LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq-context.c
// Function: gt_BWTSCRFMapAdvance
size_t
gt_BWTSCRFMapAdvance(BWTSeqContextRetrieverFactory *factory,
                  const GtUword *src,
                  size_t len)
{
  GtUword currentSfxPos;
  gt_assert(factory);
  currentSfxPos = factory->currentSfxPos;
  {
    size_t i;
    GtUword mask = factory->moduloMask,
      seqLen = factory->seqLen;
    for (i = 0; i < len; ++i)
    {
      if (!(((src[i] + seqLen - 1)%seqLen) & mask))
        addMapVal(factory, currentSfxPos + i, ((src[i] + seqLen - 1)%seqLen));
    }
  }
  factory->currentSfxPos = currentSfxPos + len;
  return len;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
testq %rdi, %rdi
je 0x1a1c37
movq %rdx, %rbp
movq 0x8(%rdi), %rax
movq %rax, 0x8(%rsp)
testq %rdx, %rdx
je 0x1a1c14
movq %rsi, %r14
movq (%rdi), %r8
movq 0x10(%rdi), %r12
leaq -0x1(%r8), %r9
xorl %r15d, %r15d
movq %r8, 0x18(%rsp)
movq %r9, 0x10(%rsp)
movq (%r14,%r15,8), %rax
addq %r9, %rax
xorl %edx, %edx
divq %r8
testq %r12, %rdx
jne 0x1a1c0c
movb 0x1a(%rdi), %cl
sarq %cl, %rdx
movq 0x8(%rsp), %rax
addq %r15, %rax
shlq $0x3, %rdx
movq %rax, 0x20(%rsp)
movq %rdi, %rbx
movq 0x20(%rdi), %r13
movq %r13, %rdi
movq %rdx, %rsi
xorl %edx, %edx
callq 0x17cf0
cmpl $-0x1, %eax
je 0x1a1c32
movl $0x8, %esi
movl $0x1, %edx
leaq 0x20(%rsp), %rdi
movq %r13, %rcx
callq 0x125658
movq %rbx, %rdi
movq 0x18(%rsp), %r8
movq 0x10(%rsp), %r9
incq %r15
cmpq %r15, %rbp
jne 0x1a1ba7
movq 0x8(%rsp), %rax
addq %rbp, %rax
movq %rax, 0x8(%rdi)
movq %rbp, %rax
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x5fac4
callq 0x5fb0b
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq-context.c
// Function: gt_BWTSeqCRLoad
BWTSeqContextRetriever *
gt_BWTSeqCRLoad(const BWTSeq *bwtSeq,
             const char *projectName,
             short mapIntervalLog2)
{
  GtUword seqLen;
  unsigned short bitsPerUlong;
  BWTSeqContextRetriever *gt_newBWTSeqCR;
  gt_assert(bwtSeq && projectName);
  seqLen = BWTSeqLength(bwtSeq);
  bitsPerUlong = requiredUlongBits(seqLen - 1);
  gt_newBWTSeqCR = gt_malloc(sizeof (*gt_newBWTSeqCR));
  gt_newBWTSeqCR->bitsPerUlong = bitsPerUlong;
  gt_newBWTSeqCR->bwtSeq = bwtSeq;
  if (mapIntervalLog2 != CTX_MAP_ILOG_AUTOSIZE)
  {
    if (!BWTSeqCRMapOpen(mapIntervalLog2, bitsPerUlong, seqLen,
                         projectName, false, gt_newBWTSeqCR))
    {
      gt_free(gt_newBWTSeqCR);
      return NULL;
    }
  }
  else
  {
    short mapIntervalLog2Max = bitsPerUlong;
    mapIntervalLog2 = 0;
    while (!BWTSeqCRMapOpen(mapIntervalLog2, bitsPerUlong, seqLen,
                            projectName, false, gt_newBWTSeqCR)
           && mapIntervalLog2 < mapIntervalLog2Max)
      ++mapIntervalLog2;
    if (!gt_newBWTSeqCR->revMap)
    {
      gt_free(gt_newBWTSeqCR);
      return NULL;
    }
  }
  gt_newBWTSeqCR->mapIntervalLog2 = mapIntervalLog2;
  gt_newBWTSeqCR->mapInterval = 1 << mapIntervalLog2;
  gt_newBWTSeqCR->mapMask = gt_newBWTSeqCR->mapInterval - 1;
  return gt_newBWTSeqCR;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x1a21b1
movq %rsi, %r14
testq %rsi, %rsi
je 0x1a21b1
movl %edx, %ebp
movq %rdi, %r12
movq (%rdi), %rax
movq 0x10(%rax), %r15
leaq -0x1(%r15), %rdi
callq 0x2f9d41
movl %eax, %r13d
leaq 0x2094ad(%rip), %rsi    # 0x3ab592
movl $0x30, %edi
movl $0x15d, %edx            # imm = 0x15D
callq 0x1092b2
movq %rax, %rbx
movw %r13w, 0x2a(%rax)
movq %r12, 0x10(%rax)
cmpw $-0x1, %bp
je 0x1a2133
movzwl %bp, %edi
movzwl %r13w, %esi
movq %r15, %rdx
movq %r14, %rcx
xorl %r8d, %r8d
movq %rbx, %r9
callq 0x1a1e2b
testb %al, %al
jne 0x1a216e
leaq 0x209469(%rip), %rsi    # 0x3ab592
movq %rbx, %rdi
movl $0x165, %edx            # imm = 0x165
jmp 0x1a2198
movl %r13d, %eax
movswl %ax, %r13d
movw $0xffff, %bp            # imm = 0xFFFF
movzwl %ax, %r12d
incl %ebp
movzwl %bp, %edi
movl %r12d, %esi
movq %r15, %rdx
movq %r14, %rcx
xorl %r8d, %r8d
movq %rbx, %r9
callq 0x1a1e2b
testb %al, %al
jne 0x1a2167
movswl %bp, %eax
cmpl %eax, %r13d
jg 0x1a2142
cmpq $0x0, 0x20(%rbx)
je 0x1a2189
movw %bp, 0x28(%rbx)
movl $0x1, %eax
movl %ebp, %ecx
shll %cl, %eax
cltq
movq %rax, (%rbx)
decq %rax
movq %rax, 0x8(%rbx)
jmp 0x1a219f
leaq 0x209402(%rip), %rsi    # 0x3ab592
movq %rbx, %rdi
movl $0x173, %edx            # imm = 0x173
callq 0x109670
xorl %ebx, %ebx
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x5fc78
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq-context.c
// Function: gt_BWTSeqCRAccessSubseq
void
gt_BWTSeqCRAccessSubseq(const BWTSeqContextRetriever *bwtSeqCR,
                     GtUword start, size_t len, Symbol subseq[])
{
  struct SeqMark currentPos;
  struct extBitsRetrieval extBits;
  const BWTSeq *bwtSeq;
  initExtBitsRetrieval(&extBits);
  gt_assert(bwtSeqCR);
  gt_assert(start < BWTSeqLength(bwtSeqCR->bwtSeq));
  bwtSeq = bwtSeqCR->bwtSeq;
  {
    GtUword end = start + len - 1;
    currentPos = BWTSeqCRNextMark(bwtSeqCR, end);
    gt_assert(currentPos.textPos >= end);
    while (currentPos.textPos > end)
    {
      currentPos.bwtPos = BWTSeqLFMap(bwtSeq, currentPos.bwtPos, &extBits);
      --currentPos.textPos;
    }
  }
  {
    GtUword i = len;
    while (i)
    {
      --i;
      subseq[i] = BWTSeqGetSym(bwtSeq, currentPos.bwtPos);
      currentPos.bwtPos = BWTSeqLFMap(bwtSeq, currentPos.bwtPos, &extBits);
#ifndef NDEBUG
      --currentPos.textPos;
#endif
    }
  }
  gt_assert(currentPos.textPos + 1 == start);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x48, %rsp
movq %rcx, 0x8(%rsp)
xorps %xmm0, %xmm0
movaps %xmm0, 0x30(%rsp)
movaps %xmm0, 0x20(%rsp)
movaps %xmm0, 0x10(%rsp)
movq $0x0, 0x40(%rsp)
testq %rdi, %rdi
je 0x1a2337
movq 0x10(%rdi), %r12
movq (%r12), %rax
movq 0x10(%rax), %rax
cmpq %rsi, %rax
jbe 0x1a233c
movq %rdx, %r15
leaq (%rsi,%rdx), %r14
decq %r14
cmpq %r14, %rax
jbe 0x1a2341
movq %rsi, (%rsp)
movq 0x8(%rdi), %rbx
leaq (%rbx,%r14), %rcx
notq %rbx
andq %rcx, %rbx
cmpq %rax, %rbx
jae 0x1a227d
movb 0x28(%rdi), %cl
movq %rbx, %r8
shrq %cl, %r8
movq 0x20(%rdi), %rax
movzwl 0x2a(%rdi), %edx
movq %rdx, %rsi
imulq %r8, %rsi
movq %rax, %rdi
callq 0x2fcc2c
movq %rax, %r13
jmp 0x1a2288
decq %rax
movq 0x30(%r12), %r13
movq %rax, %rbx
cmpq %r14, %rbx
jb 0x1a2346
jbe 0x1a22b4
leaq 0x10(%rsp), %rbp
movq %r12, %rdi
movq %r13, %rsi
movq %rbp, %rdx
callq 0x1a2350
movq %rax, %r13
decq %rbx
cmpq %r14, %rbx
ja 0x1a2298
movq %r14, %rbx
testq %r15, %r15
je 0x1a2315
subq %r15, %rbx
leaq 0x10(%rsp), %rbp
movq (%r12), %rdi
testq %rdi, %rdi
je 0x1a2332
movq 0x18(%r12), %rdx
testq %rdx, %rdx
je 0x1a2332
movq (%rdi), %rax
movq 0x8(%rdi), %r14
movq %r13, %rsi
callq *0x30(%rax)
cmpl $0x1, (%r14)
jne 0x1a232d
movzbl %al, %eax
movb 0x118(%r14,%rax), %al
movq 0x8(%rsp), %rcx
movb %al, -0x1(%rcx,%r15)
decq %r15
movq %r12, %rdi
movq %r13, %rsi
movq %rbp, %rdx
callq 0x1a2350
movq %rax, %r13
testq %r15, %r15
jne 0x1a22c1
incq %rbx
cmpq (%rsp), %rbx
jne 0x1a234b
addq $0x48, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x173b0
callq 0x5fd5a
callq 0x5fe03
callq 0x5fcea
callq 0x5fd23
callq 0x5fdca
callq 0x5fd91
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq-extinfo.c
// Function: writeLocateInfoHeader
static int
writeLocateInfoHeader(FILE *fp, void *cbData)
{
  struct locateHeader headerData;
  Definedunsignedlong rot0Pos;
  const struct locateHeaderWriteInfo *headerSrc = cbData;
  gt_assert(cbData);
  headerData.locateInterval = headerSrc->locateInterval;
  rot0Pos = SASSGetRot0Pos(headerSrc->src);
  if (!rot0Pos.defined)
  {
    fputs("Invalid index construction: position of suffix 0 unknown!\n",
          stderr);
    abort();
  }
  headerData.rot0Pos = rot0Pos.valueunsignedlong;
  headerData.featureToggles = headerSrc->featureToggles;
  gt_xfwrite(&headerData, sizeof (headerData), 1, fp);
  return 1;
}

// Assembly:
pushq %r14
pushq %rbx
subq $0x18, %rsp
testq %rsi, %rsi
je 0x1a2b81
movq %rsi, %r14
movq %rdi, %rbx
movl 0x8(%rsi), %eax
movl %eax, 0x10(%rsp)
movq (%rsi), %rdi
callq *0x18(%rdi)
testb $0x1, %al
je 0x1a2b86
leaq 0x8(%rsp), %rdi
movq %rdx, (%rdi)
movl 0xc(%r14), %eax
movl %eax, 0xc(%rdi)
movl $0x10, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x125658
movl $0x1, %eax
addq $0x18, %rsp
popq %rbx
popq %r14
retq
callq 0x6019a
callq 0x6017e
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq-extinfo.c
// Function: writeRankSortHeader
static int
writeRankSortHeader(FILE *fp, void *cbData)
{
  struct sortModeHeader *headerData = cbData;
  gt_assert(cbData);
  gt_xfwrite(&headerData->bitsPerOrigRank, sizeof (headerData->bitsPerOrigRank),
             1, fp);
  {
    size_t i, numRanges = MRAEncGetNumRanges(headerData->alphabet);
    for (i = 0; i < numRanges; ++i)
    {
      int16_t mode = headerData->rangeSort[i];
      gt_xfwrite(&mode, sizeof (mode), 1, fp);
    }
  }
  return 1;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x10, %rsp
testq %rsi, %rsi
je 0x1a2c0b
movq %rsi, %rbx
movq %rdi, %r14
movl $0x4, %esi
movl $0x1, %edx
movq %rbx, %rdi
movq %r14, %rcx
callq 0x125658
movq 0x8(%rbx), %rax
movl 0x4(%rax), %r12d
testq %r12, %r12
je 0x1a2bf8
xorl %r13d, %r13d
leaq 0xe(%rsp), %r15
movq 0x10(%rbx), %rax
movzwl (%rax,%r13,4), %eax
movw %ax, 0xe(%rsp)
movl $0x2, %esi
movl $0x1, %edx
movq %r15, %rdi
movq %r14, %rcx
callq 0x125658
incq %r13
cmpq %r13, %r12
jne 0x1a2bcd
movl $0x1, %eax
addq $0x10, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
callq 0x601d1
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq-extinfo.c
// Function: gt_BWTSeqPosHasLocateInfo
int
gt_BWTSeqPosHasLocateInfo(const BWTSeq *bwtSeq, GtUword pos,
                       struct extBitsRetrieval *extBits)
{
  if (bwtSeq->featureToggles & BWTLocateBitmap)
  {
    EISRetrieveExtraBits(bwtSeq->seqIdx, pos, EBRF_RETRIEVE_CWBITS, extBits,
                         bwtSeq->hint);
    return gt_bsGetBit(extBits->cwPart,
                       extBits->cwOffset + pos - extBits->start);
  }
  else if (bwtSeq->featureToggles & BWTLocateCount)
  {
    BitOffset markOffset = searchLocateCountMark(bwtSeq, pos, extBits);
    return markOffset != 0;
  }
#ifndef NDEBUG
  else
  {
    fputs("Trying to locate in BWT sequence index without locate information.",
          stderr);
    abort();
  }
#endif
  return 0;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdx, %r14
movq %rsi, %rbx
movl 0x40(%rdi), %eax
testb $0x1, %al
jne 0x1a32a9
testb $0x2, %al
je 0x1a32f5
movq %rbx, %rsi
movq %r14, %rdx
callq 0x1a32ff
movq %rax, %rcx
xorl %eax, %eax
testq %rcx, %rcx
setne %al
jmp 0x1a32ed
movq (%rdi), %rax
movq 0x18(%rdi), %r8
movq (%rax), %r9
movq %rax, %rdi
movq %rbx, %rsi
xorl %edx, %edx
movq %r14, %rcx
callq *0x50(%r9)
movq 0x20(%r14), %rax
testq %rax, %rax
je 0x1a32fa
addq (%r14), %rbx
subq 0x10(%r14), %rbx
movq %rbx, %rcx
shrq $0x3, %rcx
movzbl (%rax,%rcx), %ecx
notb %bl
movzbl %bl, %edx
andl $0x7, %edx
xorl %eax, %eax
btl %edx, %ecx
setb %al
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x60475
callq 0x6043c
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq-extinfo.c
// Function: searchLocateCountMark
static inline BitOffset
searchLocateCountMark(const BWTSeq *bwtSeq, GtUword pos,
                      struct extBitsRetrieval *extBits)
{
  unsigned i, numMarks, bitsPerCount;
  BitOffset markOffset;
  EISRetrieveExtraBits(bwtSeq->seqIdx, pos, EBRF_RETRIEVE_CWBITS
                       | EBRF_RETRIEVE_VARBITS, extBits, bwtSeq->hint);
  markOffset = extBits->varOffset;
  bitsPerCount = requiredUlongBits(extBits->len);
  numMarks = gt_bsGetUlong(extBits->varPart, markOffset, bitsPerCount);
  if (numMarks)
  {
    unsigned bitsPerBWTPos = requiredUlongBits(extBits->len - 1),
      bitsPerOrigPos = requiredUlongBits(
        ((bwtSeq->featureToggles & BWTReversiblySorted) ?
         (BWTSeqLength(bwtSeq) - 1) / bwtSeq->locateSampleInterval :
         BWTSeqLength(bwtSeq) - 1));
    GtUword cmpPos = pos - extBits->start;
    markOffset += bitsPerCount;
    for (i = 0; i < numMarks; ++i)
    {
      GtUword markedPos = gt_bsGetUlong(extBits->varPart, markOffset,
                                     bitsPerBWTPos);
      if (markedPos < cmpPos)
        markOffset += bitsPerBWTPos + bitsPerOrigPos;
      else if (markedPos > cmpPos)
        break;
      else if (markedPos == cmpPos)
        return markOffset + bitsPerBWTPos;
    }
  }
  return 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %rdx, %rbx
movq %rsi, %r14
movq %rdi, %r13
movq (%rdi), %rdi
movq 0x18(%r13), %r8
movq (%rdi), %rax
movl $0x2, %edx
movq %rbx, %rcx
callq *0x50(%rax)
movq 0x8(%rbx), %r15
movq 0x18(%rbx), %rdi
callq 0x2f9d41
movl %eax, %ebp
movq 0x28(%rbx), %rdi
movq %r15, %rsi
movl %eax, %edx
callq 0x2fcc2c
movq %rax, %r12
testl %r12d, %r12d
je 0x1a33f9
movl %ebp, 0x8(%rsp)
movq 0x18(%rbx), %rdi
decq %rdi
callq 0x2f9d41
movl %eax, %ebp
movq (%r13), %rax
movq 0x10(%rax), %rax
decq %rax
testb $0x4, 0x40(%r13)
je 0x1a3381
movl 0x20(%r13), %ecx
xorl %edx, %edx
divq %rcx
movq %rax, %rdi
callq 0x2f9d41
subq 0x10(%rbx), %r14
movl %eax, %r13d
movl 0x8(%rsp), %eax
addq %rax, %r15
movl %ebp, %eax
movq %rax, 0x10(%rsp)
addl %ebp, %r13d
cmpl $0x1, %r12d
adcl $0x0, %r12d
movq 0x28(%rbx), %rdi
movq %r15, %rsi
movl %ebp, %edx
callq 0x2fcc2c
cmpq %r14, %rax
jae 0x1a33c3
addq %r13, %r15
xorl %ecx, %ecx
jmp 0x1a33e9
movl $0x2, %ecx
ja 0x1a33e9
movq 0x10(%rsp), %rcx
leaq (%r15,%rcx), %rdx
xorl %ecx, %ecx
cmpq %r14, %rax
sete %cl
movq 0x8(%rsp), %rax
cmoveq %rdx, %rax
movq %rax, 0x8(%rsp)
testl %ecx, %ecx
jne 0x1a33f4
decl %r12d
jne 0x1a33a9
jmp 0x1a33f9
cmpl $0x2, %ecx
jne 0x1a33fd
xorl %eax, %eax
jmp 0x1a3402
movq 0x8(%rsp), %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/eis-bwtseq-extinfo.c
// Function: gt_BWTSeqGetRankSort
GtUword
gt_BWTSeqGetRankSort(const BWTSeq *bwtSeq, GtUword pos,
                  AlphabetRangeID range, struct extBitsRetrieval *extBits)
{
  BitOffset locVarBits;
  AlphabetRangeSize rSize;
  gt_assert(bwtSeq->rangeSort[range] == SORTMODE_RANK);
  EISRetrieveExtraBits(bwtSeq->seqIdx, pos, EBRF_RETRIEVE_CWBITS
                       | EBRF_RETRIEVE_VARBITS, extBits, bwtSeq->hint);
  locVarBits = locateVarBits(bwtSeq, extBits);
  rSize = MRAEncGetRangeSize(EISGetAlphabet(bwtSeq->seqIdx), range);
  {
    GtUword ranks[rSize * 2];
    GtUword BWTRankTotal = 0;
    AlphabetRangeSize i;
    EISPosPairRangeRank(bwtSeq->seqIdx, range, extBits->start, pos, ranks,
                        bwtSeq->hint);
    for (i = 0; i < rSize; ++i)
      BWTRankTotal += ranks[i + rSize] - ranks[i];
    return gt_bsGetUlong(extBits->varPart, extBits->varOffset + locVarBits
                       + bwtSeq->bitsPerOrigRank * BWTRankTotal,
                       bwtSeq->bitsPerOrigRank);
  }
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %rcx, %rbx
movq 0x48(%rdi), %rax
movl %edx, -0x30(%rbp)
movl %edx, %ecx
movq %rcx, -0x40(%rbp)
cmpl $0x2, (%rax,%rcx,4)
jne 0x1a396f
movq %rsi, %r15
movq %rdi, %r14
movq (%rdi), %rdi
movq 0x18(%r14), %r8
movq (%rdi), %rax
movl $0x2, %edx
movq %rbx, %rcx
callq *0x50(%rax)
movq 0x18(%rbx), %rdi
decq %rdi
callq 0x2f9d41
movl %eax, %r12d
movq (%r14), %rax
movq 0x10(%rax), %rax
decq %rax
testb $0x4, 0x40(%r14)
je 0x1a3862
movl 0x20(%r14), %ecx
xorl %edx, %edx
divq %rcx
movq %rax, %rdi
callq 0x2f9d41
movl %eax, %r13d
movl 0x40(%r14), %eax
testb $0x1, %al
jne 0x1a38b0
movl %r12d, -0x2c(%rbp)
xorl %r12d, %r12d
testb $0x2, %al
je 0x1a38c7
movq 0x8(%rbx), %rax
movq %rax, -0x38(%rbp)
movq 0x18(%rbx), %rdi
callq 0x2f9d41
movl %eax, %r12d
movq 0x28(%rbx), %rdi
movq -0x38(%rbp), %rsi
movl %eax, %edx
callq 0x2fcc2c
addl -0x2c(%rbp), %r13d
imull %eax, %r13d
addl %r12d, %r13d
jmp 0x1a38c4
movq 0x20(%rbx), %rdi
movq (%rbx), %rsi
movq 0x18(%rbx), %rdx
callq 0x2fa5fa
imull %eax, %r13d
movl %r13d, %r12d
movq (%r14), %rdi
testq %rdi, %rdi
movl -0x30(%rbp), %esi
je 0x1a3974
movq 0x8(%rdi), %rax
testq %rax, %rax
je 0x1a3979
cmpl %esi, 0x4(%rax)
jbe 0x1a397e
movq %r15, %rcx
movq 0x10(%rax), %rax
movq -0x40(%rbp), %rdx
movzwl (%rax,%rdx,2), %r15d
movl %r15d, %eax
shll $0x4, %eax
movq %rsp, %r13
subq %rax, %r13
movq %r13, %rsp
movq 0x10(%rbx), %rdx
movq 0x18(%r14), %r9
movq (%rdi), %rax
movq %r13, %r8
callq *0x20(%rax)
testl %r15d, %r15d
je 0x1a3943
leaq (,%r15,8), %rax
addq %r13, %rax
xorl %ecx, %ecx
xorl %esi, %esi
addq (%rax,%rcx,8), %rsi
subq (%r13,%rcx,8), %rsi
incq %rcx
cmpq %rcx, %r15
jne 0x1a3930
jmp 0x1a3945
xorl %esi, %esi
movl %r12d, %eax
addq 0x8(%rbx), %rax
movq 0x28(%rbx), %rdi
movl 0x44(%r14), %edx
imulq %rdx, %rsi
addq %rax, %rsi
callq 0x2fcc2c
leaq -0x28(%rbp), %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x6077e
callq 0x60825
callq 0x607ee
callq 0x607b7
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq-param.c
// Function: gt_registerPackedIndexOptions
void
gt_registerPackedIndexOptions(GtOptionParser *op,
                              struct bwtOptions *paramOutput,
                              int defaultOptimizationFlags,
                              const GtStr *projectName)
{
  GtOption *option;

  gt_registerEncIdxSeqOptions(op, &paramOutput->final.seqParams);

  paramOutput->final.featureToggles = BWTBaseFeatures;

  option = gt_option_new_uint(
    "locfreq", "specify the locate frequency\n"
    "parameter i means that each i-th position of input string is stored\n"
    "0 => no locate information", &paramOutput->final.locateInterval, 16U);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool(
    "locbitmap", "marked/unmarked positions for locate are stored as bitmaps\n"
    "this gives faster location of hits but increases the index by 1 bit per"
    " symbol", &paramOutput->useLocateBitmap, true);
  gt_option_parser_add_option(op, option);
  paramOutput->useLocateBitmapOption = option;

  option = gt_option_new_bool(
    "sprank", "build rank table for special symbols\n"
    "this produces an index which can be used to regenerate the "
    "original sequence but increases the memory used during index creation",
    &paramOutput->useSourceRank, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_int_min_max(
    "sprankilog", "specify the interval of rank sampling as log value\n"
    "parameter i means that each 2^i-th position of source is sampled for "
    "rank\nundefined => chooses default of log(log(sequence length))",
    &paramOutput->final.sourceRankInterval, -1, -1,
    sizeof (GtUword) * CHAR_BIT - 1);
  gt_option_parser_add_option(op, option);

  gt_registerCtxMapOptions(op, &paramOutput->final.ctxMapILog);

  paramOutput->final.projectName = projectName;

  paramOutput->defaultOptimizationFlags = defaultOptimizationFlags;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
movq %rcx, %r14
movl %edx, %ebx
movq %rsi, %r15
movq %rdi, %r12
callq 0x1a573c
movl $0x0, 0x10(%r15)
leaq 0x14(%r15), %rdx
leaq 0x2083ed(%rip), %rdi    # 0x3abf4d
leaq 0x2083ee(%rip), %rsi    # 0x3abf55
movl $0x10, %ecx
callq 0x10f719
movq %r12, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x2c(%r15), %rdx
leaq 0x20844a(%rip), %rdi    # 0x3abfd1
leaq 0x20844d(%rip), %rsi    # 0x3abfdb
movl $0x1, %ecx
callq 0x10f451
movq %rax, %r13
movq %r12, %rdi
movq %rax, %rsi
callq 0x10cd10
movq %r13, 0x30(%r15)
leaq 0x2d(%r15), %rdx
leaq 0x2084b0(%rip), %rdi    # 0x3ac065
leaq 0x2084b0(%rip), %rsi    # 0x3ac06c
xorl %ecx, %ecx
callq 0x10f451
movq %r12, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x18(%r15), %rdx
leaq 0x208539(%rip), %rdi    # 0x3ac112
leaq 0x20853d(%rip), %rsi    # 0x3ac11d
movl $0xffffffff, %ecx       # imm = 0xFFFFFFFF
movl $0xffffffff, %r8d       # imm = 0xFFFFFFFF
movl $0x3f, %r9d
callq 0x10f6dd
movq %r12, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x1c(%r15), %rsi
movq %r12, %rdi
callq 0x1a190c
movq %r14, 0x20(%r15)
movl %ebx, 0x28(%r15)
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq-param.c
// Function: gt_computePackedIndexDefaults
void
gt_computePackedIndexDefaults(struct bwtOptions *paramOutput, int extraToggles)
{
  if (gt_option_is_set(paramOutput->useLocateBitmapOption))
    paramOutput->final.featureToggles
      |= (paramOutput->useLocateBitmap?BWTLocateBitmap:BWTLocateCount);
  else
    paramOutput->final.featureToggles
      |= estimateBestLocateTypeFeature(paramOutput);
  if (paramOutput->final.sourceRankInterval >= 0
      || paramOutput->useSourceRank)
    paramOutput->final.featureToggles |= BWTReversiblySorted;
  paramOutput->final.featureToggles |= extraToggles;
  paramOutput->final.seqParams.EISFeatureSet
    = gt_convertBWTOptFlags2EISFeatures(paramOutput->defaultOptimizationFlags);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movl %esi, %ebp
movq %rdi, %rbx
movq 0x30(%rdi), %rdi
callq 0x10fe52
testb %al, %al
je 0x1a3c45
movzbl 0x2c(%rbx), %eax
movl $0x2, %ecx
subl %eax, %ecx
jmp 0x1a3c76
cmpl $0x0, 0x14(%rbx)
je 0x1a3c74
movq %rbx, %rdi
callq 0x1a5f68
movl %eax, %r14d
leal 0x1(%r14), %r15d
movl %eax, %edi
callq 0x2f9d04
imull %r15d, %eax
xorl %ecx, %ecx
xorl %edx, %edx
divl 0x14(%rbx)
cmpl %r14d, %eax
adcl $0x1, %ecx
jmp 0x1a3c76
xorl %ecx, %ecx
orl %ecx, 0x10(%rbx)
cmpl $0x0, 0x18(%rbx)
jns 0x1a3c85
cmpb $0x1, 0x2d(%rbx)
jne 0x1a3c89
orb $0x4, 0x10(%rbx)
orl %ebp, 0x10(%rbx)
movl 0x28(%rbx), %eax
shrl %eax
andl $0x1, %eax
movl %eax, 0x4(%rbx)
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq-sass.c
// Function: gt_BWTSeqNewSASeqSrc
SASeqSrc *
gt_BWTSeqNewSASeqSrc(const BWTSeq *bwtSeq, const BWTSeqContextRetriever *ctxMap)
{
  struct BWTSASeqSrc *newBWTSASeqSrc;
  gt_assert(bwtSeq);
  newBWTSASeqSrc = gt_malloc(sizeof (*newBWTSASeqSrc));
  {
    RandomSeqAccessor origSeqAccess;
    if (ctxMap)
    {
      origSeqAccess.accessFunc = BWTSASSAccessOrigSeq;
      origSeqAccess.state = (void *)ctxMap;
    }
    else
    {
      origSeqAccess.accessFunc = NULL;
      origSeqAccess.state = NULL;
    }
    initSASeqSrc(&newBWTSASeqSrc->baseClass,
                 BWTSeqLength(bwtSeq),
                 NULL,
                 BWTSASSCreateReader,
                 BWTSASSGetRot0Pos,
                 NULL,
                 origSeqAccess,
                 gt_deleteBWTSeqSASS,
                 BWTSASSNewMRAEnc,
                 NULL, NULL);   /* since BWTSeq can regenerate
                                 * arbitrary portions of all
                                 * associated data (when reversibly
                                 * sorted) no generator is necessary
                                 * and all readers just keep their state
                                 */
  }
  newBWTSASeqSrc->ctxMap = ctxMap;
  newBWTSASeqSrc->bwtSeq = bwtSeq;
  newBWTSASeqSrc->readerStateList = NULL;
  return &newBWTSASeqSrc->baseClass;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x1a3d8b
movq %rsi, %r14
movq %rdi, %rbx
leaq 0x20851f(%rip), %rsi    # 0x3ac1e9
movl $0xd8, %edi
movl $0x6c, %edx
callq 0x1092b2
testq %rax, %rax
je 0x1a3d90
movq %rax, %r15
movq (%rbx), %rax
movq 0x10(%rax), %rax
testq %r14, %r14
leaq 0x9f(%rip), %rcx        # 0x1a3d95
cmoveq %r14, %rcx
movq %rax, (%r15)
xorl %r12d, %r12d
movq %r12, 0x10(%r15)
leaq 0xab(%rip), %rax        # 0x1a3db6
movq %rax, 0x8(%r15)
leaq 0xd6(%rip), %rax        # 0x1a3dec
movq %rax, 0x18(%r15)
movq %r12, 0x20(%r15)
movq %rcx, 0x28(%r15)
movq %r14, 0x30(%r15)
leaq 0xd4(%rip), %rax        # 0x1a3e01
movq %rax, 0x38(%r15)
leaq 0x138(%rip), %rax       # 0x1a3e70
movq %rax, 0x40(%r15)
movq %r12, 0x48(%r15)
leaq 0x50(%r15), %rdi
movl $0x8, %ecx
xorl %esi, %esi
xorl %edx, %edx
xorl %r8d, %r8d
xorl %r9d, %r9d
callq 0x1a6cc0
movq %r15, %rdi
addq $0xb0, %rdi
callq 0x1a6be3
movq %r14, 0xc8(%r15)
movq %rbx, 0xc0(%r15)
movq %r12, 0xd0(%r15)
movq %r15, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
callq 0x6093c
callq 0x60905
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq-sass.c
// Function: BWTSASSAccessOrigSeq
static size_t
BWTSASSAccessOrigSeq(const void *state,
                     Symbol *dest,
                     GtUword pos,
                     size_t len)
{
  const BWTSeqContextRetriever *ctxMap = state;
  gt_assert(state);
  gt_BWTSeqCRAccessSubseq(ctxMap, pos, len, dest);
  return len;
}

// Assembly:
pushq %rbx
testq %rdi, %rdi
je 0x1a3db1
movq %rcx, %rbx
movq %rsi, %rcx
movq %rdx, %rsi
movq %rbx, %rdx
callq 0x1a21e2
movq %rbx, %rax
popq %rbx
retq
callq 0x60973
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq-sass.c
// Function: gt_deleteBWTSeqSASS
static void
gt_deleteBWTSeqSASS(struct SASeqSrc *baseClass)
{
  destructSASeqSrc(baseClass);
  ListDo(BWTSeqReaderState, SASS2BWTSASS(baseClass)->readerStateList,
         gt_free(p));
  gt_free(SASS2BWTSASS(baseClass));
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %rdi, %rbx
movq 0x48(%rdi), %rdi
testq %rdi, %rdi
je 0x1a3e17
callq 0x1a6aec
leaq 0xb0(%rbx), %rdi
callq 0x1a6bea
leaq 0x50(%rbx), %rdi
callq 0x1a6ceb
movq 0xd0(%rbx), %rdi
testq %rdi, %rdi
je 0x1a3e57
leaq 0x2083aa(%rip), %r14    # 0x3ac1e9
movq (%rdi), %r15
movq %r14, %rsi
movl $0x4b, %edx
callq 0x109670
movq %r15, %rdi
testq %r15, %r15
jne 0x1a3e3f
leaq 0x20838b(%rip), %rsi    # 0x3ac1e9
movq %rbx, %rdi
movl $0x4c, %edx
popq %rbx
popq %r14
popq %r15
jmp 0x109670
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq-sass.c
// Function: BWTSASSNewMRAEnc
static MRAEnc *
BWTSASSNewMRAEnc(const SASeqSrc *src)
{
  const BWTSASeqSrc *bwtSASeqSrc;
  gt_assert(src);
  bwtSASeqSrc = constSASS2BWTSASS(src);
  return gt_MRAEncCopy(EISGetAlphabet(BWTSeqGetEncIdxSeq(bwtSASeqSrc->bwtSeq)));
}

// Assembly:
pushq %rax
testq %rdi, %rdi
je 0x1a3e94
movq 0xc0(%rdi), %rax
testq %rax, %rax
je 0x1a3e99
movq (%rax), %rax
testq %rax, %rax
je 0x1a3e9e
movq 0x8(%rax), %rdi
popq %rax
jmp 0x1a6666
callq 0x60a83
callq 0x60a4a
callq 0x60a13
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq-sass.c
// Function: BWTSeqSASSAddReaderState
static BWTSeqReaderState *
BWTSeqSASSAddReaderState(BWTSASeqSrc *bwtSASeqSrc)
{
  BWTSeqReaderState *newReader = gt_malloc(sizeof (*newReader));
  gt_assert(bwtSASeqSrc);
  newReader->backLink = bwtSASeqSrc;
  newReader->nextReadPos = 0;
  newReader->next = bwtSASeqSrc->readerStateList;
  bwtSASeqSrc->readerStateList = newReader;
  return newReader;
}

// Assembly:
pushq %rbx
movq %rdi, %rbx
leaq 0x20833b(%rip), %rsi    # 0x3ac1e9
movl $0x18, %edi
movl $0xc3, %edx
callq 0x1092b2
testq %rbx, %rbx
je 0x1a3ee1
movq %rbx, 0x8(%rax)
movq $0x0, 0x10(%rax)
movq 0xd0(%rbx), %rcx
movq %rcx, (%rax)
movq %rax, 0xd0(%rbx)
popq %rbx
retq
callq 0x60aba
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq-sass.c
// Function: BWTSASSReadSufTab
static size_t
BWTSASSReadSufTab(SeqDataSrc src, void *dest, size_t len)
{
  const BWTSeq *bwtSeq;
  struct extBitsRetrieval extBits;
  gt_assert(src);
  initExtBitsRetrieval(&extBits);
  bwtSeq = ((BWTSeqReaderState *)src)->backLink->bwtSeq;
  size_t i;
  GtUword pos = ((BWTSeqReaderState *)src)->nextReadPos;
  for (i = 0; i < len; ++i)
    ((GtUword *)dest)[i] = gt_BWTSeqLocateMatch(bwtSeq,
                                                      pos + i,
                                                      &extBits);
  ((BWTSeqReaderState *)src)->nextReadPos = pos + len;
  destructExtBitsRetrieval(&extBits);
  return len;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x48, %rsp
testq %rdi, %rdi
je 0x1a3fc1
movq %rdx, %rbx
xorps %xmm0, %xmm0
movaps %xmm0, 0x30(%rsp)
movaps %xmm0, 0x20(%rsp)
movaps %xmm0, 0x10(%rsp)
movq $0x0, 0x40(%rsp)
movq %rdi, 0x8(%rsp)
movq 0x10(%rdi), %rbp
testq %rdx, %rdx
je 0x1a3f5f
movq %rsi, %r15
movq 0x8(%rsp), %rax
movq 0x8(%rax), %rax
movq 0xc0(%rax), %r12
xorl %r14d, %r14d
leaq 0x10(%rsp), %r13
leaq (%r14,%rbp), %rsi
movq %r12, %rdi
movq %r13, %rdx
callq 0x1a3411
movq %rax, (%r15,%r14,8)
incq %r14
cmpq %r14, %rbx
jne 0x1a3f44
addq %rbx, %rbp
movq 0x8(%rsp), %rax
movq %rbp, 0x10(%rax)
testb $0x1, 0x40(%rsp)
je 0x1a3f8d
movq 0x30(%rsp), %rdi
testq %rdi, %rdi
je 0x1a3f8d
leaq 0x2079f1(%rip), %rsi    # 0x3ab974
movl $0x87, %edx
callq 0x109670
testb $0x4, 0x40(%rsp)
je 0x1a3faf
movq 0x38(%rsp), %rdi
testq %rdi, %rdi
je 0x1a3faf
leaq 0x2079cf(%rip), %rsi    # 0x3ab974
movl $0x89, %edx
callq 0x109670
movq %rbx, %rax
addq $0x48, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x60af3
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq-sass.c
// Function: BWTSASSReadBWT
static size_t
BWTSASSReadBWT(SeqDataSrc src, void *dest, size_t len)
{
  const BWTSeq *bwtSeq;
  gt_assert(src);
  bwtSeq = ((BWTSeqReaderState *)src)->backLink->bwtSeq;
  size_t i;
  GtUword pos = ((BWTSeqReaderState *)src)->nextReadPos;
  for (i = 0; i < len; ++i)
    ((Symbol *)dest)[i] = BWTSeqGetSym(bwtSeq, pos + i);
  ((BWTSeqReaderState *)src)->nextReadPos = pos + len;
  return len;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x1a4067
movq %rdx, %rbx
movq %rdi, (%rsp)
movq 0x10(%rdi), %r12
testq %rdx, %rdx
je 0x1a4040
movq (%rsp), %rax
movq 0x8(%rax), %rax
movq 0xc0(%rax), %r13
testq %r13, %r13
je 0x1a406c
movq %rsi, %r15
xorl %ebp, %ebp
movq (%r13), %rdi
testq %rdi, %rdi
je 0x1a4062
movq 0x18(%r13), %rdx
testq %rdx, %rdx
je 0x1a4062
leaq (%r12,%rbp), %rsi
movq (%rdi), %rax
movq 0x8(%rdi), %r14
callq *0x30(%rax)
cmpl $0x1, (%r14)
jne 0x1a405d
movzbl %al, %eax
movb 0x118(%r14,%rax), %al
movb %al, (%r15,%rbp)
incq %rbp
cmpq %rbp, %rbx
jne 0x1a4003
addq %rbx, %r12
movq (%rsp), %rax
movq %r12, 0x10(%rax)
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x173b0
callq 0x60b2c
callq 0x60b9c
callq 0x60b63
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq.c
// Function: gt_deleteBWTSeq
void
gt_deleteBWTSeq(BWTSeq *bwtSeq)
{
  gt_MRAEncDelete(bwtSeq->alphabet);
  deleteEISHint(bwtSeq->seqIdx, bwtSeq->hint);
  gt_deleteEncIdxSeq(bwtSeq->seqIdx);
  gt_free(bwtSeq);
}

// Assembly:
pushq %rbx
movq %rdi, %rbx
movq 0x8(%rdi), %rdi
callq 0x1a6aec
movq (%rbx), %rdi
movq 0x18(%rbx), %rsi
movq (%rdi), %rax
callq *0x40(%rax)
movq (%rbx), %rdi
callq 0x1a574c
leaq 0x208014(%rip), %rsi    # 0x3ac349
movq %rbx, %rdi
movl $0x91, %edx
popq %rbx
jmp 0x109670
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq.c
// Function: gt_packedindexuniqueforward
GtUword gt_packedindexuniqueforward(const BWTSeq *bwtSeq,
                                          const GtUchar *qstart,
                                          const GtUchar *qend)
{
  GtUchar cc;
  const GtUchar *qptr;
  struct matchBound bwtbound;
  GtUwordPair seqpospair;
  Symbol curSym;
  const MRAEnc *alphabet;

  gt_assert(bwtSeq && qstart);
  alphabet = BWTSeqGetAlphabet(bwtSeq);
  qptr = qstart;
  cc = *qptr++;
#undef SKDEBUG
#ifdef SKDEBUG
  printf("# start cc=%u\n",cc);
#endif
  if (GT_ISSPECIAL(cc))
  {
    return 0;
  }
  curSym = MRAEncMapSymbol(alphabet, cc);
  bwtbound.start = bwtSeq->count[curSym];
  bwtbound.end = bwtSeq->count[curSym+1];
#ifdef SKDEBUG
  printf("# bounds="GT_WU","GT_WU" = "GT_WU""
          "occurrences\n",
         bwtbound.start,
         bwtbound.end,
         bwtbound.end - bwtbound.start);
#endif
  while (qptr < qend && bwtbound.start + 1 < bwtbound.end)
  {
    cc = *qptr;
#ifdef SKDEBUG
    printf("# cc=%u\n",cc);
#endif
    if (GT_ISSPECIAL (cc))
    {
      return 0;
    }
    curSym = MRAEncMapSymbol(alphabet, cc);
    seqpospair = BWTSeqTransformedPosPairOcc(bwtSeq, curSym,
                                             bwtbound.start,bwtbound.end);
    bwtbound.start = bwtSeq->count[curSym] + seqpospair.a;
    bwtbound.end = bwtSeq->count[curSym] + seqpospair.b;
#ifdef SKDEBUG
    printf("# bounds="GT_WU","GT_WU" = "GT_WU""
            "occurrences\n",
           bwtbound.start,
           bwtbound.end,
           bwtbound.end - bwtbound.start);
#endif
    qptr++;
  }
  if (bwtbound.start + 1 == bwtbound.end)
  {
    return (GtUword) (qptr - qstart);
  }
  return 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x1a4415
movq %rsi, %rbx
testq %rsi, %rsi
je 0x1a4415
movzbl (%rbx), %eax
cmpq $0xfd, %rax
ja 0x1a43ff
movq %rdi, %r15
movq 0x8(%rdi), %r12
cmpl $0x1, (%r12)
jne 0x1a4410
movq %rdx, %r14
movzbl 0x18(%r12,%rax), %eax
movq 0x38(%r15), %rcx
movq (%rcx,%rax,8), %rdx
movq 0x8(%rcx,%rax,8), %rcx
leaq 0x1(%rbx), %rbp
leaq 0x1(%rdx), %rsi
cmpq %r14, %rbp
jae 0x1a43f2
cmpq %rcx, %rsi
jae 0x1a43f2
movzbl (%rbp), %eax
cmpq $0xfd, %rax
ja 0x1a43ff
cmpl $0x1, (%r12)
jne 0x1a4410
movzbl 0x18(%r12,%rax), %r13d
movq %r15, %rdi
movl %r13d, %esi
callq 0x1a441a
movq %rdx, %rcx
movq 0x38(%r15), %rdx
movq (%rdx,%r13,8), %rdx
addq %rdx, %rcx
incq %rbp
leaq (%rdx,%rax), %rsi
incq %rsi
cmpq %r14, %rbp
jae 0x1a43f2
addq %rax, %rdx
jmp 0x1a43a7
cmpq %rcx, %rsi
jne 0x1a43ff
subq %rbx, %rbp
movq %rbp, %rax
jmp 0x1a4401
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x173b0
callq 0x60d8d
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq-siop.h
// Function: BWTSeqTransformedPosPairOcc
static inline GtUwordPair
BWTSeqTransformedPosPairOcc(const BWTSeq *bwtSeq, Symbol tSym,
                            GtUword posA, GtUword posB)
{
  gt_assert(bwtSeq);
  /* two counts must be treated specially:
   * 1. for the symbols mapped to the same value as the terminator
   * 2. for queries of the terminator itself */
  if (tSym < bwtSeq->bwtTerminatorFallback)
    return EISSymTransformedPosPairRank(bwtSeq->seqIdx, tSym, posA, posB,
                                        bwtSeq->hint);
  else if (tSym > bwtSeq->bwtTerminatorFallback
           && tSym != bwtSeq->alphabetSize - 1)
    return EISSymTransformedPosPairRank(bwtSeq->seqIdx, tSym, posA, posB,
                                        bwtSeq->hint);
  else if (tSym == bwtSeq->bwtTerminatorFallback)
    return EISSymTransformedPosPairRank(bwtSeq->seqIdx, tSym, posA, posB,
                                        bwtSeq->hint);
/*       - ((pos > BWTSeqTerminatorPos(bwtSeq))?1:0); */
  else /* tSym == not flattened terminator == alphabetSize - 1 */
  {
    GtUwordPair occ;
    gt_assert(tSym == bwtSeq->alphabetSize - 1);
    occ.a = (posA > BWTSeqTerminatorPos(bwtSeq))?1:0;
    occ.b = (posB > BWTSeqTerminatorPos(bwtSeq))?1:0;
    return occ;
  }
}

// Assembly:
pushq %rax
movb 0x24(%rdi), %r8b
cmpb %sil, %r8b
ja 0x1a443b
jae 0x1a4436
movzbl %sil, %eax
movq 0x10(%rdi), %r9
decq %r9
cmpq %rax, %r9
jne 0x1a4476
cmpb %sil, %r8b
jne 0x1a4450
movq (%rdi), %rax
movq 0x18(%rdi), %r8
movzbl %sil, %esi
movq %rax, %rdi
callq 0x1a52a5
popq %rcx
retq
movzbl %sil, %eax
movq 0x10(%rdi), %rsi
decq %rsi
cmpq %rax, %rsi
jne 0x1a4484
movq 0x30(%rdi), %rsi
xorl %eax, %eax
cmpq %rdx, %rsi
setb %al
xorl %edx, %edx
cmpq %rcx, %rsi
setb %dl
jmp 0x1a444e
movq (%rdi), %rsi
movq 0x18(%rdi), %r8
movq %rsi, %rdi
movl %eax, %esi
jmp 0x1a4449
callq 0x60dc6
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq.c
// Function: gt_BWTSeqMatchCount
GtUword
gt_BWTSeqMatchCount(const BWTSeq *bwtSeq, const Symbol *query, size_t queryLen,
                 bool forward)
{
  struct matchBound match;
  gt_assert(bwtSeq && query);
  getMatchBound(bwtSeq, query, queryLen, &match, forward);
  if (match.end < match.start)
    return 0;
  else
    return match.end - match.start;
}

// Assembly:
pushq %rbx
subq $0x10, %rsp
testq %rdi, %rdi
je 0x1a45af
testq %rsi, %rsi
je 0x1a45af
movzbl %cl, %r8d
movq %rsp, %rbx
movq %rbx, %rcx
callq 0x1a45b4
movq 0x8(%rbx), %rcx
xorl %eax, %eax
subq (%rbx), %rcx
cmovaeq %rcx, %rax
addq $0x10, %rsp
popq %rbx
retq
callq 0x60e36
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq.c
// Function: gt_initEMIterator
bool
gt_initEMIterator(BWTSeqExactMatchesIterator *iter, const BWTSeq *bwtSeq,
               const Symbol *query, size_t queryLen, bool forward)
{
  gt_assert(iter && bwtSeq && query);
  if (!bwtSeq->locateSampleInterval)
  {
    fputs("Index does not contain locate information.\n"
          "Localization of matches impossible!", stderr);
    return false;
  }
  getMatchBound(bwtSeq, query, queryLen, &iter->bounds, forward);
  iter->nextMatchBWTPos = iter->bounds.start;
  initExtBitsRetrieval(&iter->extBits);
  return true;
}

// Assembly:
pushq %rbp
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x1a47fb
testq %rsi, %rsi
je 0x1a47fb
testq %rdx, %rdx
je 0x1a47fb
movl 0x20(%rsi), %ebp
testl %ebp, %ebp
je 0x1a47f4
movq %rdi, %rbx
movzbl %r8b, %r8d
movq %rsi, %rdi
movq %rdx, %rsi
movq %rcx, %rdx
movq %rbx, %rcx
callq 0x1a45b4
movq (%rbx), %rax
movq %rax, 0x10(%rbx)
xorps %xmm0, %xmm0
movups %xmm0, 0x18(%rbx)
movups %xmm0, 0x28(%rbx)
movups %xmm0, 0x38(%rbx)
movq $0x0, 0x48(%rbx)
testl %ebp, %ebp
setne %al
addq $0x8, %rsp
popq %rbx
popq %rbp
retq
callq 0x60f53
jmp 0x1a47e8
callq 0x60f1a
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq.c
// Function: gt_initEmptyEMIterator
bool
gt_initEmptyEMIterator(BWTSeqExactMatchesIterator *iter, const BWTSeq *bwtSeq)
{
  gt_assert(iter && bwtSeq);
  if (!bwtSeq->locateSampleInterval)
  {
    fputs("Index does not contain locate information.\n"
          "Localization of matches impossible!", stderr);
    return false;
  }
  iter->bounds.start = iter->bounds.end = iter->nextMatchBWTPos = 0;
  initExtBitsRetrieval(&iter->extBits);
  return true;
}

// Assembly:
pushq %rbx
testq %rdi, %rdi
je 0x1a4836
testq %rsi, %rsi
je 0x1a4836
movl 0x20(%rsi), %ebx
testl %ebx, %ebx
je 0x1a482f
xorps %xmm0, %xmm0
movups %xmm0, 0x40(%rdi)
movups %xmm0, 0x30(%rdi)
movups %xmm0, 0x20(%rdi)
movups %xmm0, 0x10(%rdi)
movups %xmm0, (%rdi)
testl %ebx, %ebx
setne %al
popq %rbx
retq
callq 0x60fa2
jmp 0x1a4828
callq 0x60f69
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq.c
// Function: gt_newEMIterator
struct BWTSeqExactMatchesIterator *
gt_newEMIterator(const BWTSeq *bwtSeq, const Symbol *query, size_t queryLen,
              bool forward)
{
  struct BWTSeqExactMatchesIterator *iter;
  gt_assert(bwtSeq && query);
  iter = gt_malloc(sizeof (*iter));
  if (gt_initEMIterator(iter, bwtSeq, query, queryLen,forward))
  {
    return iter;
  }
  gt_free(iter);
  return NULL;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
testq %rdi, %rdi
je 0x1a48ad
movq %rsi, %r15
testq %rsi, %rsi
je 0x1a48ad
movl %ecx, %ebp
movq %rdx, %rbx
movq %rdi, %r12
leaq 0x207aea(%rip), %rsi    # 0x3ac349
movl $0x50, %edi
movl $0x1a1, %edx            # imm = 0x1A1
callq 0x1092b2
movq %rax, %r14
movzbl %bpl, %r8d
movq %rax, %rdi
movq %r12, %rsi
movq %r15, %rdx
movq %rbx, %rcx
callq 0x1a4799
testb %al, %al
jne 0x1a48a1
leaq 0x207ab8(%rip), %rsi    # 0x3ac349
movq %r14, %rdi
movl $0x1a6, %edx            # imm = 0x1A6
callq 0x109670
xorl %r14d, %r14d
movq %r14, %rax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
callq 0x60fb8
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-bwtseq.c
// Function: gt_EMINumMatchesLeft
GtUword
gt_EMINumMatchesLeft(const struct BWTSeqExactMatchesIterator *iter)
{
  gt_assert(iter);
  if (iter->nextMatchBWTPos > iter->bounds.end)
    return 0;
  else
    return iter->bounds.end - iter->bounds.start;
}

// Assembly:
testq %rdi, %rdi
je 0x1a4959
movq 0x8(%rdi), %rax
cmpq %rax, 0x10(%rdi)
jbe 0x1a4955
xorl %eax, %eax
retq
subq (%rdi), %rax
retq
pushq %rax
callq 0x6102a
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-encidxseq-siop.h
// Function: EISSymTransformedPosPairRank
static inline GtUwordPair
EISSymTransformedPosPairRank(EISeq *seq, Symbol tSym, GtUword posA,
                             GtUword posB, union EISHint *hint)
{
  if (tSym >= gt_MRAEncGetSize(EISGetAlphabet(seq)))
  {
    fprintf(stderr,"tsym="GT_WU",gt_MRAEncGetSize(EISGetAlphabet(seq)="
            GT_WU"\n", (GtUword) tSym,
            (GtUword) gt_MRAEncGetSize(EISGetAlphabet(seq)));
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
  gt_assert(tSym < gt_MRAEncGetSize(EISGetAlphabet(seq)));
  return seq->classInfo->posPairRank(seq, tSym, posA, posB, hint);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
testq %rdi, %rdi
je 0x1a5301
movq %r8, %rbx
movq %rcx, %r14
movq %rdx, %r15
movl %esi, %ebp
movq %rdi, %r12
movq 0x8(%rdi), %rdi
callq 0x1a67a7
movzbl %bpl, %ebp
cmpw %bp, %ax
jbe 0x1a5306
movq 0x8(%r12), %rdi
callq 0x1a67a7
cmpw %bp, %ax
jbe 0x1a5310
movq (%r12), %rax
movq 0x10(%rax), %rax
movq %r12, %rdi
movl %ebp, %esi
movq %r15, %rdx
movq %r14, %rcx
movq %rbx, %r8
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
jmpq *%rax
callq 0x614a5
movl %ebp, %edi
movq %r12, %rsi
callq 0x6142d
callq 0x6146e
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-encidxseq-construct.c
// Function: gt_createEncIdxSeq
EISeq *
gt_createEncIdxSeq(const char *projectName,
                const struct seqBaseParam *params,
                size_t numExtHeaders, const uint16_t *headerIDs,
                const uint32_t *extHeaderSizes,
                headerWriteFunc *extHeaderCallbacks, void **headerCBData,
                bitInsertFunc biFunc, BitOffset cwExtBitsPerPos,
                varExtBitsEstimator biVarBits, void *cbState,
                GtLogger *verbosity, GtError *err)
{
  Suffixarray suffixArray;
  struct encIdxSeq *newSeqIdx;
  GtUword length;
  gt_assert(projectName);
  /* map and interpret index project file */
  if (streamsuffixarray(&suffixArray,
                       SARR_SUFTAB | SARR_BWTTAB, projectName, verbosity, err))
    return NULL;
  length = gt_encseq_total_length(suffixArray.encseq) + 1;
  newSeqIdx = gt_createEncIdxSeqFromSA(&suffixArray, length,
                                      projectName, params,
                                      numExtHeaders, headerIDs,
                                      extHeaderSizes, extHeaderCallbacks,
                                      headerCBData, biFunc, cwExtBitsPerPos,
                                      biVarBits, cbState, err);
  gt_freesuffixarray(&suffixArray);
  return newSeqIdx;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x118, %rsp            # imm = 0x118
movq %r8, 0x10(%rsp)
testq %rdi, %rdi
je 0x1a53f0
movq %r9, %r14
movq %rcx, %r15
movq %rdx, %r12
movq %rsi, %r13
movq %rdi, %rbp
movq 0x180(%rsp), %rbx
movq 0x178(%rsp), %rcx
leaq 0x18(%rsp), %rdi
movl $0xa, %esi
movq %rbp, %rdx
movq %rbx, %r8
callq 0x1a9f52
testl %eax, %eax
je 0x1a5373
xorl %ebx, %ebx
jmp 0x1a53db
leaq 0x18(%rsp), %rax
movq (%rax), %rdi
movq %r14, 0x8(%rsp)
movq %rax, %r14
callq 0xec1d8
leaq 0x1(%rax), %rsi
movq %r14, %rdi
movq %rbp, %rdx
movq %r13, %rcx
movq %r12, %r8
movq %r15, %r9
pushq %rbx
pushq 0x178(%rsp)
pushq 0x178(%rsp)
pushq 0x178(%rsp)
pushq 0x178(%rsp)
pushq 0x178(%rsp)
pushq 0x38(%rsp)
pushq 0x48(%rsp)
callq 0x1a53f5
addq $0x40, %rsp
movq %rax, %rbx
movq %r14, %rdi
callq 0x1a9e1c
movq %rbx, %rax
addq $0x118, %rsp            # imm = 0x118
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x614dc
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-encidxseq-construct.c
// Function: gt_createEncIdxSeqFromSA
EISeq *
gt_createEncIdxSeqFromSA(Suffixarray *sa, GtUword totalLen,
                      const char *projectName,
                      const struct seqBaseParam *params,
                      size_t numExtHeaders, const uint16_t *headerIDs,
                      const uint32_t *extHeaderSizes,
                      headerWriteFunc *extHeaderCallbacks,
                      void **headerCBData,
                      bitInsertFunc biFunc, BitOffset cwExtBitsPerPos,
                      varExtBitsEstimator biVarBits, void *cbState,
                      GtError *err)
{
  struct encIdxSeq *newSeqIdx;
  SuffixarrayFileInterface sai;
  gt_assert(sa && projectName && err);
  gt_initSuffixarrayFileInterface(&sai, totalLen, sa);
  newSeqIdx = gt_createEncIdxSeqFromSAI(
    &sai, projectName, params, numExtHeaders, headerIDs,
    extHeaderSizes, extHeaderCallbacks, headerCBData, biFunc, cwExtBitsPerPos,
    biVarBits, cbState, err);
  gt_destructSuffixarrayFileInterface(&sai);
  return newSeqIdx;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0xe8, %rsp
testq %rdi, %rdi
je 0x1a54b4
movq %rdx, %r12
testq %rdx, %rdx
je 0x1a54b4
movq 0x158(%rsp), %rbp
testq %rbp, %rbp
je 0x1a54b4
movq %r9, %rbx
movq %r8, %r14
movq %rcx, %r15
movq %rdi, %rdx
leaq 0x8(%rsp), %r13
movq %r13, %rdi
callq 0x1a7419
subq $0x8, %rsp
movq %r13, %rdi
movq %r12, %rsi
movq %r15, %rdx
movq %r14, %rcx
movq %rbx, %r8
movq 0x128(%rsp), %r9
pushq %rbp
pushq 0x160(%rsp)
pushq 0x160(%rsp)
pushq 0x160(%rsp)
pushq 0x160(%rsp)
pushq 0x160(%rsp)
pushq 0x160(%rsp)
callq 0x1a54d4
addq $0x40, %rsp
movq %rax, %rbx
movq %r13, %rdi
callq 0x1a76ce
movq %rbx, %rax
addq $0xe8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x61513
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/eis-encidxseq-construct.c
// Function: gt_createEncIdxSeqFromSASeqSrc
static EISeq *
gt_createEncIdxSeqFromSASeqSrc(SASeqSrc *src,
                            const char *projectName,
                            const struct seqBaseParam *params,
                            size_t numExtHeaders, const uint16_t *headerIDs,
                            const uint32_t *extHeaderSizes,
                            headerWriteFunc *extHeaderCallbacks,
                            void **headerCBData, bitInsertFunc biFunc,
                            BitOffset cwExtBitsPerPos,
                            varExtBitsEstimator biVarBits, void *cbState,
                            GtError *err)
{
  SeqDataReader readSfxBWTSym;
  MRAEnc *alphabet;
  struct encIdxSeq *newSeqIdx;
  if (!SDRIsValid(readSfxBWTSym
                  = SASSCreateReader(src, SFX_REQUEST_BWTTAB)))
    return NULL;
  alphabet = SASSNewMRAEnc(src);
  newSeqIdx = gt_createEncIdxSeqGen(SASSGetLength(src), projectName,
                                 alphabet, SASSGetSeqStats(src),
                                 readSfxBWTSym, params,
                                 numExtHeaders, headerIDs, extHeaderSizes,
                                 extHeaderCallbacks, headerCBData, biFunc,
                                 cwExtBitsPerPos, biVarBits,
                                 cbState, err);
  if (!newSeqIdx)
    gt_MRAEncDelete(alphabet);
  return newSeqIdx;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq %r9, 0x18(%rsp)
movq %r8, 0x20(%rsp)
movq %rcx, %r13
movq %rdx, %r12
movq %rsi, %rbp
movq %rdi, %r15
movl $0x2, %esi
callq *0x8(%rdi)
testq %rdx, %rdx
je 0x1a5535
movq %rax, %rbx
movq %rdx, %r14
movq %r13, 0x8(%rsp)
movq %r12, 0x10(%rsp)
movq %r15, %rdi
callq *0x40(%r15)
movq %rax, %r13
movq (%r15), %r12
movq 0x20(%r15), %rax
testq %rax, %rax
je 0x1a5539
movq %r15, %rdi
callq *%rax
movq %rax, %rcx
jmp 0x1a553b
xorl %ebx, %ebx
jmp 0x1a55a8
xorl %ecx, %ecx
subq $0x8, %rsp
movq %r12, %rdi
movq %rbp, %rsi
movq %r13, %rdx
movq %rbx, %r8
movq %r14, %r9
pushq 0x98(%rsp)
pushq 0x98(%rsp)
pushq 0x98(%rsp)
pushq 0x98(%rsp)
pushq 0x98(%rsp)
pushq 0x98(%rsp)
pushq 0x98(%rsp)
pushq 0x58(%rsp)
pushq 0x68(%rsp)
pushq 0x58(%rsp)
pushq 0x68(%rsp)
callq 0x1a560e
addq $0x60, %rsp
movq %rax, %rbx
testq %rax, %rax
jne 0x1a55a8
movq %r13, %rdi
callq 0x1a6aec
movq %rbx, %rax
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq