LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O3/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 0x19ad69
testb $0x2, %al
je 0x19adb5
movq %rbx, %rsi
movq %r14, %rdx
callq 0x19adbf
movq %rax, %rcx
xorl %eax, %eax
testq %rcx, %rcx
setne %al
jmp 0x19adad
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 0x19adba
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 0x5f001
callq 0x5efc8
// File: /workspace/github_c_makefile_star2_O3/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
pushq %rax
movq %rdx, %rbx
movq %rsi, %r14
movq %rdi, %rbp
movq (%rdi), %rdi
movq 0x18(%rbp), %r8
movq (%rdi), %rax
movl $0x2, %edx
movq %rbx, %rcx
callq *0x50(%rax)
movq 0x8(%rbx), %r15
movq 0x18(%rbx), %rdi
callq 0x2f09dd
movl %eax, %r13d
movq 0x28(%rbx), %rdi
movq %r15, %rsi
movl %eax, %edx
callq 0x2f37dc
movq %rax, %r12
testl %r12d, %r12d
je 0x19ae73
movl %r13d, 0x4(%rsp)
movq 0x18(%rbx), %rdi
decq %rdi
callq 0x2f09dd
movl %eax, %r13d
movq (%rbp), %rax
movq 0x10(%rax), %rax
decq %rax
testb $0x4, 0x40(%rbp)
je 0x19ae3b
movl 0x20(%rbp), %ecx
xorl %edx, %edx
divq %rcx
movq %rax, %rdi
callq 0x2f09dd
movl %eax, %ebp
subq 0x10(%rbx), %r14
movl 0x4(%rsp), %eax
addq %rax, %r15
addl %r13d, %ebp
movq 0x28(%rbx), %rdi
movq %r15, %rsi
movl %r13d, %edx
callq 0x2f37dc
cmpq %r14, %rax
jae 0x19ae71
addq %rbp, %r15
decl %r12d
jne 0x19ae53
jmp 0x19ae73
jbe 0x19ae84
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
addq %r15, %r13
movq %r13, %rax
jmp 0x19ae75
// File: /workspace/github_c_makefile_star2_O3/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 0x19b3ea
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 0x2f09dd
movl %eax, %r12d
movq (%r14), %rax
movq 0x10(%rax), %rax
decq %rax
testb $0x4, 0x40(%r14)
je 0x19b2dd
movl 0x20(%r14), %ecx
xorl %edx, %edx
divq %rcx
movq %rax, %rdi
callq 0x2f09dd
movl %eax, %r13d
movl 0x40(%r14), %eax
testb $0x1, %al
jne 0x19b32b
movl %r12d, -0x2c(%rbp)
xorl %r12d, %r12d
testb $0x2, %al
je 0x19b342
movq 0x8(%rbx), %rax
movq %rax, -0x38(%rbp)
movq 0x18(%rbx), %rdi
callq 0x2f09dd
movl %eax, %r12d
movq 0x28(%rbx), %rdi
movq -0x38(%rbp), %rsi
movl %eax, %edx
callq 0x2f37dc
addl -0x2c(%rbp), %r13d
imull %eax, %r13d
addl %r12d, %r13d
jmp 0x19b33f
movq 0x20(%rbx), %rdi
movq (%rbx), %rsi
movq 0x18(%rbx), %rdx
callq 0x2f1242
imull %eax, %r13d
movl %r13d, %r12d
movq (%r14), %rdi
testq %rdi, %rdi
movl -0x30(%rbp), %esi
je 0x19b3ef
movq 0x8(%rdi), %rax
testq %rax, %rax
je 0x19b3f4
cmpl %esi, 0x4(%rax)
jbe 0x19b3f9
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 0x19b3be
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 0x19b3ab
jmp 0x19b3c0
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 0x2f37dc
leaq -0x28(%rbp), %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x5f30a
callq 0x5f3b1
callq 0x5f37a
callq 0x5f343
// File: /workspace/github_c_makefile_star2_O3/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 0x19d10c
movl $0x0, 0x10(%r15)
leaq 0x14(%r15), %rdx
leaq 0x207409(%rip), %rdi    # 0x3a29ed
leaq 0x20740a(%rip), %rsi    # 0x3a29f5
movl $0x10, %ecx
callq 0x10a4fd
movq %r12, %rdi
movq %rax, %rsi
callq 0x107cc0
leaq 0x2c(%r15), %rdx
leaq 0x207466(%rip), %rdi    # 0x3a2a71
leaq 0x207469(%rip), %rsi    # 0x3a2a7b
movl $0x1, %ecx
callq 0x10a235
movq %rax, %r13
movq %r12, %rdi
movq %rax, %rsi
callq 0x107cc0
movq %r13, 0x30(%r15)
leaq 0x2d(%r15), %rdx
leaq 0x2074cc(%rip), %rdi    # 0x3a2b05
leaq 0x2074cc(%rip), %rsi    # 0x3a2b0c
xorl %ecx, %ecx
callq 0x10a235
movq %r12, %rdi
movq %rax, %rsi
callq 0x107cc0
leaq 0x18(%r15), %rdx
leaq 0x207555(%rip), %rdi    # 0x3a2bb2
leaq 0x207559(%rip), %rsi    # 0x3a2bbd
movl $0xffffffff, %ecx       # imm = 0xFFFFFFFF
movl $0xffffffff, %r8d       # imm = 0xFFFFFFFF
movl $0x3f, %r9d
callq 0x10a4c1
movq %r12, %rdi
movq %rax, %rsi
callq 0x107cc0
leaq 0x1c(%r15), %rsi
movq %r12, %rdi
callq 0x1993e8
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_O3/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 0x10ac3f
testb %al, %al
je 0x19b6c9
movzbl 0x2c(%rbx), %eax
movl $0x2, %ecx
subl %eax, %ecx
jmp 0x19b6fa
cmpl $0x0, 0x14(%rbx)
je 0x19b6f8
movq %rbx, %rdi
callq 0x19d837
movl %eax, %r14d
leal 0x1(%r14), %r15d
movl %eax, %edi
callq 0x2f09a0
imull %r15d, %eax
xorl %ecx, %ecx
xorl %edx, %edx
divl 0x14(%rbx)
cmpl %r14d, %eax
adcl $0x1, %ecx
jmp 0x19b6fa
xorl %ecx, %ecx
orl 0x10(%rbx), %ecx
cmpl $0x0, 0x18(%rbx)
jns 0x19b709
cmpb $0x1, 0x2d(%rbx)
jne 0x19b70c
orl $0x4, %ecx
orl %ebp, %ecx
movl %ecx, 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_O3/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 0x19b80f
movq %rsi, %r14
movq %rdi, %rbx
leaq 0x20753b(%rip), %rsi    # 0x3a2c89
movl $0xd8, %edi
movl $0x6c, %edx
callq 0x104226
testq %rax, %rax
je 0x19b814
movq %rax, %r15
movq (%rbx), %rax
movq 0x10(%rax), %rax
testq %r14, %r14
leaq 0x9f(%rip), %rcx        # 0x19b819
cmoveq %r14, %rcx
movq %rax, (%r15)
xorl %r12d, %r12d
movq %r12, 0x10(%r15)
leaq 0xab(%rip), %rax        # 0x19b83a
movq %rax, 0x8(%r15)
leaq 0xd6(%rip), %rax        # 0x19b870
movq %rax, 0x18(%r15)
movq %r12, 0x20(%r15)
movq %rcx, 0x28(%r15)
movq %r14, 0x30(%r15)
leaq 0xd4(%rip), %rax        # 0x19b885
movq %rax, 0x38(%r15)
leaq 0x138(%rip), %rax       # 0x19b8f4
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 0x19e55c
movq %r15, %rdi
addq $0xb0, %rdi
callq 0x19e47f
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 0x5f4c8
callq 0x5f491
// File: /workspace/github_c_makefile_star2_O3/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 0x19b835
movq %rcx, %rbx
movq %rsi, %rcx
movq %rdx, %rsi
movq %rbx, %rdx
callq 0x199c9f
movq %rbx, %rax
popq %rbx
retq
callq 0x5f4ff
// File: /workspace/github_c_makefile_star2_O3/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 0x19b89b
callq 0x19e389
leaq 0xb0(%rbx), %rdi
callq 0x19e486
leaq 0x50(%rbx), %rdi
callq 0x19e587
movq 0xd0(%rbx), %rdi
testq %rdi, %rdi
je 0x19b8db
leaq 0x2073c6(%rip), %r14    # 0x3a2c89
movq (%rdi), %r15
movq %r14, %rsi
movl $0x4b, %edx
callq 0x1045eb
movq %r15, %rdi
testq %r15, %r15
jne 0x19b8c3
leaq 0x2073a7(%rip), %rsi    # 0x3a2c89
movq %rbx, %rdi
movl $0x4c, %edx
popq %rbx
popq %r14
popq %r15
jmp 0x1045eb
// File: /workspace/github_c_makefile_star2_O3/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 0x19b918
movq 0xc0(%rdi), %rax
testq %rax, %rax
je 0x19b91d
movq (%rax), %rax
testq %rax, %rax
je 0x19b922
movq 0x8(%rax), %rdi
popq %rax
jmp 0x19df36
callq 0x5f60f
callq 0x5f5d6
callq 0x5f59f
// File: /workspace/github_c_makefile_star2_O3/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 0x207357(%rip), %rsi    # 0x3a2c89
movl $0x18, %edi
movl $0xc3, %edx
callq 0x104226
testq %rbx, %rbx
je 0x19b965
movq %rbx, 0x8(%rax)
movq $0x0, 0x10(%rax)
movq 0xd0(%rbx), %rcx
movq %rcx, (%rax)
movq %rax, 0xd0(%rbx)
popq %rbx
retq
callq 0x5f646
// File: /workspace/github_c_makefile_star2_O3/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 0x19ba4c
movq %rdx, %rbx
xorps %xmm0, %xmm0
movaps %xmm0, 0x30(%rsp)
movaps %xmm0, 0x20(%rsp)
movaps %xmm0, 0x10(%rsp)
movq $0x0, 0x40(%rsp)
movq 0x10(%rdi), %rbp
testq %rdx, %rdx
je 0x19ba36
movq %rsi, %r15
movq %rdi, 0x8(%rsp)
movq 0x8(%rdi), %rax
movq 0xc0(%rax), %r12
xorl %r14d, %r14d
leaq 0x10(%rsp), %r13
leaq (%r14,%rbp), %rsi
movq %r12, %rdi
movq %r13, %rdx
callq 0x19ae8c
movq %rax, (%r15,%r14,8)
incq %r14
cmpq %r14, %rbx
jne 0x19b9c7
movl 0x40(%rsp), %eax
addq %rbx, %rbp
movq 0x8(%rsp), %rcx
movq %rbp, 0x10(%rcx)
testb $0x1, %al
je 0x19ba15
movq 0x30(%rsp), %rdi
testq %rdi, %rdi
je 0x19ba15
leaq 0x206a0d(%rip), %rsi    # 0x3a2414
movl $0x87, %edx
callq 0x1045eb
movl 0x40(%rsp), %eax
testb $0x4, %al
je 0x19ba3a
movq 0x38(%rsp), %rdi
testq %rdi, %rdi
je 0x19ba3a
leaq 0x2069ea(%rip), %rsi    # 0x3a2414
movl $0x89, %edx
callq 0x1045eb
jmp 0x19ba3a
movq %rbp, 0x10(%rdi)
movq %rbx, %rax
addq $0x48, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x5f67f
// File: /workspace/github_c_makefile_star2_O3/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 0x19baf2
movq %rdx, %rbx
movq %rdi, (%rsp)
movq 0x10(%rdi), %r12
testq %rdx, %rdx
je 0x19bacb
movq (%rsp), %rax
movq 0x8(%rax), %rax
movq 0xc0(%rax), %r13
testq %r13, %r13
je 0x19baf7
movq %rsi, %r15
xorl %ebp, %ebp
movq (%r13), %rdi
testq %rdi, %rdi
je 0x19baed
movq 0x18(%r13), %rdx
testq %rdx, %rdx
je 0x19baed
leaq (%r12,%rbp), %rsi
movq (%rdi), %rax
movq 0x8(%rdi), %r14
callq *0x30(%rax)
cmpl $0x1, (%r14)
jne 0x19bae8
movzbl %al, %eax
movb 0x118(%r14,%rax), %al
movb %al, (%r15,%rbp)
incq %rbp
cmpq %rbp, %rbx
jne 0x19ba8e
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 0x5f6b8
callq 0x5f728
callq 0x5f6ef
// File: /workspace/github_c_makefile_star2_O3/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 0x19e389
movq (%rbx), %rdi
movq 0x18(%rbx), %rsi
movq (%rdi), %rax
callq *0x40(%rax)
movq (%rbx), %rdi
callq 0x19d11c
leaq 0x207038(%rip), %rsi    # 0x3a2de9
movq %rbx, %rdi
movl $0x91, %edx
popq %rbx
jmp 0x1045eb
// File: /workspace/github_c_makefile_star2_O3/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 0x19be91
movq %rsi, %rbx
testq %rsi, %rsi
je 0x19be91
movzbl (%rbx), %eax
cmpq $0xfd, %rax
ja 0x19be7b
movq %rdi, %r15
movq 0x8(%rdi), %r12
cmpl $0x1, (%r12)
jne 0x19be8c
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 0x19be6e
cmpq %rcx, %rsi
jae 0x19be6e
movzbl (%rbp), %eax
cmpq $0xfd, %rax
ja 0x19be7b
cmpl $0x1, (%r12)
jne 0x19be8c
movzbl 0x18(%r12,%rax), %r13d
movq %r15, %rdi
movl %r13d, %esi
callq 0x19be96
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 0x19be6e
addq %rax, %rdx
jmp 0x19be23
cmpq %rcx, %rsi
jne 0x19be7b
subq %rbx, %rbp
movq %rbp, %rax
jmp 0x19be7d
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x173b0
callq 0x5f8e2
// File: /workspace/github_c_makefile_star2_O3/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 0x19beb7
jae 0x19beb2
movzbl %sil, %eax
movq 0x10(%rdi), %r9
decq %r9
cmpq %rax, %r9
jne 0x19bef2
cmpb %sil, %r8b
jne 0x19becc
movq (%rdi), %rax
movq 0x18(%rdi), %r8
movzbl %sil, %esi
movq %rax, %rdi
callq 0x19cc82
popq %rcx
retq
movzbl %sil, %eax
movq 0x10(%rdi), %rsi
decq %rsi
cmpq %rax, %rsi
jne 0x19bf00
movq 0x30(%rdi), %rsi
xorl %eax, %eax
cmpq %rdx, %rsi
setb %al
xorl %edx, %edx
cmpq %rcx, %rsi
setb %dl
jmp 0x19beca
movq (%rdi), %rsi
movq 0x18(%rdi), %r8
movq %rsi, %rdi
movl %eax, %esi
jmp 0x19bec5
callq 0x5f91b
// File: /workspace/github_c_makefile_star2_O3/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 0x19c02b
testq %rsi, %rsi
je 0x19c02b
movzbl %cl, %r8d
movq %rsp, %rbx
movq %rbx, %rcx
callq 0x19c030
movq 0x8(%rbx), %rcx
xorl %eax, %eax
subq (%rbx), %rcx
cmovaeq %rcx, %rax
addq $0x10, %rsp
popq %rbx
retq
callq 0x5f98b
// File: /workspace/github_c_makefile_star2_O3/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 0x19c277
testq %rsi, %rsi
je 0x19c277
testq %rdx, %rdx
je 0x19c277
movl 0x20(%rsi), %ebp
testl %ebp, %ebp
je 0x19c270
movq %rdi, %rbx
movzbl %r8b, %r8d
movq %rsi, %rdi
movq %rdx, %rsi
movq %rcx, %rdx
movq %rbx, %rcx
callq 0x19c030
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 0x5faa8
jmp 0x19c264
callq 0x5fa6f
// File: /workspace/github_c_makefile_star2_O3/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 0x19c2b2
testq %rsi, %rsi
je 0x19c2b2
movl 0x20(%rsi), %ebx
testl %ebx, %ebx
je 0x19c2ab
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 0x5faf7
jmp 0x19c2a4
callq 0x5fabe
// File: /workspace/github_c_makefile_star2_O3/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 0x19c329
movq %rsi, %r15
testq %rsi, %rsi
je 0x19c329
movl %ecx, %ebp
movq %rdx, %rbx
movq %rdi, %r12
leaq 0x206b0e(%rip), %rsi    # 0x3a2de9
movl $0x50, %edi
movl $0x1a1, %edx            # imm = 0x1A1
callq 0x104226
movq %rax, %r14
movzbl %bpl, %r8d
movq %rax, %rdi
movq %r12, %rsi
movq %r15, %rdx
movq %rbx, %rcx
callq 0x19c215
testb %al, %al
jne 0x19c31d
leaq 0x206adc(%rip), %rsi    # 0x3a2de9
movq %r14, %rdi
movl $0x1a6, %edx            # imm = 0x1A6
callq 0x1045eb
xorl %r14d, %r14d
movq %r14, %rax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
callq 0x5fb0d
// File: /workspace/github_c_makefile_star2_O3/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 0x19c3d7
movq 0x8(%rdi), %rax
cmpq %rax, 0x10(%rdi)
jbe 0x19c3d3
xorl %eax, %eax
retq
subq (%rdi), %rax
retq
pushq %rax
callq 0x5fb7f
// File: /workspace/github_c_makefile_star2_O3/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 0x19ccde
movq %r8, %rbx
movq %rcx, %r14
movq %rdx, %r15
movl %esi, %ebp
movq %rdi, %r12
movq 0x8(%rdi), %rdi
callq 0x19e077
movzbl %bpl, %ebp
cmpw %bp, %ax
jbe 0x19cce3
movq 0x8(%r12), %rdi
callq 0x19e077
cmpw %bp, %ax
jbe 0x19cced
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 0x5fffa
movl %ebp, %edi
movq %r12, %rsi
callq 0x5ff82
callq 0x5ffc3
nop
// File: /workspace/github_c_makefile_star2_O3/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 0x19cdcc
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 0x1a1676
testl %eax, %eax
je 0x19cd4f
xorl %ebx, %ebx
jmp 0x19cdb7
leaq 0x18(%rsp), %rax
movq (%rax), %rdi
movq %r14, 0x8(%rsp)
movq %rax, %r14
callq 0xe7b9c
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 0x19cdd1
addq $0x40, %rsp
movq %rax, %rbx
movq %r14, %rdi
callq 0x1a1540
movq %rbx, %rax
addq $0x118, %rsp            # imm = 0x118
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x60031
// File: /workspace/github_c_makefile_star2_O3/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 0x19ce90
movq %rdx, %r12
testq %rdx, %rdx
je 0x19ce90
movq 0x158(%rsp), %rbp
testq %rbp, %rbp
je 0x19ce90
movq %r9, %rbx
movq %r8, %r14
movq %rcx, %r15
movq %rdi, %rdx
leaq 0x8(%rsp), %r13
movq %r13, %rdi
callq 0x19ecc9
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 0x19ceb0
addq $0x40, %rsp
movq %rax, %rbx
movq %r13, %rdi
callq 0x19ef84
movq %rbx, %rax
addq $0xe8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x60068
// File: /workspace/github_c_makefile_star2_O3/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 0x19cf81
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 0x19cf15
movq %r15, %rdi
callq *%rax
movq %rax, %rcx
jmp 0x19cf17
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 0x19cfe6
addq $0x60, %rsp
testq %rax, %rax
jne 0x19cf83
movq %r13, %rdi
callq 0x19e389
xorl %eax, %eax
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/eis-encidxseq-construct.c
// Function: gt_createEncIdxSeqFromSfxI
EISeq *
gt_createEncIdxSeqFromSfxI(sfxInterface *sfxi,
                        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)
{
  gt_assert(sfxi && projectName && err);
  return gt_createEncIdxSeqFromSASeqSrc(
    gt_SfxI2SASS(sfxi), projectName, params,
    numExtHeaders, headerIDs, extHeaderSizes,
    extHeaderCallbacks, headerCBData, biFunc,
    cwExtBitsPerPos, biVarBits, cbState, err);
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
testq %rdi, %rdi
je 0x19cfe1
movq %rsi, %r13
testq %rsi, %rsi
je 0x19cfe1
cmpq $0x0, 0x60(%rsp)
je 0x19cfe1
movq %r9, %rbx
movq %r8, %r14
movq %rcx, %r15
movq %rdx, %r12
callq 0x19f154
movq %rax, %rdi
movq %r13, %rsi
movq %r12, %rdx
movq %r15, %rcx
movq %r14, %r8
movq %rbx, %r9
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
jmp 0x19ceb0
callq 0x600d6
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/eis-encidxseq-construct.c
// Function: gt_loadEncIdxSeqForSA
struct encIdxSeq *
gt_loadEncIdxSeqForSA(const GtAlphabet *gtalphabet,
                   const char *projectName,
                   enum seqBaseEncoding encType, int features, GtError *err)
{
  MRAEnc *alphabet;
  EISeq *seqIdx = NULL;
  gt_assert(gtalphabet!=NULL);
  alphabet = gt_SANewMRAEnc(gtalphabet);
  switch (encType)
  {
  case BWT_ON_BLOCK_ENC:
    seqIdx = gt_loadBlockEncIdxSeqGen(alphabet, projectName, features,
                                   err);
    break;
  default:
    gt_error_set(err, "Illegal/unknown/unimplemented encoding requested!");
    break;
  }
  gt_assert(seqIdx != NULL || gt_error_is_set(err));
  return seqIdx;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x19d071
movq %r8, %rbx
movl %ecx, %ebp
movl %edx, %r15d
movq %rsi, %r14
callq 0x19f128
cmpl $0x2, %r15d
jne 0x19d047
movq %rax, %rdi
movq %r14, %rsi
movl %ebp, %edx
movq %rbx, %rcx
callq 0x30a591
testq %rax, %rax
jne 0x19d066
jmp 0x19d058
leaq 0x2063fa(%rip), %rsi    # 0x3a3448
movq %rbx, %rdi
xorl %eax, %eax
callq 0xfcb67
movq %rbx, %rdi
callq 0xfcc32
testb %al, %al
je 0x19d076
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
callq 0x60146
callq 0x6010d
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/eis-encidxseq-construct.c
// Function: gt_loadEncIdxSeq
EISeq *
gt_loadEncIdxSeq(const char *projectName,
                 enum seqBaseEncoding encType, int features,
                 GT_UNUSED GtLogger *verbosity, GtError *err)
{
  struct encIdxSeq *newSeqIdx = NULL;
  GtEncseq *encseq = NULL;
  GtEncseqLoader *el = NULL;
  do
  {
    el = gt_encseq_loader_new();
    gt_encseq_loader_do_not_require_sds_tab(el);
    gt_encseq_loader_do_not_require_des_tab(el);
    gt_encseq_loader_do_not_require_ssp_tab(el);
    encseq = gt_encseq_loader_load(el, projectName, err);
    gt_encseq_loader_delete(el);
    if (encseq == NULL)
      break;
    newSeqIdx = gt_loadEncIdxSeqForSA(gt_encseq_alphabet(encseq),
                                      projectName,
                                      encType, features, err);
    gt_encseq_delete(encseq);
  } while (0);
  return newSeqIdx;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r8, %rbx
movl %edx, %ebp
movl %esi, %r14d
movq %rdi, %r15
callq 0xef0cd
movq %rax, %r13
movq %rax, %rdi
callq 0xf2408
movq %r13, %rdi
callq 0xf23ac
movq %r13, %rdi
callq 0xf23d9
movq %r13, %rdi
movq %r15, %rsi
movq %rbx, %rdx
callq 0xef129
movq %rax, %r12
movq %r13, %rdi
callq 0xefbe3
testq %r12, %r12
je 0x19d0fa
movq %r12, %rdi
callq 0xebcd9
movq %rax, %rdi
movq %r15, %rsi
movl %r14d, %edx
movl %ebp, %ecx
movq %rbx, %r8
callq 0x19d00e
movq %rax, %rbx
movq %r12, %rdi
callq 0xea375
movq %rbx, %rax
jmp 0x19d0fc
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/eis-mrangealphabet.c
// Function: gt_MRAEncGetSize
AlphabetRangeSize
gt_MRAEncGetSize(const MRAEnc *mralpha)
{
  AlphabetRangeID range, numRanges = mralpha->numRanges, sumRanges = 0;
  for (range = 0; range < numRanges; ++range)
  {
    sumRanges += mralpha->symbolsPerRange[range];
  }
  return sumRanges;
}

// Assembly:
movl 0x4(%rdi), %ecx
testq %rcx, %rcx
je 0x19e094
movq 0x10(%rdi), %rdx
xorl %esi, %esi
xorl %eax, %eax
addw (%rdx,%rsi,2), %ax
incq %rsi
cmpq %rsi, %rcx
jne 0x19e087
retq
xorl %eax, %eax
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/match/eis-mrangealphabet.c
// Function: gt_MRAEncSecondaryMapping
MRAEnc *
gt_MRAEncSecondaryMapping(const MRAEnc *srcAlpha, int selection,
                       const int *rangeSel, Symbol fallback)
{
  MRAEnc *newAlpha;
  switch (srcAlpha->encType)
  {
  case sourceUInt8:
    {
      GT_UNUSED const MRAEncUInt8 *ui8alpha;
      uint8_t *mappings, destSym;
      AlphabetRangeSize *newRanges, sym;
      AlphabetRangeID range, numRanges = MRAEncGetNumRanges(srcAlpha);
      ui8alpha = constMRAEnc2MRAEncUInt8(srcAlpha);
      mappings = gt_malloc(sizeof (uint8_t) * (UINT8_MAX + 1));
      memset(mappings, UNDEF_UCHAR, UINT8_MAX+1);
      newRanges = gt_malloc(sizeof (newRanges[0]) * numRanges);
      sym = 0;
      destSym = 0;
      for (range = 0; range < numRanges; ++range)
      {
        if (rangeSel[range] == selection)
        {
          for (; sym < srcAlpha->rangeEndIndices[range]; ++sym)
            mappings[sym] = destSym++;
          newRanges[range] = srcAlpha->symbolsPerRange[range];
        }
        else
        {
          for (; sym < srcAlpha->rangeEndIndices[range]; ++sym)
            mappings[sym] = fallback;
          newRanges[range] = 0;
        }
      }
      newAlpha = gt_newMultiRangeAlphabetEncodingUInt8(numRanges, newRanges,
                                                    mappings);
      gt_free(mappings);
      gt_free(newRanges);
    }
    break;
  default:
    abort();
    break;
  }
  return newAlpha;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rdx, (%rsp)
cmpl $0x1, (%rdi)
jne 0x19e1ba
movl %ecx, %ebx
movl %esi, %ebp
movq %rdi, %r15
movl 0x4(%rdi), %r12d
leaq 0x2056d6(%rip), %r14    # 0x3a3797
movl $0x100, %edi            # imm = 0x100
movq %r14, %rsi
movl $0xbd, %edx
callq 0x104226
movq %rax, %r13
movl $0x100, %edx            # imm = 0x100
movq %rax, %rdi
movl $0xff, %esi
callq 0x173a0
leaq (%r12,%r12), %rdi
movq %r14, %rsi
movl $0xbf, %edx
callq 0x104226
movq %rax, %r14
testq %r12, %r12
movq (%rsp), %r8
je 0x19e170
xorl %eax, %eax
xorl %ecx, %ecx
xorl %edx, %edx
movq 0x8(%r15), %rsi
movzwl (%rsi,%rax,2), %esi
cmpl %ebp, (%r8,%rax,4)
jne 0x19e144
cmpw %si, %dx
jae 0x19e13a
movzwl %dx, %esi
movb %cl, (%r13,%rsi)
incb %cl
incq %rsi
movq 0x8(%r15), %rdi
movzwl (%rdi,%rax,2), %edi
incl %edx
cmpq %rdi, %rsi
jb 0x19e121
movq 0x10(%r15), %rsi
movzwl (%rsi,%rax,2), %esi
jmp 0x19e163
cmpw %si, %dx
jae 0x19e161
movzwl %dx, %edx
movb %bl, (%r13,%rdx)
incq %rdx
movq 0x8(%r15), %rsi
movzwl (%rsi,%rax,2), %esi
cmpq %rsi, %rdx
jb 0x19e14c
xorl %esi, %esi
movw %si, (%r14,%rax,2)
incq %rax
cmpq %r12, %rax
jne 0x19e10b
movl %r12d, %edi
movq %r14, %rsi
movq %r13, %rdx
callq 0x19d84c
movq %rax, %rbx
leaq 0x20560f(%rip), %r15    # 0x3a3797
movq %r13, %rdi
movq %r15, %rsi
movl $0xd3, %edx
callq 0x1045eb
movq %r14, %rdi
movq %r15, %rsi
movl $0xd4, %edx
callq 0x1045eb
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x173b0