LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-enumcodes.c
// Function: gt_Enumcodeatposition_filledqgramcodestopatmax
bool gt_Enumcodeatposition_filledqgramcodestopatmax(
                                        GtCodetype *code,
                                        const Enumcodeatposition *ecp,
                                        unsigned int prefixindex,
                                        GtUword pos,
                                        GtCodetype stopcode)
{
  GtCodetype tmpcode;
  unsigned int idx;
  GtUchar cc;

  gt_assert(prefixindex > 0 && prefixindex < ecp->prefixlength);
  tmpcode = ecp->filltable[prefixindex];
  if (tmpcode > stopcode)
  {
    return false;
  }
  for (idx=0; idx<prefixindex; idx++)
  {
    gt_assert((GtUword) (pos + idx) < ecp->totallength);
    cc = gt_encseq_get_encoded_char_nospecial(ecp->encseq,
                                              pos + idx,
                                              ecp->readmode);
    gt_assert(GT_ISNOTSPECIAL(cc));
    tmpcode += ecp->multimappower[idx][cc];
    if (tmpcode > stopcode)
    {
      return false;
    }
  }
  *code = tmpcode;
  return true;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
testl %edx, %edx
je 0x1f5b5a
movq %rsi, %r12
cmpl %edx, 0x3c(%rsi)
jbe 0x1f5b5a
movq %r8, %rbx
movq 0x48(%r12), %rax
movl %edx, %r13d
movq (%rax,%r13,8), %rbp
cmpq %r8, %rbp
jbe 0x1f5af3
xorl %eax, %eax
jmp 0x1f5b41
movq %rcx, %r14
movq %rdi, (%rsp)
xorl %r15d, %r15d
leaq (%r14,%r15), %rsi
cmpq 0x20(%r12), %rsi
jae 0x1f5b55
movq 0x30(%r12), %rdi
movl 0x38(%r12), %edx
callq 0xec603
cmpb $-0x2, %al
jae 0x1f5b50
movq 0x40(%r12), %rcx
movq (%rcx,%r15,8), %rcx
movzbl %al, %eax
addq (%rcx,%rax,8), %rbp
cmpq %rbx, %rbp
ja 0x1f5aef
incq %r15
cmpq %r15, %r13
jne 0x1f5afd
movq (%rsp), %rax
movq %rbp, (%rax)
movb $0x1, %al
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x7a518
callq 0x7a4df
callq 0x7a551
nop
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-lcpvalues.c
// Function: gt_Outlcpinfo_reinit
void gt_Outlcpinfo_reinit(GtOutlcpinfo *outlcpinfo,
                          unsigned int numofchars,
                          unsigned int prefixlength,
                          GtUword numoflcpvalues)
{
  if (outlcpinfo != NULL)
  {
    if (prefixlength > 0)
    {
      outlcpinfo->turnwheel = gt_turningwheel_new(prefixlength,numofchars);
      outlcpinfo->sizeofinfo += gt_turningwheel_size();
    } else
    {
      outlcpinfo->turnwheel = NULL;
    }
    outlcpinfo->sizeofinfo
      += gt_tableoflcpvalues_realloc(&outlcpinfo->lcpsubtab.tableoflcpvalues,
                                     numoflcpvalues);
  }
}

// Assembly:
testq %rdi, %rdi
je 0x1f5dae
pushq %r14
pushq %rbx
pushq %rax
movq %rcx, %r14
movq %rdi, %rbx
testl %edx, %edx
je 0x1f5d90
movl %edx, %edi
callq 0x20a814
movq %rax, (%rbx)
callq 0x20a880
addq %rax, 0x18(%rbx)
jmp 0x1f5d97
movq $0x0, (%rbx)
leaq 0x40(%rbx), %rdi
movq %r14, %rsi
callq 0x1f5daf
addq %rax, 0x18(%rbx)
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-lcpvalues.c
// Function: gt_tableoflcpvalues_realloc
static size_t gt_tableoflcpvalues_realloc(GtLcpvalues *tableoflcpvalues,
                                          GtUword numoflcpvalues)
{
  if (numoflcpvalues > tableoflcpvalues->numofentries)
  {
    size_t sizeofinfo;

    tableoflcpvalues->bucketoflcpvalues
      = gt_realloc(tableoflcpvalues->bucketoflcpvalues,
                   sizeof (*tableoflcpvalues->bucketoflcpvalues) *
                   numoflcpvalues);
    sizeofinfo = sizeof (*tableoflcpvalues->bucketoflcpvalues) *
                         (numoflcpvalues - tableoflcpvalues->numofentries);
#ifndef NDEBUG
    GT_INITBITTABGENERIC(tableoflcpvalues->isset,
                         tableoflcpvalues->isset,
                         numoflcpvalues);
#endif
    sizeofinfo += GT_NUMOFINTSFORBITS(numoflcpvalues -
                                      tableoflcpvalues->numofentries)
                  * sizeof (GtBitsequence);
    tableoflcpvalues->numoflargelcpvalues = 0;
    tableoflcpvalues->numofentries = numoflcpvalues;
    tableoflcpvalues->lcptaboffset = 0;
    return sizeofinfo;
  }
  return 0;
}

// Assembly:
cmpq %rsi, 0x10(%rdi)
jae 0x1f5e72
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
movq 0x8(%rdi), %rdi
leaq (,%rsi,4), %rsi
leaq 0x1cb13e(%rip), %r15    # 0x3c0f1b
movq %r15, %rdx
movl $0x14b, %ecx            # imm = 0x14B
callq 0x1094e6
movq %rax, 0x8(%r14)
movq %rbx, %r13
subq 0x10(%r14), %r13
leaq -0x1(%rbx), %r12
shrq $0x3, %r12
andq $-0x8, %r12
movl $0x8, %ebp
addq %rbp, %r12
cmpq $0x40, %rbx
movq (%r14), %rdi
cmovbq %rbp, %r12
movq %r12, %rsi
movq %r15, %rdx
movl $0x151, %ecx            # imm = 0x151
callq 0x1094e6
movq %rax, (%r14)
movq %rax, %rdi
xorl %esi, %esi
movq %r12, %rdx
callq 0x173a0
movq %rbx, %rax
subq 0x10(%r14), %rax
leaq -0x1(%rax), %rcx
shrq $0x6, %rcx
cmpq $0x40, %rax
leaq 0x8(,%rcx,8), %rax
cmovbq %rbp, %rax
leaq (%rax,%r13,4), %rax
xorps %xmm0, %xmm0
movups %xmm0, 0x18(%r14)
movq %rbx, 0x10(%r14)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
xorl %eax, %eax
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-lcpvalues.c
// Function: gt_Outlcpinfo_prebucket
void gt_Outlcpinfo_prebucket(GtOutlcpinfo *outlcpinfo,
                             GtCodetype code,
                             GtUword lcptaboffset)
{
  if (outlcpinfo != NULL)
  {
    if (outlcpinfo->lcpsubtab.lcp2file != NULL ||
        outlcpinfo->lcpsubtab.lcpprocess != NULL)
    {
      outlcpinfo->lcpsubtab.tableoflcpvalues.numoflargelcpvalues = 0;
    } else
    {
      outlcpinfo->lcpsubtab.tableoflcpvalues.lcptaboffset = lcptaboffset;
    }
    if (code > 0)
    {
      (void) gt_turningwheel_next(outlcpinfo->turnwheel);
      if (outlcpinfo->previousbucketwasempty)
      {
        outlcpinfo->minchanged
          = GT_MIN(outlcpinfo->minchanged,
                gt_turningwheel_minchanged(outlcpinfo->turnwheel));
      } else
      {
        outlcpinfo->minchanged
          = gt_turningwheel_minchanged(outlcpinfo->turnwheel);
      }
    }
  }
}

// Assembly:
testq %rdi, %rdi
je 0x1f6281
pushq %rbp
pushq %rbx
pushq %rax
movq %rdi, %rbx
cmpq $0x0, 0x68(%rdi)
je 0x1f622d
movl $0x58, %ecx
xorl %eax, %eax
jmp 0x1f6245
xorl %eax, %eax
xorl %ecx, %ecx
cmpq $0x0, 0x70(%rbx)
sete %cl
leaq 0x58(,%rcx,8), %rcx
cmoveq %rdx, %rax
movq %rax, (%rbx,%rcx)
testq %rsi, %rsi
je 0x1f627b
movq (%rbx), %rdi
callq 0x20a886
cmpb $0x1, 0x38(%rbx)
jne 0x1f6270
movl 0x10(%rbx), %ebp
movq (%rbx), %rdi
callq 0x20a8be
cmpl %eax, %ebp
jae 0x1f6270
movl 0x10(%rbx), %eax
jmp 0x1f6278
movq (%rbx), %rdi
callq 0x20a8be
movl %eax, 0x10(%rbx)
addq $0x8, %rsp
popq %rbx
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-lcpvalues.c
// Function: outsmalllcpvalues
static void outsmalllcpvalues(Lcpoutput2file *lcp2file,
                              GtUword numoflcps)
{
  gt_assert (lcp2file != NULL);
  lcp2file->countoutputlcpvalues += numoflcps;
  gt_assert(lcp2file->outfplcptab != NULL);
  gt_xfwrite(lcp2file->smalllcpvalues,
             sizeof (*lcp2file->smalllcpvalues),
             (size_t) numoflcps,
             lcp2file->outfplcptab);
}

// Assembly:
pushq %rax
testq %rdi, %rdi
je 0x1f6778
movq %rsi, %rdx
addq %rsi, 0x38(%rdi)
movq (%rdi), %rcx
testq %rcx, %rcx
je 0x1f677d
movq 0x50(%rdi), %rdi
movl $0x1, %esi
popq %rax
jmp 0x125658
callq 0x7a89e
callq 0x7a867
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-lcpvalues.c
// Function: gt_Outlcpinfo_resizereservoir
GtLcpvalues *gt_Outlcpinfo_resizereservoir(GtOutlcpinfo *outlcpinfo,
                                           const GtBcktab *bcktab)
{
  Lcpsubtab *lcpsubtab;

  gt_assert(outlcpinfo != NULL);
  lcpsubtab = &outlcpinfo->lcpsubtab;
  if (lcpsubtab->lcp2file != NULL)
  {
    size_t sizeforlcpvalues; /* in bytes */

    gt_assert(bcktab != NULL);
    sizeforlcpvalues = gt_bcktab_sizeforlcpvalues(bcktab);
    if (lcpsubtab->lcp2file->sizereservoir < sizeforlcpvalues)
    {
      lcpsubtab->lcp2file->sizereservoir = sizeforlcpvalues;
      lcpsubtab->lcp2file->reservoir
        = gt_realloc(lcpsubtab->lcp2file->reservoir,
                     lcpsubtab->lcp2file->sizereservoir);
          /* point to the same area, since this is not used simultaneously */
          /* be careful for the parallel version */
      lcpsubtab->lcp2file->smalllcpvalues
        = (uint8_t *) lcpsubtab->lcp2file->reservoir;
#ifndef NDEBUG
      lcpsubtab->tableoflcpvalues.isset = NULL;
#endif
      lcpsubtab->tableoflcpvalues.bucketoflcpvalues
        = (GtLcpvaluetype *) lcpsubtab->lcp2file->reservoir;
      lcpsubtab->tableoflcpvalues.lcptaboffset = 0;
      lcpsubtab->tableoflcpvalues.numofentries
        = (GtUword) lcpsubtab->lcp2file->sizereservoir/
          sizeof (*lcpsubtab->tableoflcpvalues.bucketoflcpvalues);
    }
  } else
  {
    if (lcpsubtab->lcpprocess != NULL)
    {
      outlcpinfo->sizeofinfo
        += gt_tableoflcpvalues_realloc(&lcpsubtab->tableoflcpvalues,
                                       gt_bcktab_maxbucketsize(bcktab));
    }
  }
  return &lcpsubtab->tableoflcpvalues;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x1f6825
movq %rdi, %rbx
leaq 0x40(%rdi), %r14
cmpq $0x0, 0x68(%rdi)
je 0x1f67fc
testq %rsi, %rsi
je 0x1f682a
movq %rsi, %rdi
callq 0x194a57
movq 0x68(%rbx), %rcx
cmpq %rax, 0x48(%rcx)
jae 0x1f681a
movq %rax, 0x48(%rcx)
movq 0x40(%rcx), %rdi
leaq 0x1ca754(%rip), %rdx    # 0x3c0f1b
movq %rax, %rsi
movl $0x32f, %ecx            # imm = 0x32F
callq 0x1094e6
movq 0x68(%rbx), %rcx
movq %rax, 0x40(%rcx)
movq %rax, 0x50(%rcx)
xorl %edx, %edx
movq %rdx, 0x40(%rbx)
movq %rax, 0x48(%rbx)
movq %rdx, 0x60(%rbx)
movq 0x48(%rcx), %rax
shrq $0x2, %rax
movq %rax, 0x50(%rbx)
jmp 0x1f681a
cmpq $0x0, 0x70(%rbx)
je 0x1f681a
movq %rsi, %rdi
callq 0x194a71
movq %r14, %rdi
movq %rax, %rsi
callq 0x1f5daf
addq %rax, 0x18(%rbx)
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x7a90e
callq 0x7a8d5
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-linlcp.c
// Function: gt_ENCSEQ_lcp13_kasai
GtUword *gt_ENCSEQ_lcp13_kasai(const GtEncseq *encseq,
                               GtReadmode readmode,
                               GtUword partwidth,
                               GtUword totallength,
                               const ESASuffixptr *suftab,
                               GtCompactUlongStore *inversesuftab)
{
  GtUword pos, lcpvalue = 0, *lcptab;

  lcptab = gt_malloc(sizeof (*lcptab) * partwidth);
  lcptab[0] = 0;
  for (pos=0; pos <= totallength; pos++)
  {
    GtUword fillpos = gt_compact_ulong_store_get(inversesuftab, pos);
    if (fillpos > 0 && fillpos < partwidth)
    {
      GtUword previousstart = ESASUFFIXPTRGET(suftab, fillpos-1);
      while (pos+lcpvalue < totallength &&
             previousstart+lcpvalue < totallength)
      {
        GtUchar cc1, cc2;

        cc1 = gt_encseq_get_encoded_char(encseq, pos+lcpvalue, readmode);
        cc2 = gt_encseq_get_encoded_char(encseq, previousstart+lcpvalue,
                                                readmode);
        if (cc1 == cc2 && GT_ISNOTSPECIAL(cc1))
        {
          lcpvalue++;
        } else
        {
          break;
        }
      }
      lcptab[fillpos] = lcpvalue;
    }
    if (lcpvalue > 0)
    {
      lcpvalue--;
    }
  }
  return lcptab;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x48, %rsp
movq %r9, %rbx
movq %r8, 0x18(%rsp)
movq %rcx, %r15
movq %rdx, %r12
movl %esi, 0x4(%rsp)
movq %rdi, 0x30(%rsp)
leaq (,%rdx,8), %rdi
leaq 0x1ca9ea(%rip), %rsi    # 0x3c126a
movl $0x28, %edx
callq 0x1092b2
movq %rax, 0x8(%rsp)
movq $0x0, (%rax)
xorl %r14d, %r14d
xorl %ebp, %ebp
movq %rbx, 0x20(%rsp)
movq %r12, 0x10(%rsp)
movl 0x4(%rsp), %r13d
movq %rbx, %rdi
movq %r14, %rsi
callq 0xe80ec
movq %rax, %rdx
testq %rax, %rax
sete %al
cmpq %r12, %rdx
setae %cl
orb %al, %cl
jne 0x1f6956
movq 0x18(%rsp), %rax
movq %rdx, 0x28(%rsp)
movq -0x8(%rax,%rdx,8), %rax
movq %rax, 0x40(%rsp)
movq %r14, 0x38(%rsp)
leaq (%r14,%rbp), %rsi
cmpq %r15, %rsi
jae 0x1f693e
movq 0x40(%rsp), %rax
leaq (%rax,%rbp), %r12
cmpq %r15, %r12
jae 0x1f693e
movq %r15, %r14
movq 0x30(%rsp), %r15
movq %r15, %rdi
movl %r13d, %edx
callq 0xec1f8
movl %eax, %ebx
movq %r15, %rdi
movq %r14, %r15
movq 0x38(%rsp), %r14
movq %r12, %rsi
movl %r13d, %edx
callq 0xec1f8
cmpb %al, %bl
sete %al
cmpb $-0x2, %bl
setb %cl
andb %al, %cl
movzbl %cl, %eax
addq %rax, %rbp
testb %al, %al
jne 0x1f68e5
movq 0x8(%rsp), %rax
movq 0x28(%rsp), %rcx
movq %rbp, (%rax,%rcx,8)
movq 0x20(%rsp), %rbx
movq 0x10(%rsp), %r12
subq $0x1, %rbp
movl $0x0, %eax
cmovbq %rax, %rbp
incq %r14
cmpq %r15, %r14
jbe 0x1f68aa
movq 0x8(%rsp), %rax
addq $0x48, %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/sfx-mappedstr.c
// Function: gt_kmerstream_delete
static void gt_kmerstream_delete(GtKmerstream *spwp)
{
  if (spwp != NULL) {
    gt_free(spwp->filltable);
    gt_multimappower_delete(spwp->multimappower);
    special_queue_delete(&spwp->specialqueue);
    gt_free(spwp);
  }
}

// Assembly:
testq %rdi, %rdi
je 0x1f7c94
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq 0x60(%rdi), %rdi
leaq 0x1c9bbc(%rip), %r14    # 0x3c1813
movq %r14, %rsi
movl $0x1a4, %edx            # imm = 0x1A4
callq 0x109670
movq 0x68(%rbx), %rdi
callq 0x1bef6c
movq (%rbx), %rdi
movq %r14, %rsi
movl $0x11e, %edx            # imm = 0x11E
callq 0x109670
movq %rbx, %rdi
movq %r14, %rsi
movl $0x1a7, %edx            # imm = 0x1A7
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-mappedstr.c
// Function: gt_kmerstream_new
static GtKmerstream *gt_kmerstream_new(unsigned int numofchars,
                                       unsigned int kmersize)
{
  GtKmerstream *spwp;

  gt_assert(kmersize <= 32);
  spwp = gt_malloc(sizeof (*spwp));
  spwp->multimappower = gt_initmultimappower(numofchars,kmersize);
  gt_kmerstream_init(spwp, numofchars, kmersize);
  special_queue_init(&spwp->specialqueue,kmersize);
  spwp->filltable = gt_filllargestchartable(numofchars,kmersize);
  return spwp;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
cmpl $0x21, %esi
jae 0x1f7f9a
movl %esi, %ebx
movl %edi, %ebp
leaq 0x1c98ff(%rip), %r15    # 0x3c1813
movl $0x80, %edi
movq %r15, %rsi
movl $0x133, %edx            # imm = 0x133
callq 0x1092b2
movq %rax, %r14
movl %ebp, %edi
movl %ebx, %esi
callq 0x1bee83
movq %rax, 0x68(%r14)
xorl %r12d, %r12d
movl %r12d, 0x50(%r14)
movq %r12, 0x58(%r14)
movl %ebx, 0x44(%r14)
movl %ebp, 0x40(%r14)
movq %r12, 0x48(%r14)
movl %ebx, 0x18(%r14)
movl %ebx, %edi
shll $0x4, %edi
movq %r15, %rsi
movl $0xef, %edx
callq 0x1092b2
movq %rax, (%r14)
movl %r12d, 0x1c(%r14)
movl 0x18(%r14), %ecx
shlq $0x4, %rcx
addq %rcx, %rax
addq $-0x10, %rax
movq %rax, 0x8(%r14)
movq %rax, 0x10(%r14)
movl %ebp, %edi
movl %ebx, %esi
callq 0x1bedb1
movq %rax, 0x60(%r14)
movq %r14, %rax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
callq 0x7b04b
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-mappedstr.c
// Function: gt_kmercodeiterator_encseq_next
const GtKmercode *gt_kmercodeiterator_encseq_next(
                             GtKmercodeiterator *kmercodeiterator)
{
  if (!kmercodeiterator->hasprocessedfirst)
  {
    gt_assert(kmercodeiterator->currentposition
              == kmercodeiterator->startpos + kmercodeiterator->spwp->kmersize);
    gt_kmerstream_newcode(&kmercodeiterator->kmercode, kmercodeiterator->spwp);
    kmercodeiterator->hasprocessedfirst = true;
    return &kmercodeiterator->kmercode;
  }
  if (kmercodeiterator->currentposition < kmercodeiterator->totallength)
  {
    GtUchar charcode
      = gt_encseq_reader_next_encoded_char(kmercodeiterator->esr);
    gt_kmerstream_shiftrightwithchar(kmercodeiterator->spwp,charcode);
    gt_kmerstream_newcode(&kmercodeiterator->kmercode, kmercodeiterator->spwp);
    kmercodeiterator->currentposition++;
    return &kmercodeiterator->kmercode;
  }
  if (kmercodeiterator->currentposition < kmercodeiterator->totallength +
                                          kmercodeiterator->spwp->kmersize)
  {
    gt_kmerstream_shiftrightwithchar(kmercodeiterator->spwp,
                                     (GtUchar) GT_WILDCARD);
    gt_kmerstream_newcode(&kmercodeiterator->kmercode, kmercodeiterator->spwp);
    kmercodeiterator->currentposition++;
    return &kmercodeiterator->kmercode;
  }
  return NULL;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq 0x10(%rdi), %rax
cmpb $0x0, 0x18(%rdi)
je 0x1f7fca
movq (%rbx), %rcx
cmpq %rcx, %rax
jae 0x1f7fec
movq 0x28(%rbx), %rdi
callq 0xec7be
movq 0x38(%rbx), %rdi
movzbl %al, %esi
jmp 0x1f8000
movq 0x38(%rbx), %rsi
movl 0x44(%rsi), %ecx
addq 0x8(%rbx), %rcx
cmpq %rcx, %rax
jne 0x1f8029
leaq 0x40(%rbx), %r14
movq %r14, %rdi
callq 0x1f802e
movb $0x1, 0x18(%rbx)
jmp 0x1f801e
movq 0x38(%rbx), %rdi
movl 0x44(%rdi), %edx
addq %rdx, %rcx
cmpq %rcx, %rax
jae 0x1f801b
movl $0xfe, %esi
callq 0x1f806f
leaq 0x40(%rbx), %r14
movq 0x38(%rbx), %rsi
movq %r14, %rdi
callq 0x1f802e
incq 0x10(%rbx)
jmp 0x1f801e
xorl %r14d, %r14d
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x7b084
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-mappedstr.c
// Function: gt_kmerstream_newcode
static void gt_kmerstream_newcode(GtKmercode *kmercode,
                                  const GtKmerstream *spwp)
{
  {
    if (special_queue_is_empty(&spwp->specialqueue))
    {
      kmercode->definedspecialposition = false;
      kmercode->specialposition = 0;
      kmercode->code = spwp->codewithoutspecial;
    } else
    {
      GtSpecialcontext *head = special_queue_head_get(&spwp->specialqueue);
      gt_assert(head->lengthofleftcontext < spwp->kmersize);
      kmercode->code = head->codeofleftcontext +
                       spwp->filltable[head->lengthofleftcontext];
      kmercode->definedspecialposition = true;
      kmercode->specialposition = head->lengthofleftcontext;
    }
  }
}

// Assembly:
cmpl $0x0, 0x1c(%rsi)
je 0x1f8056
movq 0x10(%rsi), %rcx
movl (%rcx), %eax
cmpl 0x44(%rsi), %eax
jae 0x1f8069
movq 0x60(%rsi), %rdx
movq (%rdx,%rax,8), %rdx
addq 0x8(%rcx), %rdx
movq %rdx, 0x8(%rdi)
movb $0x1, (%rdi)
movl %eax, 0x4(%rdi)
retq
movb $0x0, (%rdi)
movl $0x0, 0x4(%rdi)
movq 0x58(%rsi), %rax
movq %rax, 0x8(%rdi)
retq
pushq %rax
callq 0x7b0bd
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-mappedstr.c
// Function: gt_kmerstream_shiftrightwithchar
static void gt_kmerstream_shiftrightwithchar(GtKmerstream *spwp,
                                             GtUchar charcode)
{
  gt_assert(spwp->windowwidth == spwp->kmersize);
  gt_kmerstream_updatespecialpositions(spwp,charcode,true,
                                       spwp->cyclicwindow[spwp->firstindex]);
  spwp->cyclicwindow[spwp->firstindex] = charcode;
  if (spwp->firstindex < spwp->kmersize-1)
  {
    spwp->firstindex++;
  } else
  {
    spwp->firstindex = 0;
  }
}

// Assembly:
pushq %rbp
pushq %rbx
pushq %rax
movl 0x48(%rdi), %eax
cmpl 0x44(%rdi), %eax
jne 0x1f80b9
movq %rdi, %rbx
movl 0x4c(%rdi), %eax
movzbl 0x20(%rdi,%rax), %ecx
movzbl %sil, %ebp
movl %ebp, %esi
movl $0x1, %edx
callq 0x1f7c95
movl 0x4c(%rbx), %eax
movb %bpl, 0x20(%rbx,%rax)
movl 0x44(%rbx), %eax
movl 0x4c(%rbx), %ecx
decl %eax
leal 0x1(%rcx), %edx
xorl %esi, %esi
cmpl %eax, %ecx
cmovbl %edx, %esi
movl %esi, 0x4c(%rbx)
addq $0x8, %rsp
popq %rbx
popq %rbp
retq
callq 0x7b0f6
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-mappedstr.c
// Function: gt_kmercodeiterator_encseq_nonspecial_next
const GtKmercode *gt_kmercodeiterator_encseq_nonspecial_next(
                             GtKmercodeiterator *kmercodeiterator)
{
  while (true) {
    if (!kmercodeiterator->hasprocessedfirst) {
      gt_assert(kmercodeiterator->currentposition
                == kmercodeiterator->startpos +
                   kmercodeiterator->spwp->kmersize);
      gt_kmerstream_newcode(&kmercodeiterator->kmercode,
                            kmercodeiterator->spwp);
      kmercodeiterator->hasprocessedfirst = true;
      if (!kmercodeiterator->kmercode.definedspecialposition)
        return &kmercodeiterator->kmercode;
    }
    else {
      if (kmercodeiterator->currentposition < kmercodeiterator->totallength) {
        GtUchar charcode
          = gt_encseq_reader_next_encoded_char(kmercodeiterator->esr);
        gt_kmerstream_shiftrightwithchar(kmercodeiterator->spwp,charcode);
        gt_kmerstream_newcode(&kmercodeiterator->kmercode,
                              kmercodeiterator->spwp);
        kmercodeiterator->currentposition++;
        if (!kmercodeiterator->kmercode.definedspecialposition)
          return &kmercodeiterator->kmercode;
      }
      else
        break;
    }
  }
  return NULL;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %rdi, %r15
leaq 0x40(%rdi), %r14
cmpb $0x0, 0x18(%r15)
jne 0x1f80f8
movq 0x38(%r15), %rsi
movl 0x44(%rsi), %eax
addq 0x8(%r15), %rax
cmpq %rax, 0x10(%r15)
jne 0x1f8143
movq %r14, %rdi
callq 0x1f802e
movb $0x1, 0x18(%r15)
cmpb $0x0, 0x40(%r15)
jne 0x1f80ca
jmp 0x1f8133
movq 0x10(%r15), %rax
cmpq (%r15), %rax
jae 0x1f813f
movq 0x28(%r15), %rdi
callq 0xec7be
movq 0x38(%r15), %rdi
movzbl %al, %esi
callq 0x1f806f
movq 0x38(%r15), %rsi
movq %r14, %rdi
callq 0x1f802e
incq 0x10(%r15)
cmpb $0x0, 0x40(%r15)
cmoveq %r14, %rbx
jne 0x1f80ca
jmp 0x1f8136
movq %r14, %rbx
movq %rbx, %rax
popq %rbx
popq %r14
popq %r15
retq
xorl %ebx, %ebx
jmp 0x1f8136
callq 0x7b12f
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-mappedstr.c
// Function: gt_kmercodeiterator_delete
void gt_kmercodeiterator_delete(GtKmercodeiterator *kmercodeiterator)
{
  if (kmercodeiterator != NULL)
  {
    gt_encseq_reader_delete(kmercodeiterator->esr);
    gt_kmerstream_delete(kmercodeiterator->spwp);
    gt_sequence_buffer_delete(kmercodeiterator->fb);
    gt_free(kmercodeiterator);
  }
}

// Assembly:
testq %rdi, %rdi
je 0x1f82b4
pushq %rbx
movq %rdi, %rbx
movq 0x28(%rdi), %rdi
callq 0xed7bf
movq 0x38(%rbx), %rdi
callq 0x1f7c40
movq 0x50(%rbx), %rdi
callq 0x11ab5d
leaq 0x1c956d(%rip), %rsi    # 0x3c1813
movq %rbx, %rdi
movl $0x2d4, %edx            # imm = 0x2D4
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-mappedstr.c
// Function: gt_kmercodeiterator_filetab_next
int gt_kmercodeiterator_filetab_next(const GtKmercode **kmercodeptr,
                                     GtKmercodeiterator *kmercodeiterator,
                                     GtError *err)
{
  if (!kmercodeiterator->inputexhausted)
  {
    if (kmercodeiterator->hasprocessedfirst)
    {
      GtUchar charcode;
      int retval;

      retval = gt_sequence_buffer_next(kmercodeiterator->fb,&charcode,err);
      if (retval < 0)
      {
        *kmercodeptr = NULL;
        return -1;
      }
      if (retval != 0)
      {
        gt_kmerstream_shiftrightwithchar(kmercodeiterator->spwp,charcode);
        gt_kmerstream_newcode(&kmercodeiterator->kmercode,
                              kmercodeiterator->spwp);
        kmercodeiterator->currentposition++,
        *kmercodeptr = &kmercodeiterator->kmercode;
        return 0;
      }
      kmercodeiterator->inputexhausted = true;
      kmercodeiterator->totallength = kmercodeiterator->currentposition;
    } else
    {
      gt_kmerstream_newcode(&kmercodeiterator->kmercode,
                            kmercodeiterator->spwp);
      kmercodeiterator->hasprocessedfirst = true;
      *kmercodeptr = &kmercodeiterator->kmercode;
      return 0;
    }
  }
  if (kmercodeiterator->currentposition < kmercodeiterator->totallength +
                                          kmercodeiterator->spwp->kmersize)
  {
    gt_kmerstream_shiftrightwithchar(kmercodeiterator->spwp,
                                     (GtUchar) GT_WILDCARD);
    gt_kmerstream_newcode(&kmercodeiterator->kmercode, kmercodeiterator->spwp);
    kmercodeiterator->currentposition++,
    *kmercodeptr = &kmercodeiterator->kmercode;
  } else
  {
    *kmercodeptr = NULL;
  }
  return 0;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
subq $0x10, %rsp
movq %rsi, %r14
movq %rdi, %rbx
cmpb $0x0, 0x19(%rsi)
je 0x1f82fa
movq 0x38(%r14), %rdi
movl 0x44(%rdi), %eax
addq (%r14), %rax
cmpq %rax, 0x10(%r14)
jae 0x1f833e
movl $0xfe, %esi
callq 0x1f806f
leaq 0x40(%r14), %r15
movq 0x38(%r14), %rsi
movq %r15, %rdi
callq 0x1f802e
incq 0x10(%r14)
jmp 0x1f8358
cmpb $0x1, 0x18(%r14)
jne 0x1f8343
movq 0x50(%r14), %rdi
leaq 0xf(%rsp), %rsi
callq 0x11ae1e
testl %eax, %eax
js 0x1f8367
je 0x1f8377
movq 0x38(%r14), %rdi
movzbl 0xf(%rsp), %esi
callq 0x1f806f
leaq 0x40(%r14), %r15
movq 0x38(%r14), %rsi
movq %r15, %rdi
callq 0x1f802e
incq 0x10(%r14)
movq %r15, (%rbx)
xorl %eax, %eax
jmp 0x1f8373
xorl %r15d, %r15d
jmp 0x1f8358
leaq 0x40(%r14), %r15
movq 0x38(%r14), %rsi
movq %r15, %rdi
callq 0x1f802e
movb $0x1, 0x18(%r14)
movq %r15, (%rbx)
xorl %eax, %eax
addq $0x10, %rsp
popq %rbx
popq %r14
popq %r15
retq
movq $0x0, (%rbx)
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
xorl %ecx, %ecx
jmp 0x1f8385
movb $0x1, 0x19(%r14)
movq 0x10(%r14), %rax
movq %rax, (%r14)
movb $0x1, %cl
testb %cl, %cl
jne 0x1f82ca
jmp 0x1f835d
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-maprange.c
// Function: gt_Sfxmappedrange_map_entire
void *gt_Sfxmappedrange_map_entire(GtSfxmappedrange *sfxmappedrange,
                                   GtError *err)
{
  size_t mappedsize;

  gt_assert(sfxmappedrange != NULL);
  sfxmappedrange->entire = gt_fa_mmap_read(gt_str_get(sfxmappedrange->filename),
                                           &mappedsize,err);
  if (sfxmappedrange->entire == NULL)
  {
    return NULL;
  }
  if (mappedsize != gt_Sfxmappedrange_size_entire(sfxmappedrange))
  {
    gt_error_set(err,
                 "map file %s: mapped size = "GT_WU" != "
                 GT_WU" = expected size",
                 gt_str_get(sfxmappedrange->filename), (GtUword) mappedsize,
                 (GtUword) gt_Sfxmappedrange_size_entire(sfxmappedrange));
    gt_fa_xmunmap(sfxmappedrange->entire);
    sfxmappedrange->entire = NULL;
    return NULL;
  }
  gt_log_log("map %s completely ("GT_WU" units of size %u)",
              gt_str_get(sfxmappedrange->tablename),
              (GtUword) sfxmappedrange->numofunits,
              (unsigned int) sfxmappedrange->sizeofunit);
  return sfxmappedrange->entire;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
subq $0x10, %rsp
testq %rdi, %rdi
je 0x1f860f
movq %rsi, %r14
movq %rdi, %rbx
movq 0x18(%rdi), %rdi
callq 0x120d23
leaq 0x1c9532(%rip), %rdx    # 0x3c1a9b
leaq 0x8(%rsp), %rsi
movq %rax, %rdi
movl $0x58, %ecx
movq %r14, %r8
callq 0x102572
movq %rax, 0x8(%rbx)
testq %rax, %rax
je 0x1f85be
movq 0x30(%rbx), %rax
imulq 0x38(%rbx), %rax
cmpq %rax, 0x8(%rsp)
jne 0x1f85c3
movq 0x20(%rbx), %rdi
callq 0x120d23
movq 0x30(%rbx), %rdx
movl 0x38(%rbx), %ecx
leaq 0x1c9559(%rip), %rdi    # 0x3c1b07
movq %rax, %rsi
xorl %eax, %eax
callq 0x108e02
movq 0x8(%rbx), %r15
jmp 0x1f8602
xorl %r15d, %r15d
jmp 0x1f8602
movq 0x18(%rbx), %rdi
callq 0x120d23
movq 0x8(%rsp), %rcx
movq 0x30(%rbx), %r8
imulq 0x38(%rbx), %r8
leaq 0x1c94f0(%rip), %rsi    # 0x3c1ad1
xorl %r15d, %r15d
movq %r14, %rdi
movq %rax, %rdx
xorl %eax, %eax
callq 0x1019cf
movq 0x8(%rbx), %rdi
callq 0x102b12
movq $0x0, 0x8(%rbx)
movq %r15, %rax
addq $0x10, %rsp
popq %rbx
popq %r14
popq %r15
retq
callq 0x7b1d8
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-maprange.c
// Function: gt_Sfxmappedrange_new
GtSfxmappedrange *gt_Sfxmappedrange_new(const char *tablename,
                                        GtUword numofentries,
                                        GtSfxmappedrangetype type,
                                        GtSfxmappedrangetransformfunc
                                          transformfunc,
                                        const void *transformfunc_data)
{
  GtSfxmappedrange *sfxmappedrange;

  sfxmappedrange = gt_malloc(sizeof (*sfxmappedrange));
  sfxmappedrange->ptr = NULL;
  sfxmappedrange->pagesize = gt_pagesize();
  sfxmappedrange->usedptrptr = NULL;
  sfxmappedrange->filename = NULL;
  sfxmappedrange->writable = false;
  sfxmappedrange->entire = NULL;
  sfxmappedrange->transformfunc = transformfunc;
  sfxmappedrange->transformfunc_data = transformfunc_data;
  sfxmappedrange->type = type;
  sfxmappedrange->tablename = gt_str_new_cstr(tablename);
  sfxmappedrange->currentminindex = sfxmappedrange->currentmaxindex = 0;
  sfxmappedrange->indexrange_defined = false;
  switch (type)
  {
    case GtSfxGtBitsequence:
      sfxmappedrange->sizeofunit = sizeof (GtBitsequence);
      sfxmappedrange->numofunits = GT_NUMOFINTSFORBITS(numofentries);
      break;
    case GtSfxuint32_t:
      sfxmappedrange->sizeofunit = sizeof (uint32_t);
      sfxmappedrange->numofunits = (size_t) numofentries;
      break;
    case GtSfxunsignedlong:
      sfxmappedrange->sizeofunit = sizeof (GtUword);
      sfxmappedrange->numofunits = (size_t) numofentries;
      break;
    default:
      gt_assert(false);
      break;
  }
  return sfxmappedrange;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r8, (%rsp)
movq %rcx, %r12
movl %edx, %ebp
movq %rsi, %rbx
movq %rdi, %r13
leaq 0x1c9466(%rip), %rsi    # 0x3c1a9b
movl $0x78, %edi
movl $0x78, %edx
callq 0x1092b2
movq %rax, %r14
xorl %r15d, %r15d
movq %r15, (%rax)
callq 0xe837d
movq %rax, 0x28(%r14)
movb %r15b, 0x70(%r14)
xorps %xmm0, %xmm0
movups %xmm0, 0x8(%r14)
movq %r15, 0x18(%r14)
movq %r12, 0x60(%r14)
movq (%rsp), %rax
movq %rax, 0x68(%r14)
movl %ebp, 0x40(%r14)
movq %r13, %rdi
callq 0x120955
movq %rax, 0x20(%r14)
xorps %xmm0, %xmm0
movups %xmm0, 0x48(%r14)
movb %r15b, 0x58(%r14)
cmpl $0x2, %ebp
je 0x1f86c8
cmpl $0x1, %ebp
je 0x1f86be
testl %ebp, %ebp
jne 0x1f86e6
movq $0x8, 0x38(%r14)
leaq -0x1(%rbx), %rax
shrq $0x6, %rax
incq %rax
cmpq $0x40, %rbx
movl $0x1, %ebx
cmovaeq %rax, %rbx
jmp 0x1f86d0
movq $0x8, 0x38(%r14)
jmp 0x1f86d0
movq $0x4, 0x38(%r14)
movq %rbx, 0x30(%r14)
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x7b20f
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-maprange.c
// Function: gt_Sfxmappedrange_storetmp
static void gt_Sfxmappedrange_storetmp(GtSfxmappedrange *sfxmappedrange,
                                       GtSfxStoretype usedptrptr,
                                       GtSfxmappedrangetype type,
                                       bool writable)
{
  FILE *outfp;

  gt_assert(sfxmappedrange != NULL);
  sfxmappedrange->ptr = NULL;
  sfxmappedrange->filename = gt_str_new();
  sfxmappedrange->writable = writable;
  outfp = gt_xtmpfp(sfxmappedrange->filename);
  gt_assert(outfp != NULL);
  gt_log_log("write %s to file %s ("GT_WU" units of "GT_WU" bytes)",
             gt_str_get(sfxmappedrange->tablename),
             gt_str_get(sfxmappedrange->filename),
             (GtUword) sfxmappedrange->numofunits,
             (GtUword) sfxmappedrange->sizeofunit);
  switch (type) {
    case GtSfxGtBitsequence:
      gt_xfwrite(*(usedptrptr.bs),sfxmappedrange->sizeofunit,
                 sfxmappedrange->numofunits,outfp);
      sfxmappedrange->usedptrptr = (void**) usedptrptr.bs;
      gt_free(*(usedptrptr.bs));
      *(usedptrptr.bs) = NULL;
      break;
    case GtSfxunsignedlong:
      gt_xfwrite(*(usedptrptr.ulong),sfxmappedrange->sizeofunit,
                 sfxmappedrange->numofunits,outfp);
      sfxmappedrange->usedptrptr = (void**) usedptrptr.ulong;
      gt_free(*(usedptrptr.ulong));
      *(usedptrptr.ulong) = NULL;
      break;
    case GtSfxuint32_t:
      gt_xfwrite(*(usedptrptr.uint32),sfxmappedrange->sizeofunit,
                 sfxmappedrange->numofunits,outfp);
      sfxmappedrange->usedptrptr = (void**) usedptrptr.uint32;
      gt_free(*(usedptrptr.uint32));
      *(usedptrptr.uint32) = NULL;
      break;
   }
   gt_fa_fclose(outfp);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x1f87da
movl %ecx, %ebp
movl %edx, %r14d
movq %rsi, %rbx
movq %rdi, %r15
movq $0x0, (%rdi)
callq 0x1208f8
movq %rax, 0x18(%r15)
movb %bpl, 0x70(%r15)
leaq 0x1c9361(%rip), %rdx    # 0x3c1a9b
movq %rax, %rdi
xorl %esi, %esi
movl $0xab, %ecx
callq 0x1021c2
testq %rax, %rax
je 0x1f87df
movq %rax, %r12
movq 0x20(%r15), %rdi
callq 0x120d23
movq %rax, %r13
movq 0x18(%r15), %rdi
callq 0x120d23
movq 0x30(%r15), %rcx
movq 0x38(%r15), %r8
leaq 0x1c96be(%rip), %rdi    # 0x3c1e37
movq %r13, %rsi
movq %rax, %rdx
xorl %eax, %eax
callq 0x108e02
movq (%rbx), %rdi
movq 0x30(%r15), %rdx
movq 0x38(%r15), %rsi
movq %r12, %rcx
callq 0x125658
movq %rbx, 0x10(%r15)
movq (%rbx), %rdi
leal (,%r14,8), %edx
subl %r14d, %edx
addl $0xb7, %edx
leaq 0x1c92e3(%rip), %rsi    # 0x3c1a9b
callq 0x109670
movq $0x0, (%rbx)
movq %r12, %rdi
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x101e80
callq 0x7b2ba
callq 0x7b281
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-maprange.c
// Function: gt_Sfxmappedrange_usetmp
void gt_Sfxmappedrange_usetmp(GtSfxmappedrange *sfxmappedrange,
                              const GtStr *tmpfilename,
                              void **usedptrptr,
                              GtUword numofentries,
                              bool writable)
{
  gt_assert(sfxmappedrange != NULL);
  sfxmappedrange->ptr = NULL;
  /*gt_assert(usedptrptr != NULL && *usedptrptr == NULL);*/
  sfxmappedrange->usedptrptr = usedptrptr;
  sfxmappedrange->filename = gt_str_clone(tmpfilename);
  sfxmappedrange->writable = writable;
  if (sfxmappedrange->type == GtSfxGtBitsequence)
  {
    sfxmappedrange->numofunits = GT_NUMOFINTSFORBITS(numofentries);
  } else
  {
    sfxmappedrange->numofunits = (size_t) numofentries;
  }
  gt_log_log("use file %s for table %s ("GT_WU" units of "GT_WU" bytes)",
             gt_str_get(sfxmappedrange->filename),
             gt_str_get(sfxmappedrange->tablename),
             (GtUword) sfxmappedrange->numofunits,
             (GtUword) sfxmappedrange->sizeofunit);
  gt_free(*sfxmappedrange->usedptrptr);
  *sfxmappedrange->usedptrptr = NULL;
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0x1f88bd
movl %r8d, %ebp
movq %rcx, %r14
movq %rdi, %rbx
movq $0x0, (%rdi)
movq %rdx, 0x10(%rdi)
movq %rsi, %rdi
callq 0x120e13
movq %rax, 0x18(%rbx)
movb %bpl, 0x70(%rbx)
cmpl $0x0, 0x40(%rbx)
jne 0x1f8861
leaq -0x1(%r14), %rcx
shrq $0x6, %rcx
incq %rcx
cmpq $0x40, %r14
movl $0x1, %r14d
cmovaeq %rcx, %r14
movq %r14, 0x30(%rbx)
movq %rax, %rdi
callq 0x120d23
movq %rax, %r14
movq 0x20(%rbx), %rdi
callq 0x120d23
movq 0x30(%rbx), %rcx
movq 0x38(%rbx), %r8
leaq 0x1c9354(%rip), %rdi    # 0x3c1bdc
movq %r14, %rsi
movq %rax, %rdx
xorl %eax, %eax
callq 0x108e02
movq 0x10(%rbx), %rax
movq (%rax), %rdi
leaq 0x1c91f8(%rip), %rsi    # 0x3c1a9b
movl $0x105, %edx            # imm = 0x105
callq 0x109670
movq 0x10(%rbx), %rax
movq $0x0, (%rax)
popq %rbx
popq %r14
popq %rbp
retq
callq 0x7b365
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-maprange.c
// Function: gt_Sfxmappedrange_size_mapped
GtUword gt_Sfxmappedrange_size_mapped(const GtSfxmappedrange
                                                      *sfxmappedrange,
                                            GtUword minindex,
                                            GtUword maxindex)
{
  gt_assert(sfxmappedrange != NULL);
  if (sfxmappedrange->transformfunc != NULL)
  {
    sfxmappedrange->transformfunc(&minindex,&maxindex,
                                  sfxmappedrange->transformfunc_data);
  }
  if (minindex <= maxindex)
  {
    GtMappedrange lbrange;

    gt_Sfxmapped_offset_end(&lbrange,
                            sfxmappedrange->sizeofunit,
                            sfxmappedrange->pagesize,
                            minindex,
                            maxindex);
    return lbrange.mapend - lbrange.mapoffset + 1;
  }
  return 0;
}

// Assembly:
pushq %rbx
subq $0x10, %rsp
movq %rsi, 0x8(%rsp)
movq %rdx, (%rsp)
testq %rdi, %rdi
je 0x1f8941
movq %rdi, %rbx
movq 0x60(%rdi), %rax
testq %rax, %rax
je 0x1f88ef
movq 0x68(%rbx), %rdx
leaq 0x8(%rsp), %rdi
movq %rsp, %rsi
callq *%rax
movq 0x8(%rsp), %rcx
movq (%rsp), %rsi
cmpq %rsi, %rcx
jbe 0x1f8901
xorl %eax, %eax
jmp 0x1f893b
movq 0x28(%rbx), %r8
movq 0x38(%rbx), %r9
imulq %r9, %rcx
movq %rcx, %rax
xorl %edx, %edx
divq %r8
movq %rdx, %rdi
imulq %r9, %rsi
movq %rsi, %rax
xorl %edx, %edx
divq %r8
addq %rsi, %r8
subq %rdx, %r8
testq %rdx, %rdx
cmoveq %rsi, %r8
subq %rcx, %rdi
leaq (%rdi,%r8), %rax
incq %rax
addq $0x10, %rsp
popq %rbx
retq
callq 0x7b39e
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-maprange.c
// Function: gt_Sfxmappedrange_unmap
void gt_Sfxmappedrange_unmap(GtSfxmappedrange *sfxmappedrange)
{
  gt_assert(sfxmappedrange != NULL);
  if (sfxmappedrange->ptr != NULL)
  {
    gt_fa_xmunmap(sfxmappedrange->ptr);
  }
  sfxmappedrange->ptr = 0;
}

// Assembly:
pushq %rbx
testq %rdi, %rdi
je 0x1f8965
movq %rdi, %rbx
movq (%rdi), %rdi
testq %rdi, %rdi
je 0x1f895c
callq 0x102b12
movq $0x0, (%rbx)
popq %rbx
retq
callq 0x7b3d7
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-maprange.c
// Function: gt_Sfxmappedrange_delete
void gt_Sfxmappedrange_delete(GtSfxmappedrange *sfxmappedrange)
{
  if (sfxmappedrange == NULL)
  {
    return;
  }
  gt_fa_xmunmap(sfxmappedrange->ptr);
  sfxmappedrange->ptr = NULL;
  gt_fa_xmunmap(sfxmappedrange->entire);
  sfxmappedrange->entire = NULL;
  if (sfxmappedrange->usedptrptr != NULL)
  {
    *sfxmappedrange->usedptrptr = NULL;
  }
  if (sfxmappedrange->filename != NULL)
  {
    gt_xunlink(gt_str_get(sfxmappedrange->filename));
  }
  gt_str_delete(sfxmappedrange->tablename);
  gt_str_delete(sfxmappedrange->filename);
  gt_free(sfxmappedrange);
}

// Assembly:
testq %rdi, %rdi
je 0x1f8c30
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x102b12
xorl %r14d, %r14d
movq %r14, (%rbx)
movq 0x8(%rbx), %rdi
callq 0x102b12
movq %r14, 0x8(%rbx)
movq 0x10(%rbx), %rax
testq %rax, %rax
je 0x1f8bed
movq $0x0, (%rax)
movq 0x18(%rbx), %rdi
testq %rdi, %rdi
je 0x1f8c03
callq 0x120d23
movq %rax, %rdi
callq 0x1259fb
movq 0x20(%rbx), %rdi
callq 0x121b03
movq 0x18(%rbx), %rdi
callq 0x121b03
leaq 0x1c8e7f(%rip), %rsi    # 0x3c1a9b
movq %rbx, %rdi
movl $0x198, %edx            # imm = 0x198
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-maprange.c
// Function: gt_Sfxmappedrangelist_add
void gt_Sfxmappedrangelist_add(GtSfxmappedrangelist *sfxmrlist,
                               GtSfxmappedrange *sfxmappedrange)
{
  gt_assert(sfxmrlist != NULL);

  if (sfxmrlist->nextfree >= sfxmrlist->allocated)
  {
    sfxmrlist->allocated += 4UL;
    sfxmrlist->arr = gt_realloc(sfxmrlist->arr,sizeof (*sfxmrlist->arr) *
                                               sfxmrlist->allocated);
  }
  sfxmrlist->arr[sfxmrlist->nextfree++] = sfxmappedrange;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x1f8cb3
movq %rsi, %rbx
movq %rdi, %r14
movq 0x10(%rdi), %rax
cmpq %rax, 0x8(%rdi)
jb 0x1f8c98
leaq 0x4(%rax), %rcx
movq %rcx, 0x10(%r14)
movq (%r14), %rdi
leaq 0x20(,%rax,8), %rsi
leaq 0x1c8e10(%rip), %rdx    # 0x3c1a9b
movl $0x1b3, %ecx            # imm = 0x1B3
callq 0x1094e6
movq %rax, (%r14)
movq (%r14), %rax
movq 0x8(%r14), %rcx
leaq 0x1(%rcx), %rdx
movq %rdx, 0x8(%r14)
movq %rbx, (%rax,%rcx,8)
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x7b5d8
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-maprange.c
// Function: gt_Sfxmappedrangelist_size_mapped
GtUword gt_Sfxmappedrangelist_size_mapped(const GtSfxmappedrangelist *sfxmrlist,
                                          GtUword minindex,
                                          GtUword maxindex)
{
  if (sfxmrlist == NULL)
  {
    gt_assert(maxindex >= minindex);
    return maxindex - minindex + 1;
  } else
  {
    GtUword idx, sumsize = 0;

    for (idx = 0; idx < sfxmrlist->nextfree; idx++)
    {
      GtSfxmappedrange *sfxmappedrange = sfxmrlist->arr[idx];
      if (sfxmappedrange != NULL)
      {
        /*printf("size_mapped %s "GT_WU" "GT_WU" => "GT_WU"\n",
                    gt_str_get(sfxmappedrange->tablename),
                    minindex,maxindex,
                    gt_Sfxmappedrange_size_mapped(sfxmappedrange,minindex,
                                                  maxindex));*/
        sumsize += gt_Sfxmappedrange_size_mapped(sfxmappedrange,
                                                 minindex,
                                                 maxindex);
      }
    }
    return sumsize;
  }
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
movq %rdx, %rbx
movq %rsi, %r14
testq %rdi, %rdi
je 0x1f8d01
movq %rdi, %r15
cmpq $0x0, 0x8(%rdi)
je 0x1f8d0e
xorl %r12d, %r12d
xorl %r13d, %r13d
movq (%r15), %rax
movq (%rax,%r13,8), %rdi
testq %rdi, %rdi
je 0x1f8cf6
movq %r14, %rsi
movq %rbx, %rdx
callq 0x1f88c2
addq %rax, %r12
incq %r13
cmpq 0x8(%r15), %r13
jb 0x1f8cdc
jmp 0x1f8d11
subq %r14, %rbx
jb 0x1f8d1e
incq %rbx
movq %rbx, %r12
jmp 0x1f8d11
xorl %r12d, %r12d
movq %r12, %rax
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
callq 0x7b611
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-maprange.c
// Function: gt_Sfxmappedrangelist_size_entire
GtUword gt_Sfxmappedrangelist_size_entire(const GtSfxmappedrangelist *sfxmrlist)
{
  if (sfxmrlist == NULL)
  {
    return 0;
  } else
  {
    GtUword idx, sumsize = 0;

    for (idx = 0; idx < sfxmrlist->nextfree; idx++)
    {
      GtSfxmappedrange *sfxmappedrange = sfxmrlist->arr[idx];
      if (sfxmappedrange != NULL)
      {
        sumsize += gt_Sfxmappedrange_size_entire(sfxmappedrange);
      }
    }
    return sumsize;
  }
}

// Assembly:
testq %rdi, %rdi
je 0x1f8d56
movq 0x8(%rdi), %rcx
testq %rcx, %rcx
je 0x1f8d56
movq (%rdi), %rdx
xorl %eax, %eax
xorl %esi, %esi
movq (%rdx,%rsi,8), %rdi
testq %rdi, %rdi
je 0x1f8d4d
movq 0x30(%rdi), %r8
imulq 0x38(%rdi), %r8
addq %r8, %rax
incq %rsi
cmpq %rsi, %rcx
jne 0x1f8d38
retq
xorl %eax, %eax
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-partssuf.c
// Function: gt_suftabparts_variance
double gt_suftabparts_variance(const GtSuftabparts *suftabparts)
{

  gt_assert(suftabparts->numofparts > 0);
  if (suftabparts->numofparts == 1U)
  {
    return 0.0;
  } else
  {
    double meanwidth, difference, sum = 0.0;
    unsigned int part;

    meanwidth
      = (double)
        gt_suftabparts_sumofwidth(suftabparts->numofparts-1,suftabparts)/
        suftabparts->numofparts;
    for (part = 0; part < suftabparts->numofparts; part++)
    {
      difference = (double) suftabparts->components[part].widthofpart
                   - meanwidth;
      sum += difference * difference;
    }
    return sum/(double) (suftabparts->numofparts-1);
  }
}

// Assembly:
pushq %rbx
movq %rdi, %rbx
movl 0xc(%rdi), %edi
xorpd %xmm0, %xmm0
cmpl $0x1, %edi
je 0x1f9058
testl %edi, %edi
je 0x1f905a
decl %edi
movq %rbx, %rsi
callq 0x1f8f18
movl 0xc(%rbx), %ecx
testq %rcx, %rcx
je 0x1f9046
movq %rax, %xmm0
punpckldq 0x15790d(%rip), %xmm0 # xmm0 = xmm0[0],mem[0],xmm0[1],mem[1]
subpd 0x157915(%rip), %xmm0   # 0x3508f0
movapd %xmm0, %xmm1
unpckhpd %xmm0, %xmm1            # xmm1 = xmm1[1],xmm0[1]
addsd %xmm0, %xmm1
xorps %xmm0, %xmm0
cvtsi2sd %rcx, %xmm0
divsd %xmm0, %xmm1
movq (%rbx), %rax
movq %rcx, %rdx
shlq $0x4, %rdx
leaq (%rdx,%rdx,2), %rdx
xorpd %xmm0, %xmm0
xorl %esi, %esi
movsd 0x1578d1(%rip), %xmm2   # 0x3508e0
movapd 0x1578d9(%rip), %xmm3   # 0x3508f0
movsd (%rax,%rsi), %xmm4
unpcklps %xmm2, %xmm4            # xmm4 = xmm4[0],xmm2[0],xmm4[1],xmm2[1]
subpd %xmm3, %xmm4
movapd %xmm4, %xmm5
unpckhpd %xmm4, %xmm5            # xmm5 = xmm5[1],xmm4[1]
addsd %xmm4, %xmm5
subsd %xmm1, %xmm5
mulsd %xmm5, %xmm5
addsd %xmm5, %xmm0
addq $0x30, %rsi
cmpq %rsi, %rdx
jne 0x1f9017
jmp 0x1f904a
xorpd %xmm0, %xmm0
decl %ecx
xorps %xmm1, %xmm1
cvtsi2sd %rcx, %xmm1
divsd %xmm1, %xmm0
popq %rbx
retq
callq 0x7b763
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-run.c
// Function: gt_parseargsandcallsuffixerator
int gt_parseargsandcallsuffixerator(bool doesa,int argc,
                                    const char **argv,GtError *err)
{
  Suffixeratoroptions so;
  int retval;
  bool haserr = false;

  gt_error_check(err);
  retval = gt_suffixeratoroptions(&so,doesa,argc,argv,err);
  if (retval == 0)
  {
    GtLogger *logger = gt_logger_new(so.beverbose,
                                     GT_LOGGER_DEFLT_PREFIX, stdout);

    gt_logger_log(logger,"sizeof (GtUword)="GT_WU"",
                  (GtUword) (sizeof (GtUword) * CHAR_BIT));
    if (gt_runsuffixerator(doesa,&so,NULL,logger,err) < 0)
    {
      haserr = true;
    }
    gt_logger_delete(logger);
    logger = NULL;
  } else
  {
    if (retval < 0)
    {
      haserr = true;
    }
  }
  gt_sfxoptions_delete(&so);
  return haserr ? -1 : 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
subq $0x38, %rsp
movq %rcx, %rbx
movq %rdx, %r14
movl %esi, %r15d
movl %edi, %ebp
testq %rcx, %rcx
je 0x1fa936
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0x1fa9c1
movzbl %bpl, %ebp
movq %rsp, %rdi
movl %ebp, %esi
movl %r15d, %edx
movq %r14, %rcx
movq %rbx, %r8
callq 0x3345db
movl %eax, %r14d
testl %eax, %eax
jne 0x1fa9a7
movq %rsp, %r14
movzbl (%r14), %edi
movq 0x2c9586(%rip), %rax    # 0x4c3ee8
movq (%rax), %rdx
leaq 0x154f68(%rip), %rsi    # 0x34f8d4
callq 0x108ed0
movq %rax, %r15
leaq 0x1c7bba(%rip), %rsi    # 0x3c2535
movl $0x40, %edx
movq %rax, %rdi
xorl %eax, %eax
callq 0x10906e
movl %ebp, %edi
movq %r14, %rsi
xorl %edx, %edx
movq %r15, %rcx
movq %rbx, %r8
callq 0x1f9b10
movl %eax, %r14d
movq %r15, %rdi
callq 0x10916a
sarl $0x1f, %r14d
movq %rsp, %rdi
callq 0x3345a0
movl %r14d, %eax
addq $0x38, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
callq 0x7bde4
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sfx-run.c
// Function: gt_suflcptab2genomediff
static void gt_suflcptab2genomediff(void *data,
                                    const GtSuffixsortspace *sssp,
                                    const GtLcpvalues *tableoflcpvalues,
                                    GtUword bucketoffset,
                                    GtUword numberofsuffixes,
                                    GtUword posoffset)
{
  (void) gt_sfx_multiesa2shulengthdist(
                  (GtBUstate_shulen *) data,
                  gt_suffixsortspace_getptr_ulong(sssp,bucketoffset+posoffset),
                  gt_suffixsortspace_getptr_uint32(sssp,bucketoffset+posoffset),
                  gt_lcptab_getptr(tableoflcpvalues,bucketoffset),
                  numberofsuffixes,
                  NULL);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r8, (%rsp)
movq %rcx, %r14
movq %rdx, %r15
movq %rsi, %r12
movq %rdi, %r13
leaq (%r9,%rcx), %rbp
movq %rsi, %rdi
movq %rbp, %rsi
callq 0x206081
movq %rax, %rbx
movq %r12, %rdi
movq %rbp, %rsi
callq 0x2060b0
movq %rax, %r12
movq %r15, %rdi
movq %r14, %rsi
callq 0x1f5b60
movq %r13, %rdi
movq %rbx, %rsi
movq %r12, %rdx
movq %rax, %rcx
movq (%rsp), %r8
xorl %r9d, %r9d
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x1af575
nop