LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-contigs-graph.c
// Function: gt_contigs_graph_rm_optional_neighbours
void gt_contigs_graph_rm_optional_neighbours(GtContigsGraph *cg,
    GtUword cnum, unsigned int incoming)
{
  GtContigsGraphSpmEdge *edge;
  for (GT_CONTIGS_GRAPH_EACH_SPM_EDGE(cg, cnum, incoming, edge))
  {
    if (edge->deleted)
      continue;
    if (GT_CONTIGS_GRAPH_IS_OPTIONAL(cg, edge->dest))
    {
      /*gt_log_log("rm edge "GT_WU" -- %u", cnum, edge->dest);*/
      gt_contigs_graph_rm_spm_edge(cg, cnum, incoming, edge);
      /* if optional is now untraversable, rm it */
      if (cg->v_spm[0][edge->dest].deg == 0 ||
          cg->v_spm[1][edge->dest].deg == 0)
      {
        gt_contigs_graph_rm_vertex(cg, (GtUword)edge->dest);
      }
    }
  }
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
movl %edx, %ebx
movl %edx, %r13d
movq 0x18(%rdi,%r13,8), %rax
movq 0x80(%rdi,%r13,8), %rcx
movq (%rax,%rsi,8), %rdx
movq 0x8(%rax,%rsi,8), %rax
shrq $0x10, %rdx
leaq (%rcx,%rdx,8), %r12
shrq $0x10, %rax
leaq (%rcx,%rax,8), %rax
cmpq %rax, %r12
jae 0x1d052f
movq %rsi, %r14
movq %rdi, %r15
testb $0x40, 0x7(%r12)
jne 0x1d050c
movq 0x38(%r15), %rax
movl (%r12), %ecx
testb $0x2, (%rax,%rcx)
je 0x1d050c
movq %r15, %rdi
movq %r14, %rsi
movl %ebx, %edx
movq %r12, %rcx
callq 0x1d0296
movq 0x18(%r15), %rax
movl (%r12), %esi
cmpw $0x0, (%rax,%rsi,8)
je 0x1d0504
movq 0x20(%r15), %rax
cmpw $0x0, (%rax,%rsi,8)
jne 0x1d050c
movq %r15, %rdi
callq 0x1d038c
addq $0x8, %r12
movq 0x18(%r15,%r13,8), %rax
movq 0x8(%rax,%r14,8), %rax
shrq $0xd, %rax
andq $-0x8, %rax
addq 0x80(%r15,%r13,8), %rax
cmpq %rax, %r12
jb 0x1d04c4
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-contigs-graph.c
// Function: gt_contigs_graph_simplify
void gt_contigs_graph_simplify(GtContigsGraph *cg, bool restrict_rm_optionals)
{
  GtUword cnum;
  gt_assert(cg != NULL);
  for (cnum = 0; cnum < cg->nof_v; cnum++)
  {
    cg->v_m[cnum].mark0 = false;
    cg->v_m[cnum].mark1 = false;
    cg->v_m[cnum].visited = false;
  }
  for (cnum = 0; cnum < cg->nof_v; cnum++)
  {
    if (!cg->v_m[cnum].deleted &&
        GT_CONTIGS_GRAPH_IS_SINGLE_COPY(cg, cnum))
    {
      if (!cg->v_m[cnum].mark0)
      {
        /*gt_log_log("simplify from contig "GT_WU" (incoming=0, deg=%u)", cnum,
              cg->v_spm[0U][cnum].deg);*/
        gt_contigs_graph_simplify_from_contig(cg, cnum, 0U,
            restrict_rm_optionals);
      }
      if (!cg->v_m[cnum].mark1)
      {
        /*gt_log_log("simplify from contig "GT_WU" (incoming=1, deg=%u)", cnum,
              cg->v_spm[1U][cnum].deg);*/
        gt_contigs_graph_simplify_from_contig(cg, cnum, 1U,
            restrict_rm_optionals);
      }
    }
  }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x1d075b
movq %rdi, %rbx
cmpq $0x0, (%rdi)
je 0x1d06e2
xorl %eax, %eax
movq 0x38(%rbx), %rcx
andb $-0x41, (%rcx,%rax)
movq 0x38(%rbx), %rcx
andb $0x7f, (%rcx,%rax)
movq 0x38(%rbx), %rcx
andb $-0x11, (%rcx,%rax)
incq %rax
cmpq (%rbx), %rax
jb 0x1d06c2
cmpq $0x0, (%rbx)
je 0x1d0750
movl $0x1c, %r15d
xorl %r14d, %r14d
movzbl %sil, %ebp
movq 0x38(%rbx), %rax
movb (%rax,%r14), %al
testb $0x1, %al
jne 0x1d0744
movq 0x30(%rbx), %rcx
movss (%rcx,%r15), %xmm0
ucomiss 0x1e6102(%rip), %xmm0   # 0x3b6814
jb 0x1d0744
testb $0x40, %al
jne 0x1d0727
movq %rbx, %rdi
movq %r14, %rsi
xorl %edx, %edx
movl %ebp, %ecx
callq 0x1d0539
movq 0x38(%rbx), %rax
cmpb $0x0, (%rax,%r14)
js 0x1d0744
movq %rbx, %rdi
movq %r14, %rsi
movl $0x1, %edx
movl %ebp, %ecx
callq 0x1d0539
incq %r14
addq $0x20, %r15
cmpq (%rbx), %r14
jb 0x1d06f5
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
callq 0x6bb75
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-contigs-writer.c
// Function: gt_contigs_writer_new
GtContigsWriter *gt_contigs_writer_new(const GtEncseq *reads, GtFile *outfp)
{
  GtContigsWriter *contigs_writer;

  gt_assert(reads != NULL);

  contigs_writer = gt_malloc(sizeof (GtContigsWriter));
  contigs_writer->reads = reads;
  contigs_writer->outfp = outfp;
  contigs_writer->show_paths = false;
  contigs_writer->nofseqs = gt_encseq_num_of_sequences(contigs_writer->reads);
  contigs_writer->contignum = 0;
  contigs_writer->arrival_rate = (double)0;
  contigs_writer->depthinfo.firstread_copynum = (float)1;
  contigs_writer->depthinfo.internal_copynum = (float)0;
  contigs_writer->depthinfo.lastread_copynum = (float)1;
  contigs_writer->depthinfo.depth = 0;
  contigs_writer->depthinfo.length = 0;
  contigs_writer->depthinfo.astat = (float)0;
  contigs_writer->rlen = 0;
  contigs_writer->calculate_astat = false;
  GT_INITARRAY(&contigs_writer->contig, char);
  contigs_writer->contig_desc = gt_str_new();
  contigs_writer->path_desc = gt_str_new();
  contigs_writer->asc = gt_assembly_stats_calculator_new();
  contigs_writer->esr = gt_encseq_create_reader_with_readmode(reads,
      GT_READMODE_FORWARD, 0);
  contigs_writer->rcn = NULL;
  contigs_writer->depthinfo_fp = NULL;
  return contigs_writer;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0x1d12c3
movq %rsi, %r15
movq %rdi, %rbx
leaq 0x1e629f(%rip), %rsi    # 0x3b74ca
movl $0xa8, %edi
movl $0x34, %edx
callq 0x1092b2
movq %rax, %r14
movq %rbx, (%rax)
movq %r15, 0x8(%rax)
xorl %r15d, %r15d
movb %r15b, 0x10(%rax)
movq %rbx, %rdi
callq 0xec1e8
movq %rax, 0x60(%r14)
movq %r15, 0x50(%r14)
movaps 0x1e623e(%rip), %xmm0   # 0x3b74a0
movups %xmm0, 0x88(%r14)
xorps %xmm0, %xmm0
movups %xmm0, 0x68(%r14)
movb %r15b, 0x11(%r14)
movups %xmm0, 0x28(%r14)
movq %r15, 0x38(%r14)
movups %xmm0, 0x78(%r14)
callq 0x1208f8
movq %rax, 0x40(%r14)
callq 0x1208f8
movq %rax, 0x48(%r14)
callq 0x12b8c8
movq %rax, 0x18(%r14)
movq %rbx, %rdi
xorl %esi, %esi
xorl %edx, %edx
callq 0xed76d
movq %rax, 0x20(%r14)
xorps %xmm0, %xmm0
movups %xmm0, 0x98(%r14)
movq %r14, %rax
popq %rbx
popq %r14
popq %r15
retq
callq 0x6bde8
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-contigs-writer.c
// Function: gt_contigs_writer_enable_astat_calculation
void gt_contigs_writer_enable_astat_calculation(GtContigsWriter *contigs_writer,
    double coverage, unsigned char *rcn, FILE *depthinfo_fp)
{
  contigs_writer->calculate_astat = true;
  if (gt_encseq_accesstype_get(contigs_writer->reads) ==
      GT_ACCESS_TYPE_EQUALLENGTH)
    contigs_writer->rlen = gt_encseq_equallength(contigs_writer->reads);
  else
    contigs_writer->rlen = gt_encseq_total_length(contigs_writer->reads) /
      gt_encseq_num_of_sequences(contigs_writer->reads);
  contigs_writer->arrival_rate = coverage / (double)contigs_writer->rlen;
  gt_log_log("arrival_rate = %.4f", contigs_writer->arrival_rate);
  contigs_writer->rcn = rcn;
  contigs_writer->depthinfo_fp = depthinfo_fp;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rdx, %rbx
movq %rsi, %r14
movsd %xmm0, (%rsp)
movq %rdi, %r15
movb $0x1, 0x11(%rdi)
movq (%rdi), %rdi
callq 0xfac0f
movq (%r15), %rdi
cmpl $0x2, %eax
jne 0x1d12fe
callq 0xfac12
jmp 0x1d1319
callq 0xec1d8
movq %rax, %r12
movq (%r15), %rdi
callq 0xec1e8
movq %rax, %rcx
movq %r12, %rax
xorl %edx, %edx
divq %rcx
movq %rax, %xmm0
punpckldq 0x17f5ba(%rip), %xmm0 # xmm0 = xmm0[0],mem[0],xmm0[1],mem[1]
movq %rax, 0x68(%r15)
subpd 0x17f5be(%rip), %xmm0   # 0x3508f0
movapd %xmm0, %xmm1
unpckhpd %xmm0, %xmm1            # xmm1 = xmm1[1],xmm0[1]
addsd %xmm0, %xmm1
movsd (%rsp), %xmm0
divsd %xmm1, %xmm0
movsd %xmm0, 0x70(%r15)
leaq 0x1e6195(%rip), %rdi    # 0x3b74e9
movb $0x1, %al
callq 0x108e02
movq %r14, 0x98(%r15)
movq %rbx, 0xa0(%r15)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-contigs-writer.c
// Function: gt_contigs_writer_delete
void gt_contigs_writer_delete(GtContigsWriter *contigs_writer)
{
  if (contigs_writer == NULL)
    return;
  GT_FREEARRAY(&contigs_writer->contig, char);
  gt_str_delete(contigs_writer->contig_desc);
  gt_str_delete(contigs_writer->path_desc);
  gt_assembly_stats_calculator_delete(contigs_writer->asc);
  gt_encseq_reader_delete(contigs_writer->esr);
  gt_free(contigs_writer);
}

// Assembly:
testq %rdi, %rdi
je 0x1d13ed
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq 0x28(%rdi), %rdi
testq %rdi, %rdi
je 0x1d13ae
leaq 0x28(%rbx), %r14
leaq 0x1e6135(%rip), %rsi    # 0x3b74ca
movl $0x68, %edx
callq 0x109670
xorps %xmm0, %xmm0
movups %xmm0, (%r14)
movq $0x0, 0x10(%r14)
movq 0x40(%rbx), %rdi
callq 0x121b03
movq 0x48(%rbx), %rdi
callq 0x121b03
movq 0x18(%rbx), %rdi
callq 0x12b910
movq 0x20(%rbx), %rdi
callq 0xed7bf
leaq 0x1e60f1(%rip), %rsi    # 0x3b74ca
movq %rbx, %rdi
movl $0x6d, %edx
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-contigs-writer.c
// Function: gt_contigs_writer_start
void gt_contigs_writer_start(GtContigsWriter *contigs_writer,
    GtUword seqnum)
{
  GtUword pos, nofchars, i;
  gt_assert(contigs_writer != NULL);
  pos = gt_encseq_seqstartpos(contigs_writer->reads, seqnum);
  nofchars = gt_encseq_seqlength(contigs_writer->reads, seqnum);
  for (i = 0; i < nofchars; i++, pos++)
  {
    char *c;
    GT_GETNEXTFREEINARRAY(c, &contigs_writer->contig, char,
        GT_CONTIGS_WRITER_CONTIG_INC);
    *c = gt_encseq_get_encoded_char_nospecial(contigs_writer->reads, pos,
        GT_READMODE_FORWARD)["acgt"];
  }
  contigs_writer->depthinfo.depth++;
  gt_str_append_uword(contigs_writer->path_desc,
      GT_CONTIGS_WRITER_READNUM(seqnum, contigs_writer->nofseqs));
  gt_str_append_char(contigs_writer->path_desc,
      GT_CONTIGS_WRITER_LETTER(seqnum, contigs_writer->nofseqs));
  if (contigs_writer->rcn != NULL)
  {
    contigs_writer->depthinfo.firstread_copynum = (float)contigs_writer->rcn[
      GT_CONTIGS_WRITER_READNUM(seqnum, contigs_writer->nofseqs)];
  }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x1d19e8
movq %rsi, %r14
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0xefce0
movq %rax, %r15
movq (%rbx), %rdi
movq %r14, (%rsp)
movq %r14, %rsi
callq 0xeffd3
testq %rax, %rax
je 0x1d195d
movq %rax, %r12
leaq 0x195a85(%rip), %rbp    # 0x36737c
movq 0x30(%rbx), %rsi
cmpq %rsi, 0x38(%rbx)
jb 0x1d1925
addq $0x4000, %rsi           # imm = 0x4000
movq %rsi, 0x30(%rbx)
movq 0x28(%rbx), %rdi
leaq 0x1e5bb3(%rip), %rdx    # 0x3b74ca
movl $0x11f, %ecx            # imm = 0x11F
callq 0x1094e6
movq %rax, 0x28(%rbx)
movq 0x28(%rbx), %r14
testq %r14, %r14
je 0x1d19e3
movq (%rbx), %rdi
movq 0x38(%rbx), %r13
leaq 0x1(%r13), %rax
movq %rax, 0x38(%rbx)
movq %r15, %rsi
xorl %edx, %edx
callq 0xec603
movzbl %al, %eax
movb (%rax,%rbp), %al
movb %al, (%r14,%r13)
incq %r15
decq %r12
jne 0x1d18f7
incq 0x78(%rbx)
movq 0x48(%rbx), %rdi
movq 0x60(%rbx), %rsi
movq %rsi, %rax
shrq %rax
movq (%rsp), %r14
movq %r14, %r15
notq %r15
addq %r15, %rsi
cmpq %r14, %rax
cmovaq %r14, %rsi
callq 0x120af4
movq 0x48(%rbx), %rdi
movq 0x60(%rbx), %rax
shrq %rax
xorl %ecx, %ecx
cmpq %r14, %rax
seta %cl
leal (%rcx,%rcx,2), %esi
addl $0x42, %esi
callq 0x120ba5
movq 0x98(%rbx), %rax
testq %rax, %rax
je 0x1d19d4
movq 0x60(%rbx), %rcx
addq %rcx, %r15
shrq %rcx
cmpq %r14, %rcx
cmovaq %r14, %r15
movzbl (%rax,%r15), %eax
cvtsi2ss %eax, %xmm0
movss %xmm0, 0x88(%rbx)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x6bf03
callq 0x6bf3c
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-contigs-writer.c
// Function: gt_contigs_writer_show_stats
void gt_contigs_writer_show_stats(GtContigsWriter *contigs_writer,
    GtLogger *logger)
{
  gt_assert(contigs_writer != NULL);
  if (contigs_writer->contignum > 0)
    gt_assembly_stats_calculator_show(contigs_writer->asc, logger);
  else
    gt_logger_log(logger, "no contigs respect the given cutoff parameters");
}

// Assembly:
testq %rdi, %rdi
je 0x1d1a16
cmpq $0x0, 0x50(%rdi)
je 0x1d1a02
movq 0x18(%rdi), %rdi
jmp 0x12bc49
leaq 0x1e5bec(%rip), %rax    # 0x3b75f5
movq %rsi, %rdi
movq %rax, %rsi
xorl %eax, %eax
jmp 0x10906e
pushq %rax
callq 0x6bf75
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-errfind.c
// Function: processleafedge_errfind
static int processleafedge_errfind(GT_UNUSED bool firstsucc,
    GtUword fatherdepth,
    GT_UNUSED GtBUinfo_errfind *father, GtUword leafnumber,
    GtBUstate_errfind *state, GT_UNUSED GtError *err)
{
#ifdef RDJ_ERRFIND_DEBUG
  if (leafnumber == state->debug_value)
    gt_log_enable();
  RDJ_ERRFIND_SHOW_KMER;
#endif
  if (fatherdepth < state->k - 1)
  {
    gt_errfind_reset(state);
  }
  else if (!state->seprange)
  {
    if (fatherdepth == state->k - 1 &&
        RDJ_ERRFIND_IS_SEPRANGE(state->encseq, leafnumber + fatherdepth))
    {
      state->seprange = true;
    }
    if (!state->seprange && state->currentchar < state->alphasize)
    {
      gt_errfind_process_kmer(leafnumber, state);
      if (fatherdepth == state->k - 1)
      {
        state->currentchar++;
#ifdef RDJ_ERRFIND_DEBUG
        gt_log_log("currentchar incremented, now is %u", state->currentchar);
#endif
      }
    }
  }
  return 0;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
movq %rdx, %rbx
movq 0x20(%rdx), %rax
decq %rax
cmpq %rdi, %rax
jbe 0x1d2623
movl $0x0, 0x1c(%rbx)
movl 0x18(%rbx), %edx
testq %rdx, %rdx
je 0x1d261a
movq 0x38(%rbx), %rdi
shlq $0x3, %rdx
xorl %esi, %esi
callq 0x173a0
movb $0x0, 0x40(%rbx)
jmp 0x1d26c4
cmpb $0x0, 0x40(%rbx)
jne 0x1d26c4
movq %rsi, %r15
movq %rdi, %r14
cmpq %rdi, %rax
jne 0x1d2660
leaq (%r15,%r14), %r12
movq 0x10(%rbx), %rdi
callq 0xec1d8
cmpq %rax, %r12
je 0x1d265c
movq 0x10(%rbx), %rdi
movq %r12, %rsi
xorl %edx, %edx
callq 0xec754
testb %al, %al
je 0x1d2660
movb $0x1, 0x40(%rbx)
cmpb $0x0, 0x40(%rbx)
jne 0x1d26c4
movl 0x1c(%rbx), %eax
cmpl 0x18(%rbx), %eax
jae 0x1d26c4
movq 0x38(%rbx), %rcx
movq (%rcx,%rax,8), %r12
leaq 0x1(%r12), %rdx
movq %rdx, (%rcx,%rax,8)
cmpq 0x28(%rbx), %rdx
ja 0x1d26b5
decq %r15
movq 0x20(%rbx), %r13
addq %r15, %r13
movq 0x10(%rbx), %rdi
callq 0xec1d8
cmpq %rax, %r13
jae 0x1d26ce
addq 0x20(%rbx), %r15
movl 0x1c(%rbx), %eax
imulq 0x28(%rbx), %rax
shlq $0x3, %rax
addq 0x30(%rbx), %rax
movq %r15, (%rax,%r12,8)
movq 0x20(%rbx), %rax
decq %rax
cmpq %r14, %rax
jne 0x1d26c4
incl 0x1c(%rbx)
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
callq 0x6c2aa
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-errfind.c
// Function: processlcpinterval_errfind
static int processlcpinterval_errfind(GtUword lcp,
    GT_UNUSED GtBUinfo_errfind *info, GtBUstate_errfind *state,
    GT_UNUSED GtError *err)
{
  if (lcp == state->k - 1 && !gt_errfind_are_all_trusted(state))
  {
    GtUchar trusted_char = gt_errfind_trusted_char(state);
    if (trusted_char != (GtUchar)GT_UNDEF_UCHAR)
    {
      unsigned int cnum;
      for (cnum = 0; cnum < state->alphasize && state->count[cnum] > 0; cnum++)
      {
        if (state->count[cnum] < state->c)
        {
          GtUword i;
          for (i = 0; i < state->count[cnum]; i++)
          {
            GtUword pos = state->kpositions[cnum * state->c + i];
            GtUchar newchar = trusted_char;
            if (pos >= state->firstmirrorpos)
            {
              pos = state->totallength - 1UL - pos;
              newchar = (GtUchar)3 - newchar;
            }
            if (state->editor != NULL)
            {
#ifdef RDJ_ERRFIND_DEBUG
              printf(""GT_WU":%u\n", pos, (unsigned int)newchar);
#endif
              gt_twobitenc_editor_edit(state->editor, pos, newchar);
            }
          }
        }
      }
    }
  }
  return 0;
}

// Assembly:
movq 0x20(%rsi), %rax
decq %rax
cmpq %rdi, %rax
jne 0x1d281f
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, %rbx
movl 0x18(%rsi), %eax
testq %rax, %rax
je 0x1d2811
movq 0x28(%rbx), %rcx
movq 0x38(%rbx), %rsi
movb $0x1, %dl
movl $0x1, %edi
xorl %r8d, %r8d
cmpq %rcx, -0x8(%rsi,%rdi,8)
movzbl %dl, %edx
cmovbl %r8d, %edx
cmpq %rax, %rdi
jae 0x1d2728
incq %rdi
testb $0x1, %dl
jne 0x1d270f
testb $0x1, %dl
jne 0x1d2811
movb $-0x1, %bpl
testq %rax, %rax
je 0x1d2782
xorl %r14d, %r14d
movq 0x28(%rbx), %rax
movq 0x38(%rbx), %rcx
movq (%rcx,%r14,8), %rcx
cmpq %rax, %rcx
setb %dl
testq %rcx, %rcx
sete %cl
orb %dl, %cl
jne 0x1d2771
movq 0x10(%rbx), %rdi
movq 0x30(%rbx), %rcx
imulq %r14, %rax
movq (%rcx,%rax,8), %rsi
xorl %edx, %edx
callq 0xec603
movl %eax, %ebp
incq %r14
movl 0x18(%rbx), %eax
cmpq %rax, %r14
jae 0x1d2782
cmpb $-0x1, %bpl
je 0x1d273c
cmpb $-0x1, %bpl
je 0x1d2811
cmpl $0x0, 0x18(%rbx)
je 0x1d2811
movb $0x3, %r14b
subb %bpl, %r14b
xorl %r15d, %r15d
xorl %r12d, %r12d
movq 0x38(%rbx), %rax
movl %r12d, %r12d
movq (%rax,%r12,8), %rax
testq %rax, %rax
je 0x1d2811
cmpq 0x28(%rbx), %rax
jae 0x1d2804
movq 0x38(%rbx), %rax
cmpq $0x0, (%rax,%r12,8)
je 0x1d2804
xorl %r13d, %r13d
movq 0x28(%rbx), %rax
imulq %r15, %rax
addq 0x30(%rbx), %rax
movq (%rax,%r13,8), %rsi
cmpq 0x58(%rbx), %rsi
jae 0x1d27dc
movl %ebp, %eax
jmp 0x1d27e6
notq %rsi
addq 0x60(%rbx), %rsi
movl %r14d, %eax
movq 0x68(%rbx), %rdi
testq %rdi, %rdi
je 0x1d27f7
movzbl %al, %edx
callq 0x1e46f5
incq %r13
movq 0x38(%rbx), %rax
cmpq (%rax,%r12,8), %r13
jb 0x1d27c2
incl %r12d
addq $0x8, %r15
cmpl 0x18(%rbx), %r12d
jb 0x1d279e
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/sarr-def.h
// Function: lcptable_get
static inline GtUword lcptable_get(
                       const Suffixarray *suffixarray,
                       GtUword pos)
{
  GtUchar smalllcpvalue;
  const Largelcpvalue *largelcpvalue;

  gt_assert(pos <= gt_encseq_total_length(suffixarray->encseq));
  smalllcpvalue = suffixarray->lcptab[pos];
  if (smalllcpvalue != (GtUchar) LCPOVERFLOW)
  {
    return (GtUword) smalllcpvalue;
  }
  largelcpvalue = getlargelcpvalue(suffixarray,pos);
  gt_assert(largelcpvalue != NULL);
  return largelcpvalue->value;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
movq (%rdi), %rdi
callq 0xec1d8
cmpq %rbx, %rax
jb 0x1d346e
movq 0x60(%r14), %rax
movzbl (%rax,%rbx), %eax
cmpq $0xff, %rax
jne 0x1d3466
cmpb $0x0, 0x8(%r14)
je 0x1d3473
movq 0x10(%r14), %rax
movq 0x68(%r14), %rcx
shlq $0x4, %rax
addq %rcx, %rax
addq $-0x10, %rax
cmpq %rax, %rcx
ja 0x1d345b
movq %rax, %rsi
subq %rcx, %rsi
sarq %rsi
andq $-0x10, %rsi
leaq (%rcx,%rsi), %rdx
cmpq %rbx, (%rcx,%rsi)
jbe 0x1d3450
addq $-0x10, %rdx
movq %rdx, %rax
jmp 0x1d342b
jae 0x1d345d
addq $0x10, %rdx
movq %rdx, %rcx
jmp 0x1d342b
xorl %edx, %edx
testq %rdx, %rdx
je 0x1d3478
movq 0x8(%rdx), %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x6c54c
callq 0x6c4dc
callq 0x6c513
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-pairwise.c
// Function: rdj_pairwise_check_arguments
static inline bool rdj_pairwise_check_arguments(GtOvlfindMode m, void *proc,
    void *procdata, GtBitsequence *cntreads_in, GtBitsequence **cntreads_out,
    bool cntfilter)
{
  gt_assert(m == GT_OVLFIND_CNT || m == GT_OVLFIND_ALL || m == GT_OVLFIND_SPM);
  if (proc == NULL)
  {
    gt_assert(m == GT_OVLFIND_CNT);
    gt_assert(procdata == NULL);
  }
  else
    gt_assert(m == GT_OVLFIND_SPM || m == GT_OVLFIND_ALL);
  if (cntfilter || (cntreads_out != NULL))
    gt_assert((m == GT_OVLFIND_CNT) ||
              (m == GT_OVLFIND_ALL) ||
              (cntreads_in != NULL));
  return true; /* allow to wrap in gt_assert() */
}

// Assembly:
pushq %rax
movl %edi, %eax
subl $0x3, %eax
jae 0x1d3553
testq %rsi, %rsi
je 0x1d3529
testb $0x1, %dil
je 0x1d3533
callq 0x6c5be
cmpl $0x1, %edi
jne 0x1d355d
testq %rdx, %rdx
jne 0x1d3562
cmpl $-0x2, %eax
setb %al
testq %r8, %r8
setne %dl
orb %r9b, %dl
testq %rcx, %rcx
sete %cl
andb %al, %cl
andb %dl, %cl
cmpb $0x1, %cl
je 0x1d3558
popq %rax
retq
callq 0x6c585
callq 0x6c669
callq 0x6c5f7
callq 0x6c630
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-pairwise.c
// Function: find_exact_overlaps
static inline GtContfind find_exact_overlaps(struct Data *d, bool use_kmp,
    GtUword min_length, bool find_nonmaximal)
{
  GtContfind retval;

  if (d->u->seqnum == d->v->seqnum && d->v->direct)
  {
    if (!(d->mode == GT_OVLFIND_SPM || d->mode == GT_OVLFIND_ALL))
      return GT_CONTFIND_EQ;
    if (use_kmp)
      retval = gt_ovlfind_kmp(d->u->seq, d->u->len, d->u->pi, NULL, 0, NULL,
          d->mode, min_length, find_nonmaximal, call_spmproc, d);
    else
      retval = gt_ovlfind_bf(d->u->seq, d->u->len, NULL, 0, d->mode,
          min_length, find_nonmaximal, call_spmproc, d);
  }
  else
  {
    if (use_kmp)
      retval = gt_ovlfind_kmp(d->u->seq, d->u->len, d->u->pi, d->v->seq,
          d->v->len, d->v->pi, d->mode, min_length, find_nonmaximal,
          call_spmproc, d);
    else
      retval = gt_ovlfind_bf(d->u->seq, d->u->len, d->v->seq, d->v->len,
          d->mode, min_length, find_nonmaximal, call_spmproc, d);
  }
  return retval;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rdx, %rax
movq %rdi, %r10
movq 0x18(%rdi), %rdx
movq 0x20(%rdi), %r9
movq 0x10(%rdx), %rdi
cmpq 0x10(%r9), %rdi
jne 0x1d3e40
cmpb $0x1, 0x18(%r9)
jne 0x1d3e40
movl 0x28(%r10), %r11d
testl $0xfffffffd, %r11d      # imm = 0xFFFFFFFD
jne 0x1d3ec1
movq (%rdx), %rdi
movq 0x8(%rdx), %r8
testb %sil, %sil
je 0x1d3ecc
movq 0x20(%rdx), %rdx
subq $0x8, %rsp
leaq 0x12f(%rip), %rbx       # 0x1d3f56
movzbl %cl, %r14d
movq %r8, %rsi
xorl %ecx, %ecx
xorl %r8d, %r8d
xorl %r9d, %r9d
pushq %r10
pushq %rbx
pushq %r14
pushq %rax
pushq %r11
jmp 0x1d3e7d
movq (%rdx), %rdi
movq 0x8(%rdx), %r11
testb %sil, %sil
je 0x1d3e88
movq 0x20(%rdx), %rdx
movq (%r9), %rbx
movq 0x8(%r9), %r8
movq 0x20(%r9), %r9
movl 0x28(%r10), %r14d
subq $0x8, %rsp
leaq 0xec(%rip), %r15        # 0x1d3f56
movzbl %cl, %r12d
movq %r11, %rsi
movq %rbx, %rcx
pushq %r10
pushq %r15
pushq %r12
pushq %rax
pushq %r14
callq 0x3327eb
addq $0x38, %rsp
jmp 0x1d3eb9
movq (%r9), %rdx
movq 0x8(%r9), %r9
movl 0x28(%r10), %r8d
subq $0x8, %rsp
leaq 0xb8(%rip), %rbx        # 0x1d3f56
movzbl %cl, %r14d
movq %r11, %rsi
movq %r9, %rcx
movq %rax, %r9
pushq %r10
pushq %rbx
pushq %r14
callq 0x32ef5c
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
movl $0x2, %eax
addq $0x8, %rsp
jmp 0x1d3eb9
subq $0x8, %rsp
leaq 0x7f(%rip), %rbx        # 0x1d3f56
movzbl %cl, %r14d
movq %r8, %rsi
xorl %edx, %edx
xorl %ecx, %ecx
movl %r11d, %r8d
jmp 0x1d3ea8
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-pairwise.c
// Function: call_spmproc_a
static void call_spmproc_a(GtUword length_on_u, GtUword length_on_v,
    GtUword unit_edist, bool suffix_of_u, void *data)
{
  struct Data *d = data;
  if (suffix_of_u)
    d->proc_a(d->u->seqnum, d->v->seqnum, length_on_u, length_on_v,
              unit_edist, d->u->direct, d->v->direct, d->procdata);
  else
    d->proc_a(d->v->seqnum, d->u->seqnum, length_on_v, length_on_u,
              unit_edist, d->v->direct, d->u->direct, d->procdata);
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %rdx, %r11
movq %rsi, %r10
movq %rdi, %rax
movq 0x8(%r8), %rbx
movq 0x10(%r8), %r14
testl %ecx, %ecx
je 0x1d3f23
movq 0x18(%r8), %rcx
movq 0x20(%r8), %rdx
movq 0x10(%rcx), %rdi
movq 0x10(%rdx), %rsi
movzbl 0x18(%rcx), %r9d
movzbl 0x18(%rdx), %r15d
movq %rax, %rdx
movq %r10, %rcx
jmp 0x1d3f43
movq 0x18(%r8), %rcx
movq 0x20(%r8), %rdx
movq 0x10(%rdx), %rdi
movq 0x10(%rcx), %rsi
movzbl 0x18(%rdx), %r9d
movzbl 0x18(%rcx), %r15d
movq %r10, %rdx
movq %rax, %rcx
movq %r11, %r8
pushq %r14
pushq %r15
callq *%rbx
addq $0x10, %rsp
popq %rbx
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-spmfind.c
// Function: processleafedge_spmvar
static inline int processleafedge_spmvar(bool firstsucc,
    GtUword fatherdepth,
    GtBUinfo_spmeq *father, GtUword seqnum, GtUword relpos,
    GtBUstate_spmeq *state, GT_UNUSED GtError *err)
{
  if (fatherdepth >= state->minmatchlength)
  {
    GtUword seqlen = gt_encseq_seqlength(state->encseq, seqnum);
    if (firstsucc)
    {
      gt_assert(father != NULL);
      father->w_left = state->w_nextfree;
    }
    if (relpos == 0)
    {
      appendtowset_spm(seqnum, state);
      if (fatherdepth == seqlen)
      {
        GtUword readnum = GT_READJOINER_READNUM(seqnum,
            state->first_revcompl, state->nofreads);
        (void)fwrite(&(readnum), sizeof (GtUword), (size_t)1,
            state->cntfile);
        state->nof_contained++;
      }
    }
    if (relpos + fatherdepth == seqlen)
      appendtolset_spm(seqnum, state);
  }
  else
  {
#ifdef GT_READJOINER_STATISTICS
    reset_subtree_stats(state);
#endif
    state->w_nextfree = 0;
  }
  return 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r9, %rbx
cmpq %rsi, 0x20(%r9)
jbe 0x1d400c
movq $0x0, 0x80(%rbx)
jmp 0x1d40f2
movq %r8, %r15
movq %rcx, %r14
movq %rdx, %rbp
movq %rsi, %r12
movl %edi, %r13d
movq 0x38(%rbx), %rdi
movq %rcx, %rsi
callq 0xeffd3
testb %r13b, %r13b
je 0x1d4040
testq %rbp, %rbp
je 0x1d4101
movq 0x80(%rbx), %rcx
movq %rcx, (%rbp)
testq %r15, %r15
jne 0x1d409a
movq %r14, %rdi
movq %rbx, %rsi
movq %rax, %r13
callq 0x1d54e9
movq %r13, %rax
cmpq %r12, %r13
jne 0x1d409a
movq 0x58(%rbx), %rcx
decq %rcx
movq %r14, %rax
cmpq %r14, %rcx
jae 0x1d4074
movq %r14, %rax
notq %rax
addq 0x50(%rbx), %rax
movq %rsp, %rdi
movq %rax, (%rdi)
movq 0xe0(%rbx), %rcx
movl $0x8, %esi
movl $0x1, %edx
callq 0x17fa0
incq 0xe8(%rbx)
movq %r13, %rax
addq %r12, %r15
cmpq %rax, %r15
jne 0x1d40f2
movq 0x70(%rbx), %rax
cmpq %rax, 0x68(%rbx)
jne 0x1d40e2
leaq 0x400(%rax), %rcx
movq %rcx, 0x70(%rbx)
movq 0x60(%rbx), %rdi
leaq 0x2000(,%rax,8), %rsi
leaq 0x1e3a52(%rip), %rdx    # 0x3b7b1c
movl $0xf7, %ecx
callq 0x1094e6
movq %rax, 0x60(%rbx)
movq 0x68(%rbx), %rax
cmpq 0x70(%rbx), %rax
jae 0x1d4106
movq 0x60(%rbx), %rax
movq 0x68(%rbx), %rcx
movq %r14, (%rax,%rcx,8)
incq 0x68(%rbx)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x6c8dc
callq 0x6c8a3
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-spmfind.c
// Function: appendtowset_spm
static inline void appendtowset_spm(GtUword seqnum,
  GtBUstate_spm *state)
{
  WholereadInfo *w;

  state->w_count++;
  if (state->w_count <= state->w_offset)
    return;

  if (state->w_count > state->w_offset + state->w_maxsize)
  {
    state->w_overflow = true;
    return;
  }

  /* realloc if necessary */
  if (state->w_nextfree == state->w_allocated)
    expandwset_spm(state);

  /* add element */
#ifdef GT_READJOINER_DEBUG
  gt_log_log("-- add to wset: "GT_WU"", seqnum);
  gt_log_log("offset: "GT_WU"", state->w_offset);
#endif
  w = state->w_set + state->w_nextfree;
  state->w_nextfree++;

  w->seqnum = seqnum;
  /* get a new blind trie or recycle old one */
  if (w->blindtrie == NULL)
    w->blindtrie = gt_blindtrie_new(NULL, 0,
        GT_SPMFIND_BLTRIE_ALLOC, state->encseq, false, NULL,
        NULL, GT_READMODE_REVERSE);
  else
    gt_blindtrie_reset(w->blindtrie);

#ifdef GT_READJOINER_STATISTICS
  /* statistics */
  if (state->w_nextfree > state->max_w_nextfree)
    state->max_w_nextfree = state->w_nextfree;
#endif
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq 0x90(%rsi), %rax
movq 0x98(%rsi), %rcx
incq %rcx
movq %rcx, 0x98(%rsi)
cmpq %rax, %rcx
jbe 0x1d5684
movq %rsi, %rbx
addq 0xa0(%rsi), %rax
cmpq %rax, %rcx
jbe 0x1d552a
movb $0x1, 0xa8(%rbx)
jmp 0x1d5684
movq %rdi, %r14
movq 0x88(%rbx), %r15
cmpq %r15, 0x80(%rbx)
jne 0x1d5629
leaq 0x400(%r15), %rsi
movq %rsi, 0x88(%rbx)
movq 0x78(%rbx), %rdi
shlq $0x4, %rsi
leaq 0x1e25be(%rip), %rdx    # 0x3b7b1c
movl $0x8d, %ecx
callq 0x1094e6
movq %rax, 0x78(%rbx)
movq 0x88(%rbx), %rcx
movq %rcx, %rsi
subq %r15, %rsi
jbe 0x1d5620
leaq 0x1(%rsi), %rdx
andq $-0x2, %rdx
decq %rsi
movq %rsi, %xmm0
pshufd $0x44, %xmm0, %xmm0     # xmm0 = xmm0[0,1,0,1]
shlq $0x4, %r15
addq %r15, %rax
addq $0x18, %rax
xorl %esi, %esi
movdqa 0x18c4c7(%rip), %xmm1   # 0x361a70
movdqa 0x18c4cf(%rip), %xmm2   # 0x361a80
pxor %xmm2, %xmm0
pcmpeqd %xmm3, %xmm3
movq %rsi, %xmm4
pshufd $0x44, %xmm4, %xmm4     # xmm4 = xmm4[0,1,0,1]
por %xmm1, %xmm4
pxor %xmm2, %xmm4
movdqa %xmm4, %xmm5
pcmpgtd %xmm0, %xmm5
pcmpeqd %xmm0, %xmm4
pshufd $0xf5, %xmm4, %xmm6     # xmm6 = xmm4[1,1,3,3]
pand %xmm5, %xmm6
pshufd $0xf5, %xmm5, %xmm4     # xmm4 = xmm5[1,1,3,3]
por %xmm6, %xmm4
movd %xmm4, %edi
notl %edi
testb $0x1, %dil
je 0x1d55fd
movq $0x0, -0x10(%rax)
pxor %xmm3, %xmm4
pextrw $0x4, %xmm4, %edi
testb $0x1, %dil
je 0x1d5613
movq $0x0, (%rax)
addq $0x2, %rsi
addq $0x20, %rax
cmpq %rsi, %rdx
jne 0x1d55b9
cmpq %rcx, 0x80(%rbx)
jae 0x1d568a
movq 0x78(%rbx), %r15
movq 0x80(%rbx), %rcx
movq %rcx, %rax
shlq $0x4, %rax
incq %rcx
movq %rcx, 0x80(%rbx)
movq %r14, (%r15,%rax)
movq 0x8(%r15,%rax), %rdi
testq %rdi, %rdi
je 0x1d565d
popq %rbx
popq %r14
popq %r15
jmp 0x1ef8f9
addq %rax, %r15
movq 0x38(%rbx), %rcx
xorl %edi, %edi
xorl %esi, %esi
movl $0x40, %edx
xorl %r8d, %r8d
xorl %r9d, %r9d
pushq $0x1
pushq $0x0
callq 0x1ef774
addq $0x10, %rsp
movq %rax, 0x8(%r15)
popq %rbx
popq %r14
popq %r15
retq
callq 0x6cfc3
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-spmfind.c
// Function: processlcpinterval_spmvar
static int processlcpinterval_spmvar(GtUword lcp,
    GtBUinfo_spmvar *info, GtBUstate_spmvar *state, GT_UNUSED GtError *err)
{
  if (lcp >= state->minmatchlength)
  {
    GtUword i;
    for (i = 0; i < state->l_nextfree; i++)
    {
      combine_terminal_with_wset(state->l_set[i],
          gt_encseq_seqstartpos(state->encseq, state->l_set[i]),
          gt_encseq_seqlength(state->encseq, state->l_set[i]), info->w_left,
          lcp, state);
    }
    state->l_nextfree = 0;
  }
  return 0;
}

// Assembly:
cmpq %rdi, 0x20(%rdx)
ja 0x1d5945
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rdx, %rbx
cmpq $0x0, 0x68(%rdx)
je 0x1d592f
movq %rsi, %r14
movq %rdi, %r15
xorl %ebp, %ebp
movq 0x38(%rbx), %rdi
movq 0x60(%rbx), %rax
movq (%rax,%rbp,8), %r12
movq %r12, %rsi
callq 0xefce0
movq %rax, %r13
movq 0x38(%rbx), %rdi
movq 0x60(%rbx), %rax
movq (%rax,%rbp,8), %rsi
callq 0xeffd3
movq (%r14), %rcx
movq %r12, %rdi
movq %r13, %rsi
movq %rax, %rdx
movq %r15, %r8
movq %rbx, %r9
callq 0x1d568f
incq %rbp
cmpq 0x68(%rbx), %rbp
jb 0x1d58e7
movq $0x0, 0x68(%rbx)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
nop
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-spmlist.c
// Function: gt_spmlist_parse_ascii_approx
int gt_spmlist_parse_ascii_approx(const char* filename,
    GtUword min_length, GtSpmprocA processoverlap, void *data,
    GtError *err)
{
  int retval = 0;
  GtFile *infp;

  /*@i1@*/ gt_error_check(err);
  infp = gt_file_new(filename, "r", err);
  if (infp == NULL) return -1;
  retval = gt_spmlist_parse_ascii_generic(infp, min_length, NULL,
      processoverlap, data, err);
  gt_file_delete(infp);
  return retval;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
movq %r8, %rbx
movq %rcx, %r14
movq %rdx, %r15
movq %rsi, %r12
movq %rdi, %r13
testq %r8, %r8
je 0x1d5a42
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0x1d5a8f
leaq 0x18e480(%rip), %rsi    # 0x363ec9
movq %r13, %rdi
movq %rbx, %rdx
callq 0x103957
testq %rax, %rax
je 0x1d5a80
movq %rax, %r13
movq %rax, %rdi
movq %r12, %rsi
xorl %edx, %edx
movq %r15, %rcx
movq %r14, %r8
movq %rbx, %r9
callq 0x1d5a94
movl %eax, %ebx
movq %r13, %rdi
callq 0x1040fc
movl %ebx, %eax
jmp 0x1d5a85
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
callq 0x6d22a
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-spmlist.c
// Function: gt_spmlist_parse_ascii_generic
static int gt_spmlist_parse_ascii_generic(GtFile *infp,
    GtUword min_length, GtSpmproc proc_e, GtSpmprocA proc_a, void *data,
    GtError *err)
{
  int had_err = 0;
  GtStr *line;
  gt_error_check(err);
  line = gt_str_new();
  while (!had_err && gt_str_read_next_line_generic(line, infp) != EOF)
  {
    had_err = parse_line(line, min_length, proc_e, proc_a, data, err);
    gt_str_reset(line);
  }
  gt_str_delete(line);
  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %r9, %rbx
movq %r8, 0x10(%rsp)
movq %rcx, 0x8(%rsp)
movq %rdx, %r12
movq %rsi, %r13
movq %rdi, %rbp
testq %r9, %r9
je 0x1d5ac9
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0x1d5b3b
callq 0x1208f8
movq %rax, %r14
movq %rax, %rdi
movq %rbp, %rsi
callq 0x121005
cmpl $-0x1, %eax
je 0x1d5b1e
movq %r14, %rdi
movq %r13, %rsi
movq %r12, %rdx
movq 0x8(%rsp), %rcx
movq 0x10(%rsp), %r8
movq %rbx, %r9
callq 0x1d719b
movl %eax, %r15d
movq %r14, %rdi
callq 0x120db4
testl %r15d, %r15d
jne 0x1d5b21
movq %r14, %rdi
movq %rbp, %rsi
callq 0x121005
cmpl $-0x1, %eax
jne 0x1d5ae1
jmp 0x1d5b21
xorl %r15d, %r15d
movq %r14, %rdi
callq 0x121b03
movl %r15d, %eax
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x6d263
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-spmproc.c
// Function: gt_spmproc_skip
void gt_spmproc_skip(GtUword suffix_seqnum, GtUword prefix_seqnum,
  GtUword length, bool suffixseq_direct, bool prefixseq_direct,
  void *data)
{
  GtSpmprocSkipData *d = data;

  if (d->to_skip != NULL)
  {
    if ((bool)GT_ISIBITSET(d->to_skip, suffix_seqnum) ||
        (bool)GT_ISIBITSET(d->to_skip, prefix_seqnum))
    {
      d->skipped_counter++;
      return;
    }
  }
  if (d->out.e.proc != NULL)
  {
    d->out.e.proc(suffix_seqnum, prefix_seqnum, length, suffixseq_direct,
                  prefixseq_direct, d->out.e.data);
  }
}

// Assembly:
movl %ecx, %eax
movq (%r9), %r10
testq %r10, %r10
je 0x1d75cf
movq %rdi, %rcx
shrq $0x6, %rcx
movq (%r10,%rcx,8), %r11
movl %edi, %ecx
shlq %cl, %r11
shrq $0x3f, %r11
jne 0x1d75ca
movabsq $-0x8000000000000000, %r11 # imm = 0x8000000000000000
movl %esi, %ecx
shrq %cl, %r11
movq %rsi, %rcx
shrq $0x6, %rcx
testq %r11, (%r10,%rcx,8)
je 0x1d75cf
incq 0x18(%r9)
retq
movq 0x8(%r9), %r11
testq %r11, %r11
je 0x1d75e6
movq 0x10(%r9), %r9
movzbl %al, %ecx
movzbl %r8b, %r8d
jmpq *%r11
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-spmproc.c
// Function: gt_spmproc_a_skip
void gt_spmproc_a_skip(GtUword suffix_seqnum,
                       GtUword prefix_seqnum,
                       GtUword suffix_length,
                       GtUword prefix_length,
                       GtUword unit_edist,
                       bool suffixseq_direct,
                       bool prefixseq_direct,
                       void *data)
{
  GtSpmprocSkipData *d = data;

  if (d->to_skip != NULL)
  {
    if ((bool)GT_ISIBITSET(d->to_skip, suffix_seqnum) ||
        (bool)GT_ISIBITSET(d->to_skip, prefix_seqnum))
    {
      d->skipped_counter++;
      return;
    }
  }

  if (d->out.a.proc != NULL)
  {
    d->out.a.proc(suffix_seqnum, prefix_seqnum, suffix_length, prefix_length,
                unit_edist, suffixseq_direct, prefixseq_direct, d->out.a.data);
  }
}

// Assembly:
pushq %rbx
movq %rcx, %rax
movq 0x18(%rsp), %r10
movq (%r10), %r11
testq %r11, %r11
je 0x1d7630
movq %rdi, %rcx
shrq $0x6, %rcx
movq (%r11,%rcx,8), %rbx
movl %edi, %ecx
shlq %cl, %rbx
shrq $0x3f, %rbx
jne 0x1d762a
movabsq $-0x8000000000000000, %rbx # imm = 0x8000000000000000
movl %esi, %ecx
shrq %cl, %rbx
movq %rsi, %rcx
shrq $0x6, %rcx
testq %rbx, (%r11,%rcx,8)
je 0x1d7630
incq 0x18(%r10)
jmp 0x1d7653
movq 0x8(%r10), %r11
testq %r11, %r11
je 0x1d7653
movb 0x10(%rsp), %cl
movzbl %cl, %ebx
movzbl %r9b, %r9d
movq %rax, %rcx
pushq 0x10(%r10)
pushq %rbx
callq *%r11
addq $0x10, %rsp
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-spmproc.c
// Function: gt_spmproc_skip_unit_test
int gt_spmproc_skip_unit_test(GtError *err)
{
  int had_err = 0;
  GtSpmprocSkipData d;
  bool skipped;

  gt_error_check(err);
  GT_INITBITTAB(d.to_skip, 4);
  GT_SETIBIT(d.to_skip, 1);
  GT_SETIBIT(d.to_skip, 2);
  GT_SPMPROC_SKIP_TEST(0UL, 1UL, true);
  GT_SPMPROC_SKIP_TEST(1UL, 2UL, true);
  GT_SPMPROC_SKIP_TEST(2UL, 3UL, true);
  GT_SPMPROC_SKIP_TEST(0UL, 3UL, false);

  gt_free(d.to_skip);

  return had_err;
}

// Assembly:
pushq %rbx
testq %rdi, %rdi
je 0x1d7664
callq 0x101a9a
testb %al, %al
jne 0x1d76a0
leaq 0x1e1147(%rip), %rbx    # 0x3b87b2
movl $0x8, %esi
xorl %edi, %edi
movq %rbx, %rdx
movl $0x7e, %ecx
callq 0x1094e6
movabsq $0x6000000000000000, %rcx # imm = 0x6000000000000000
movq %rcx, (%rax)
movq %rax, %rdi
movq %rbx, %rsi
movl $0x86, %edx
callq 0x109670
xorl %eax, %eax
popq %rbx
retq
callq 0x6d643
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-strgraph.c
// Function: gt_strgraph_show_limits
void gt_strgraph_show_limits(void)
{
  printf("# max number of reads: "GT_WU"\n", (GtUword) GT_STRGRAPH_N_READS_MAX);
  printf("# max read length: "FormatGtStrgraphLength"\n",
      PRINTGtStrgraphLengthcast(GT_STRGRAPH_LENGTH_MAX));
  printf("# max degree of a vertex: "FormatGtStrgraphVEdgenum"\n",
      PRINTGtStrgraphVEdgenumcast(GT_STRGRAPH_V_EDGENUM_MAX));
  printf("# max number of spm: "FormatGtStrgraphEdgenum"\n",
      PRINTGtStrgraphEdgenumcast(GT_STRGRAPH_NOFSPM_MAX));
  printf("# compile-time chosen representations\n");
  printf("# - counts: %s\n",   GT_STRGRAPH_COUNTS_REPRESENTATION);
  printf("# - vertices: %s\n", GT_STRGRAPH_VERTICES_REPRESENTATION);
  printf("# - edges: %s\n",    GT_STRGRAPH_EDGES_REPRESENTATION);
}

// Assembly:
pushq %rbx
leaq 0x1e1120(%rip), %rdi    # 0x3b8845
movabsq $0x7ffffffffffffffe, %rbx # imm = 0x7FFFFFFFFFFFFFFE
movq %rbx, %rsi
xorl %eax, %eax
callq 0x17070
leaq 0x1e1121(%rip), %rdi    # 0x3b8861
movq $-0x1, %rsi
xorl %eax, %eax
callq 0x17070
leaq 0x1e1124(%rip), %rdi    # 0x3b8879
movq $-0x2, %rsi
xorl %eax, %eax
callq 0x17070
incq %rbx
leaq 0x1e112b(%rip), %rdi    # 0x3b8898
movq %rbx, %rsi
xorl %eax, %eax
callq 0x17070
leaq 0x1e3e9e(%rip), %rdi    # 0x3bb61c
callq 0x17bd0
leaq 0x1e1128(%rip), %rdi    # 0x3b88b2
leaq 0x1e1131(%rip), %rsi    # 0x3b88c2
xorl %eax, %eax
callq 0x17070
leaq 0x1e113b(%rip), %rdi    # 0x3b88da
leaq 0x1e1097(%rip), %rsi    # 0x3b883d
xorl %eax, %eax
callq 0x17070
leaq 0x1e1138(%rip), %rdi    # 0x3b88ec
leaq 0x1e107b(%rip), %rsi    # 0x3b8836
xorl %eax, %eax
popq %rbx
jmp 0x17070
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-strgraph.c
// Function: gt_strgraph_longest_read
GtStrgraphLength gt_strgraph_longest_read(GtStrgraph *strgraph)
{
  if (strgraph->fixlen > 0)
  {
    return strgraph->fixlen;
  }
  else
  {
    GtStrgraphLength seqlen, maxseqlen;
    GtStrgraphVnum i;

    gt_assert(strgraph->encseq != NULL);
    maxseqlen = 0;
    for (i = 0; i < GT_STRGRAPH_NOFREADS(strgraph); i++)
    {
      seqlen = (GtStrgraphLength)gt_encseq_seqlength(strgraph->encseq,
          (GtUword)i);
      if (seqlen > maxseqlen)
        maxseqlen = seqlen;
    }
    gt_assert(maxseqlen > 0);
    gt_assert(sizeof (GtStrgraphLength) >= sizeof (GtUword) ||
        maxseqlen <= GT_STRGRAPH_LENGTH_MAX);
    return maxseqlen;
  }
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq 0x8(%rdi), %r14
testq %r14, %r14
jne 0x1d7818
movq %rdi, %rbx
cmpq $0x0, (%rdi)
je 0x1d7821
cmpq $0x2, 0x80(%rbx)
jae 0x1d77e9
xorl %r14d, %r14d
jmp 0x1d7813
xorl %r15d, %r15d
xorl %r14d, %r14d
movq (%rbx), %rdi
movq %r15, %rsi
callq 0xeffd3
cmpq %r14, %rax
cmovaq %rax, %r14
incq %r15
movq 0x80(%rbx), %rax
shrq %rax
cmpq %rax, %r15
jb 0x1d77ef
testq %r14, %r14
je 0x1d7826
movq %r14, %rax
popq %rbx
popq %r14
popq %r15
retq
callq 0x6d6b3
callq 0x6d67a
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-strgraph.c
// Function: gt_strgraph_largest_count
GtStrgraphCount gt_strgraph_largest_count(GtStrgraph *strgraph)
{
  GtStrgraphCount count, maxcount;
  GtStrgraphVnum i;
  maxcount = 0;

  gt_assert(strgraph != NULL &&\
            strgraph->__small_counts != NULL &&
            strgraph->__large_counts != NULL);
  for (i = 0; i < (GT_STRGRAPH_NOFVERTICES(strgraph)); i++)
  {
    GT_STRGRAPH_GET_COUNT(strgraph, count, i);
    if (count > maxcount)
      maxcount = count;
  }
  return maxcount;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x1d78b2
movq %rdi, %rbx
cmpq $0x0, 0x40(%rdi)
je 0x1d78b2
cmpq $0x0, 0x48(%rbx)
je 0x1d78b2
cmpq $0x0, 0x80(%rbx)
je 0x1d789b
xorl %r12d, %r12d
movq %rsp, %r15
xorl %r14d, %r14d
movq 0x40(%rbx), %rax
movzbl (%rax,%r12), %eax
cmpq $0xff, %rax
jne 0x1d7886
movq 0x48(%rbx), %rdi
movq %r12, (%rsp)
movq %r15, %rsi
callq 0x10620e
testq %rax, %rax
je 0x1d78ad
movq 0x8(%rax), %rax
cmpq %r14, %rax
cmovaq %rax, %r14
incq %r12
cmpq 0x80(%rbx), %r12
jb 0x1d785c
jmp 0x1d789e
xorl %r14d, %r14d
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
callq 0x6d6ec
callq 0x6d725
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-strgraph.c
// Function: gt_strgraph_counts_sum
GtStrgraphEdgenum gt_strgraph_counts_sum(GtStrgraph *strgraph)
{
  GtStrgraphCount count;
  GtStrgraphEdgenum sum;
  GtStrgraphVnum i;
  sum = 0;
  for (i = 0; i < (GT_STRGRAPH_NOFVERTICES(strgraph)); i++)
  {
    gt_assert(sizeof (GtStrgraphEdgenum) >= sizeof (GtStrgraphVEdgenum));
    GT_STRGRAPH_GET_COUNT(strgraph, count, i);
    sum += count;
  }
  return sum;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
cmpq $0x0, 0x80(%rdi)
je 0x1d7910
movq %rdi, %rbx
xorl %r12d, %r12d
movq %rsp, %r15
xorl %r14d, %r14d
movq 0x40(%rbx), %rax
movzbl (%rax,%r12), %eax
cmpq $0xff, %rax
jne 0x1d78ff
movq 0x48(%rbx), %rdi
movq %r12, (%rsp)
movq %r15, %rsi
callq 0x10620e
testq %rax, %rax
je 0x1d7922
movq 0x8(%rax), %rax
addq %rax, %r14
incq %r12
cmpq 0x80(%rbx), %r12
jb 0x1d78d5
jmp 0x1d7913
xorl %r14d, %r14d
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
callq 0x6d75e
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-strgraph.c
// Function: gt_strgraph_new
GtStrgraph* gt_strgraph_new(GtUword nofreads)
{
  GtStrgraph *strgraph;
  strgraph = gt_calloc((size_t)1, sizeof (GtStrgraph));
  strgraph->state = GT_STRGRAPH_PREPARATION;
  strgraph->load_self_spm = false;
  strgraph->minmatchlen = GT_STRGRAPH_LENGTH_MAX;
  strgraph->rlt = NULL;
  gt_strgraph_show_limits_debug_log();
  GT_STRGRAPH_CHECK_NOFREADS(nofreads);
  GT_STRGRAPH_SET_NOFVERTICES(strgraph, (GtStrgraphVnum)nofreads << 1);
  GT_STRGRAPH_ALLOC_COUNTS(strgraph, GT_STRGRAPH_NOFVERTICES(strgraph));
  return strgraph;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
subq $0x30, %rsp
movq %rdi, %r14
leaq 0x1e0ff3(%rip), %r15    # 0x3b892d
movl $0x1, %edi
movl $0xa0, %esi
movq %r15, %rdx
movl $0x191, %ecx            # imm = 0x191
callq 0x1093ef
movq %rax, %rbx
movl $0x0, 0x10(%rax)
movb $0x0, 0x28(%rax)
movq $-0x1, 0x30(%rax)
movq $0x0, 0x38(%rax)
leaq 0x1e0e8e(%rip), %rdi    # 0x3b8804
leaq 0x1e0ec0(%rip), %rsi    # 0x3b883d
leaq 0x1e0eb2(%rip), %rdx    # 0x3b8836
xorl %eax, %eax
callq 0x108e02
addq %r14, %r14
movq %r14, 0x80(%rbx)
movl $0x1, %esi
movq %r14, %rdi
movq %r15, %rdx
movl $0x199, %ecx            # imm = 0x199
callq 0x1093ef
movq %rax, 0x40(%rbx)
movups 0x2edbbb(%rip), %xmm0   # 0x4c5570
movups %xmm0, 0x20(%rsp)
movups 0x2edb9f(%rip), %xmm0   # 0x4c5560
movups %xmm0, 0x10(%rsp)
movups 0x2edb83(%rip), %xmm0   # 0x4c5550
movups %xmm0, (%rsp)
callq 0x1060b4
movq %rax, 0x48(%rbx)
movq 0x80(%rbx), %rax
movq %rax, 0x50(%rbx)
movq %rbx, %rax
addq $0x30, %rsp
popq %rbx
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-strgraph.c
// Function: gt_strgraph_delete
void gt_strgraph_delete(GtStrgraph *strgraph)
{
  if (strgraph != NULL)
  {
    GT_STRGRAPH_FREE_VERTICES(strgraph);
    GT_STRGRAPH_FREE_EDGES(strgraph);
    GT_STRGRAPH_FREE_COUNTS(strgraph);
    gt_reads_libraries_table_delete(strgraph->rlt);
    gt_free(strgraph);
  }
}

// Assembly:
testq %rdi, %rdi
je 0x1d7f08
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq 0x58(%rdi), %r14
testq %r14, %r14
je 0x1d7e00
movq (%r14), %rdi
leaq 0x192005(%rip), %r15    # 0x369de8
movq %r15, %rsi
movl $0x5d, %edx
callq 0x109670
movq %r14, %rdi
movq %r15, %rsi
movl $0x5e, %edx
callq 0x109670
movq 0x70(%rbx), %r14
testq %r14, %r14
je 0x1d7e30
movq (%r14), %rdi
leaq 0x191fd5(%rip), %r15    # 0x369de8
movq %r15, %rsi
movl $0x5d, %edx
callq 0x109670
movq %r14, %rdi
movq %r15, %rsi
movl $0x5e, %edx
callq 0x109670
leaq 0x58(%rbx), %r12
movq 0x60(%rbx), %r14
testq %r14, %r14
je 0x1d7e64
movq (%r14), %rdi
leaq 0x191fa1(%rip), %r15    # 0x369de8
movq %r15, %rsi
movl $0x5d, %edx
callq 0x109670
movq %r14, %rdi
movq %r15, %rsi
movl $0x5e, %edx
callq 0x109670
movq $0x0, 0x70(%rbx)
xorps %xmm0, %xmm0
movups %xmm0, (%r12)
movq 0x88(%rbx), %r14
testq %r14, %r14
je 0x1d7ea7
movq (%r14), %rdi
leaq 0x191f5e(%rip), %r15    # 0x369de8
movq %r15, %rsi
movl $0x5d, %edx
callq 0x109670
movq %r14, %rdi
movq %r15, %rsi
movl $0x5e, %edx
callq 0x109670
xorl %r14d, %r14d
movq %r14, 0x88(%rbx)
movq 0x40(%rbx), %rdi
leaq 0x1e0a71(%rip), %rsi    # 0x3b892d
movl $0x1ce, %edx            # imm = 0x1CE
callq 0x109670
movq %r14, 0x40(%rbx)
movq 0x48(%rbx), %rdi
testq %rdi, %rdi
je 0x1d7ed8
callq 0x106d10
movq $0x0, 0x48(%rbx)
movq 0x38(%rbx), %rdi
callq 0x1e8c73
leaq 0x1e0a3d(%rip), %rsi    # 0x3b892d
movq %rbx, %rdi
movl $0x1d0, %edx            # imm = 0x1D0
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-strgraph.c
// Function: gt_strgraph_load_reads_library_table
int gt_strgraph_load_reads_library_table(GtStrgraph *strgraph,
    FILE *rlt_fp, GtError *err)
{
  gt_assert(strgraph != NULL);
  gt_assert(strgraph->rlt == NULL);
  strgraph->rlt = gt_reads_libraries_table_load(rlt_fp, err);
  return (strgraph->rlt == NULL) ? -1 : 0;
}

// Assembly:
pushq %rbx
testq %rdi, %rdi
je 0x1d7f34
movq %rdi, %rbx
cmpq $0x0, 0x38(%rdi)
jne 0x1d7f39
movq %rsi, %rdi
movq %rdx, %rsi
callq 0x1e8df1
movq %rax, 0x38(%rbx)
xorl %ecx, %ecx
cmpq $0x1, %rax
sbbl %ecx, %ecx
movl %ecx, %eax
popq %rbx
retq
callq 0x6d8ed
callq 0x6d8b4
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/rdj-strgraph.c
// Function: gt_strgraph_get_file
static GtFile* gt_strgraph_get_file(const char *indexname, const char *suffix,
    bool write, bool gzipped)
{
  GtFile *file;
  GtStr *filename;
  GtError *err;

  err = gt_error_new();
  filename = gt_str_new_cstr(indexname);
  gt_str_append_cstr(filename, suffix);
  if (!write && !gt_file_exists(gt_str_get(filename)))
  {
    fprintf(stderr, "file %s does not exist\n", gt_str_get(filename));
    exit(EXIT_FAILURE);
  }
  file = gt_file_open(gzipped ? GT_FILE_MODE_GZIP : GT_FILE_MODE_UNCOMPRESSED,
      gt_str_get(filename), write ? "wb" : "r", err);
  if (file == NULL)
  {
    fprintf(stderr, "%s", gt_error_get(err));
    exit(EXIT_FAILURE);
  }
  gt_str_delete(filename);
  gt_error_delete(err);
  return file;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movl %ecx, %ebp
movl %edx, %r15d
movq %rsi, %r12
movq %rdi, %r14
callq 0x1019b4
movq %rax, %rbx
movq %r14, %rdi
callq 0x120955
movq %rax, %r14
movq %rax, %rdi
movq %r12, %rsi
callq 0x12097f
testl %r15d, %r15d
je 0x1d8964
leaq 0x1861ab(%rip), %r15    # 0x35eb0d
jmp 0x1d897f
movq %r14, %rdi
callq 0x120d23
movq %rax, %rdi
callq 0x10415c
testb %al, %al
je 0x1d89c7
leaq 0x18b54a(%rip), %r15    # 0x363ec9
movzbl %bpl, %ebp
movq %r14, %rdi
callq 0x120d23
movl %ebp, %edi
movq %rax, %rsi
movq %r15, %rdx
movq %rbx, %rcx
callq 0x1039a2
testq %rax, %rax
je 0x1d89bf
movq %rax, %r15
movq %r14, %rdi
callq 0x121b03
movq %rbx, %rdi
callq 0x101b35
movq %r15, %rax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
movq %rbx, %rdi
callq 0x6df8e
movq %r14, %rdi
callq 0x6df62