcx, %r8
jae 0x1ada2a
movq %rdi, %rsi
movq %r12, %rdi
movq %r8, %rcx
movq %r8, %rbx
callq 0xed48e
movq %rbx, %r8
movq %r8, %r13
cmpq %r15, %r8
jae 0x1ada7a
movq 0x40(%rsp), %rbp
addq 0x8(%r14), %rbp
movq %r8, (%rsp)
movq %r8, %r13
movq (%r14), %rax
cmpq 0x20(%rax), %rbp
jae 0x1ada76
movq %r12, %rdi
callq 0xec7be
cmpb $-0x3, %al
ja 0x1ada76
movl %eax, %ebx
movq (%r14), %rdi
movq %rbp, %rsi
callq 0x1ada8f
cmpb %al, %bl
jne 0x1ada76
incq %r13
incq %rbp
cmpq %r13, %r15
jne 0x1ada42
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_O1/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 0x1adaf5
movq %rsi, %rax
movq %rdi, %rbx
movq 0x20(%rdi), %rsi
cmpq %rax, %rsi
jbe 0x1adafa
movq %rax, %rcx
notq %rcx
addq %rcx, %rsi
cmpl $0x0, 0x10(%rbx)
cmoveq %rax, %rsi
addq 0x18(%rbx), %rsi
movq (%rbx), %rax
testq %rax, %rax
je 0x1adac6
movb (%rax,%rsi), %al
jmp 0x1adad6
movq 0x8(%rbx), %rdi
testq %rdi, %rdi
je 0x1adaff
xorl %edx, %edx
callq 0xec1f8
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 0x63b29
callq 0x63abb
callq 0x63af2
// File: /workspace/github_c_makefile_star2_O1/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 0x20036f(%rip), %r14    # 0x3ae424
movl $0x58, %edi
movq %r14, %rsi
movl $0x23, %edx
callq 0x1092b2
movq %rax, %rbx
movl $0x100, %edi            # imm = 0x100
movq %r14, %rsi
movl $0x24, %edx
callq 0x1092b2
movq %rax, (%rbx)
testl %ebp, %ebp
je 0x1ae0ec
leaq -0x4198(%rip), %r9      # 0x1a9f52
jmp 0x1ae0f3
leaq -0x35d3(%rip), %r9      # 0x1aab20
movq %rax, %rdi
movl %r13d, %esi
movq %r12, %rdx
movq %r15, %rcx
movq (%rsp), %r8
callq *%r9
testl %eax, %eax
je 0x1ae135
movq (%rbx), %rdi
leaq 0x200310(%rip), %r14    # 0x3ae424
movq %r14, %rsi
movl $0x2b, %edx
callq 0x109670
movq %rbx, %rdi
movq %r14, %rsi
movl $0x2c, %edx
callq 0x109670
xorl %ebx, %ebx
jmp 0x1ae195
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 0x1ae1a7
movq (%rax), %rdi
movq %rdi, 0x38(%rbx)
movl 0x48(%rax), %eax
movl %eax, 0x50(%rbx)
callq 0xec1d8
incq %rax
movq %rax, 0x10(%rbx)
movq 0x38(%rbx), %rdi
callq 0xec1d8
movq %rax, %r14
movq 0x38(%rbx), %rdi
callq 0xf0b87
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 0x63d22
// File: /workspace/github_c_makefile_star2_O1/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), %rax
movq (%rax), %rdi
testq %rdi, %rdi
je 0x1ae1d7
callq 0x1a9e1c
movq (%rbx), %rax
movq (%rax), %rdi
leaq 0x200257(%rip), %rsi    # 0x3ae424
movl $0x43, %edx
callq 0x109670
movq (%rbx), %rdi
leaq 0x200243(%rip), %rsi    # 0x3ae424
movl $0x45, %edx
popq %rbx
jmp 0x109670
// File: /workspace/github_c_makefile_star2_O1/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 0x1ae53a
movq %rdi, %rbx
movq (%rsi), %r15
cmpb $0x1, 0x40(%rsi)
jne 0x1ae491
cmpq $0x0, 0xb0(%r15)
je 0x1ae4b3
movl 0xa4(%r15), %eax
cmpl 0xa0(%r15), %eax
jb 0x1ae477
movq 0xa8(%r15), %rdi
movq 0xb0(%r15), %rcx
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 0x1ae53f
movl $0x0, 0xa4(%r15)
testl %r14d, %r14d
je 0x1ae52a
movq 0xa8(%r15), %rax
movl 0xa4(%r15), %ecx
leal 0x1(%rcx), %edx
movl %edx, 0xa4(%r15)
jmp 0x1ae4a1
movq 0x58(%r15), %rax
movq 0x18(%rsi), %rcx
leaq 0x1(%rcx), %rdx
movq %rdx, 0x18(%rsi)
movq (%rax,%rcx,8), %rcx
movl $0x1, %eax
movq %rcx, (%rbx)
popq %rbx
popq %r14
popq %r15
retq
movl 0x8c(%r15), %eax
cmpl 0x88(%r15), %eax
jb 0x1ae50a
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 0x1ae544
movl $0x0, 0x8c(%r15)
testl %r14d, %r14d
je 0x1ae531
movq 0x90(%r15), %rax
movl 0x8c(%r15), %ecx
leal 0x1(%rcx), %edx
movl %edx, 0x8c(%r15)
movl (%rax,%rcx,4), %ecx
jmp 0x1ae4a5
xorl %eax, %eax
jmp 0x1ae4ad
xorl %ecx, %ecx
xorl %eax, %eax
jmp 0x1ae4aa
callq 0x63e67
callq 0x63e17
callq 0x63e3f
// File: /workspace/github_c_makefile_star2_O1/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 0x1ae584
cmpb $0x1, 0x40(%rdi)
jne 0x1ae579
addq $0x30, %rdi
jmp 0x1ae580
movq (%rdi), %rdi
addq $0x58, %rdi
movq (%rdi), %rax
retq
pushq %rax
callq 0x63f12
// File: /workspace/github_c_makefile_star2_O1/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 0x20005d(%rip), %rsi    # 0x3ae709
movl $0x48, %edi
movl $0x17e, %edx            # imm = 0x17E
callq 0x1092b2
movq %rax, %rbx
movq %r15, %rdi
callq 0xf4233
movq %rax, (%rbx)
movq %r15, 0x10(%rbx)
movq %rax, %rdi
callq 0x1ae746
movq %rax, 0x8(%rbx)
movq %r12, %rdi
movq %rbx, %rsi
movq %r14, %rdx
callq 0x1ae7d7
movl %eax, %ebp
testl %eax, %eax
jne 0x1ae6fb
movq (%rbx), %rdx
movq 0x8(%rbx), %rsi
xorl %edi, %edi
callq 0x1af169
movq 0x8(%rbx), %rax
movq (%rax), %rdi
leaq 0x200000(%rip), %r14    # 0x3ae709
movq %r14, %rsi
movl $0x191, %edx            # imm = 0x191
callq 0x109670
movq 0x8(%rbx), %rdi
movq %r14, %rsi
movl $0x191, %edx            # imm = 0x191
callq 0x109670
movq %rbx, %rdi
movq %r14, %rsi
movl $0x195, %edx            # imm = 0x195
callq 0x109670
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_O1/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 0x1fffa9(%rip), %r12    # 0x3ae709
movq %r14, %rdi
movq %r12, %rsi
movl $0x145, %edx            # imm = 0x145
callq 0x1092b2
movq %rax, %r15
movq %r14, %rdi
imulq %rbx, %rdi
movq %r12, %rsi
movl $0x145, %edx            # imm = 0x145
callq 0x1092b2
movq %rax, (%r15)
cmpq $0x2, %rbx
jb 0x1ae7aa
movq (%r15), %rax
addq %r14, %rax
movl $0x1, %ecx
movq %rax, (%r15,%rcx,8)
incq %rcx
addq %r14, %rax
cmpq %rcx, %rbx
jne 0x1ae79b
testq %rbx, %rbx
je 0x1ae7c8
xorl %r12d, %r12d
movq (%r15,%r12,8), %rdi
xorl %esi, %esi
movq %r14, %rdx
callq 0x173a0
incq %r12
cmpq %r12, %rbx
jne 0x1ae7b2
movq %r15, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O1/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 0x1ff6bc(%rip), %rdi    # 0x3ae840
movq %rdx, %rsi
xorl %eax, %eax
callq 0x17070
testq %rbx, %rbx
je 0x1af218
leaq 0x205cba(%rip), %r12    # 0x3b4e58
leaq 0x1ff6b0(%rip), %r13    # 0x3ae855
xorl %ebp, %ebp
movq %r15, (%rsp)
testq %r15, %r15
je 0x1af1c7
movq %r15, %rdi
movq %rbp, %rsi
callq 0x121cfa
leaq 0x1afb0e(%rip), %rdi    # 0x35ecd0
movq %rax, %rsi
jmp 0x1af1cd
movq %r12, %rdi
movq %rbp, %rsi
xorl %eax, %eax
callq 0x17070
xorl %r15d, %r15d
cmpq %r15, %rbp
jne 0x1af1e8
movq %r13, %rdi
xorl %eax, %eax
callq 0x17070
jmp 0x1af1fa
movq (%r14,%r15,8), %rax
movq (%rax,%rbp,8), %rsi
movq %r12, %rdi
xorl %eax, %eax
callq 0x17070
incq %r15
cmpq %r15, %rbx
jne 0x1af1d7
movl $0xa, %edi
callq 0x17a20
incq %rbp
cmpq %rbx, %rbp
movq (%rsp), %r15
jne 0x1af1ab
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/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 0x1ff2a7(%rip), %rsi    # 0x3ae709
movl $0x48, %edi
movl $0x21c, %edx            # imm = 0x21C
callq 0x1092b2
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 0x1ae7d7
movl %eax, %ebx
movq %rbp, %rdi
leaq 0x1ff264(%rip), %rsi    # 0x3ae709
movl $0x22f, %edx            # imm = 0x22F
callq 0x109670
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_O1/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 0x1ff233(%rip), %rsi    # 0x3ae709
movl $0x48, %edi
movl $0x238, %edx            # imm = 0x238
callq 0x1092b2
movq %rax, %rbx
movq %r15, 0x10(%rax)
movq $-0x1, 0x28(%rax)
movq $0x0, 0x20(%rax)
movb $0x0, 0x30(%rax)
testq %r14, %r14
je 0x1af50a
movq (%r14), %rax
jmp 0x1af512
movq %r15, %rdi
callq 0x207fe7
movq %rax, 0x38(%rbx)
movq %r15, %rdi
callq 0xf4233
movq %rax, (%rbx)
movq 0x38(%rbx), %rcx
movq 0x20(%rcx), %rcx
movq %rcx, 0x18(%rbx)
testq %r14, %r14
je 0x1af538
movq 0x8(%r14), %rax
jmp 0x1af540
movq %rax, %rdi
callq 0x1ae746
movq %rax, 0x8(%rbx)
leaq 0x1ff19c(%rip), %rsi    # 0x3ae6e7
movl $0x18, %edi
movl $0x5f, %edx
callq 0x1092b2
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_O1/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 0x1afbb9
movq %rsi, %rax
movq %rdi, %rbx
movq 0x8(%rdi), %rsi
testq %rsi, %rsi
je 0x1afbc1
testq %rax, %rax
jne 0x1afb95
movq (%rbx), %rdx
movq 0x38(%rbx), %rax
movq 0x18(%rax), %rdi
callq 0x1af169
movq 0x8(%rbx), %rax
movq (%rax), %rdi
leaq 0x1feb9b(%rip), %r14    # 0x3ae709
movq %r14, %rsi
movl $0x295, %edx            # imm = 0x295
callq 0x109670
movq 0x8(%rbx), %rdi
movq %r14, %rsi
movl $0x295, %edx            # imm = 0x295
callq 0x109670
movq 0x38(%rbx), %rdi
callq 0x207fa2
movq 0x40(%rbx), %rdi
callq 0x1ae61f
leaq 0x1feb64(%rip), %rsi    # 0x3ae709
movq %rbx, %rdi
movl $0x29c, %edx            # imm = 0x29C
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x109670
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x646b1
// File: /workspace/github_c_makefile_star2_O1/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, %r15
movq %rdx, %rbx
movq %rsi, %r12
movl %edi, %ebp
movq 0x10(%r8), %rdi
movq 0x18(%r8), %r13
movq %rcx, %rsi
callq 0xfab4f
movq %rax, %r14
testq %r13, %r13
je 0x1afcdd
movq (%r13,%r14,8), %r14
testb %bpl, %bpl
je 0x1afd24
testq %rbx, %rbx
je 0x1afd7f
cmpq $0x0, (%rbx)
jne 0x1afd0c
movq (%r15), %rdi
shlq $0x3, %rdi
leaq 0x1fea0a(%rip), %rsi    # 0x3ae709
movl $0xeb, %edx
callq 0x1092b2
movq %rax, (%rbx)
movq (%r15), %rdx
testq %rdx, %rdx
je 0x1afd69
movq (%rbx), %rdi
shlq $0x3, %rdx
xorl %esi, %esi
callq 0x173a0
jmp 0x1afd69
cmpq $0x0, (%r15)
je 0x1afd69
movq (%rbx), %rax
incq %r12
xorl %ecx, %ecx
cmpq %rcx, %r14
je 0x1afd61
cmpq $0x0, (%rax,%rcx,8)
je 0x1afd61
movq 0x8(%r15), %rdx
movq (%rdx,%rcx,8), %rsi
addq %r12, (%rsi,%r14,8)
cmpq $0x0, (%rax,%r14,8)
jne 0x1afd61
movq (%rax,%rcx,8), %rsi
imulq %r12, %rsi
movq (%rdx,%r14,8), %rdx
addq %rsi, (%rdx,%rcx,8)
incq %rcx
cmpq (%r15), %rcx
jb 0x1afd32
movq (%rbx), %rax
incq (%rax,%r14,8)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x6475a
// File: /workspace/github_c_makefile_star2_O1/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
cmpq $0x0, (%rdi)
je 0x1afe8a
incq %rsi
xorl %eax, %eax
cmpq $0x0, (%rdx,%rax,8)
je 0x1afe82
cmpq $0x0, (%rcx,%rax,8)
jne 0x1afe82
cmpq $0x0, (%rdi)
je 0x1afe82
xorl %r8d, %r8d
movq (%rcx,%r8,8), %r9
testq %r9, %r9
je 0x1afe7a
cmpq %r8, %rax
je 0x1afe8c
movq 0x8(%rdi), %r10
imulq %rsi, %r9
movq (%r10,%rax,8), %r10
addq %r9, (%r10,%r8,8)
incq %r8
cmpq (%rdi), %r8
jb 0x1afe5c
incq %rax
cmpq (%rdi), %rax
jb 0x1afe45
popq %rax
retq
callq 0x647cc
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O1/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 0x1afee7
movq 0x8(%rsp), %rdi
movl (%rsp), %edx
callq 0xec1f8
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 0x1aff0b
movq 0x8(%rsp), %rdi
movl (%rsp), %edx
callq 0xec1f8
movl %eax, %ebx
movzbl %bl, %r12d
cmpl %r12d, 0x4(%rsp)
je 0x1aff4d
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 0x1aff7b
addq $0x10, %rsp
cmpb %bpl, %r12b
je 0x1aff5b
cmpb %bpl, %bl
ja 0x1aff57
incq %rax
movq %rax, %r13
jmp 0x1afeec
cmpb %bpl, %bl
movq 0x60(%rsp), %rcx
je 0x1aff5e
xorl %eax, %eax
jmp 0x1aff6c
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_O1/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 0x1afffe
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 0x1affe4
movq 0x10(%rsp), %rdi
movl 0xc(%rsp), %edx
callq 0xec1f8
movl 0x8(%rsp), %edi
movzbl %al, %eax
cmpl %edi, %eax
ja 0x1affed
movq %r13, %r12
jmp 0x1afff3
movq %r13, %rbp
movq %r12, %r13
leaq 0x1(%r13), %rax
cmpq %rax, %rbp
ja 0x1affb7
jmp 0x1b0001
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_O1/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 0x1b008b
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 0x1b008f
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 0x1afe94
testb %al, %al
je 0x1b0093
incq %rbx
cmpq %rbx, %r14
jne 0x1b0049
movq %r14, %rbx
jmp 0x1b0093
xorl %ebx, %ebx
jmp 0x1b0093
cmpb $-0x1, %al
je 0x1b00a5
movq %rbx, %rax
addq $0x38, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x64805
// File: /workspace/github_c_makefile_star2_O1/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 0x1b0248
movq %r12, %rdi
movl %r15d, %edx
movq %rcx, %rbp
callq 0xec1f8
movq %rbp, %rcx
movl %eax, %ebp
addq (%rbx,%rcx,8), %r14
movl $0xff, %eax
cmpq %r13, %r14
je 0x1b0267
movq %r12, %rdi
movq %r14, %rsi
movl %r15d, %edx
callq 0xec1f8
movzbl %al, %eax
cmpb $-0x3, %bpl
ja 0x1b0281
movzbl %bpl, %ecx
cmpl %ecx, %eax
jne 0x1b0281
cmpb 0x4(%rsp), %bpl
jb 0x1b0287
callq 0x648ae
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
// File: /workspace/github_c_makefile_star2_O1/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 0x1b02c2
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0x1b037c
movq %r15, %rdi
movl $0x7, %esi
movl $0x1, %edx
movq %r14, %rcx
movq %rbx, %r8
callq 0x1ae094
movq %rax, 0x8(%rsp)
testq %rax, %rax
sete %r12b
je 0x1b0357
movq %rax, %rdi
callq 0x1ae599
movq %rax, %r14
movq 0x8(%rsp), %rdi
callq 0x1ae549
movq %rax, %r15
movq 0x8(%rsp), %rdi
callq 0x1ae559
movl %eax, %ebp
movq 0x8(%rsp), %rdi
callq 0x1ae5df
movq %r15, %rdi
movl %ebp, %esi
movl %eax, %edx
movq %rbx, %rcx
callq 0x1b0e99
movq %rax, %r15
movq 0x8(%rsp), %rdi
movq %rax, %rsi
movq %rbx, %rdx
callq 0x31a073
movb $0x1, %bl
testl %eax, %eax
jne 0x1b034c
movq %r15, %rdi
movq %r14, %rsi
callq 0x1b0f42
movl %r12d, %ebx
movq %r15, %rdi
callq 0x1b1324
movl %ebx, %r12d
cmpq $0x0, 0x8(%rsp)
je 0x1b0369
leaq 0x8(%rsp), %rdi
callq 0x1ae1ac
movzbl %r12b, %eax
negl %eax
addq $0x10, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
callq 0x648e7
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O1/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 0x1fe614(%rip), %rsi    # 0x3aea14
movl $0x70, %edi
movl $0x87, %edx
callq 0x1092b2
movq %rax, %r13
movq %r12, (%rax)
movl %r15d, 0x8(%rax)
movq %r12, %rdi
callq 0xec1d8
movq %rax, 0x10(%r13)
movq %r14, 0x18(%r13)
movb %bpl, 0x30(%r13)
movb %bl, 0x31(%r13)
movq $0x0, 0x20(%r13)
callq 0x319fe0
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