LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/match/rdj-contfinder.c
// Function: gt_contfinder_radixsort_str_eqlen_tester
void gt_contfinder_radixsort_str_eqlen_tester(GtContfinder *contfinder,
    bool mirrored, GtUword depth,
    GtUword maxdepth, bool print)
{
  GtUword *suffixes, totallength, width, i;
  GtRadixsortstringinfo *rsi;

  totallength = (GtUword) contfinder->nofseqs * contfinder->len - 1;
  width = mirrored ? GT_MULT2(totallength + 1) : (totallength + 1);
  rsi = gt_radixsort_str_new(contfinder->twobitencoding,
                             totallength,
                             (GtUword) contfinder->len,
                             GT_MULT2(width));
  suffixes = gt_malloc(sizeof (GtUword) * width);
  for (i = 0; i < width; i++)
  {
    suffixes[i] = i;
  }
  gt_radixsort_str_eqlen(rsi, suffixes, NULL, 0, depth, maxdepth, width);
  if (print)
  {
    for (i = 0; i < width; i++)
    {
      printf(""GT_WU"\n", suffixes[i]);
    }
  }
  gt_free(suffixes);
  gt_radixsort_str_delete(rsi);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rcx, %r14
movl %esi, %ecx
movl 0xc(%rdi), %r13d
movq 0x18(%rdi), %rax
imulq %rax, %r13
leaq -0x1(%r13), %rsi
shlq %cl, %r13
movl %r8d, %ebp
movq %rdx, %r12
movq (%rdi), %rdi
leaq (,%r13,2), %rcx
movq %rax, %rdx
callq 0x2c1918
movq %rax, %rbx
leaq (,%r13,8), %rdi
leaq 0x1d7e7a(%rip), %rsi    # 0x34d2d5
movl $0x3c0, %edx            # imm = 0x3C0
callq 0x93160
movq %rax, %r15
xorl %eax, %eax
cmpq %rax, %r13
je 0x175478
movq %rax, (%r15,%rax,8)
incq %rax
jmp 0x17546a
movq %r13, (%rsp)
movq %rbx, %rdi
movq %r15, %rsi
xorl %edx, %edx
xorl %ecx, %ecx
movq %r12, %r8
movq %r14, %r9
callq 0x2c1b30
testb %bpl, %bpl
je 0x1754b8
leaq 0x17b59e(%rip), %r14    # 0x2f0a3b
xorl %r12d, %r12d
cmpq %r12, %r13
je 0x1754b8
movq (%r15,%r12,8), %rsi
movq %r14, %rdi
xorl %eax, %eax
callq 0x17070
incq %r12
jmp 0x1754a0
leaq 0x1d7e16(%rip), %rsi    # 0x34d2d5
movq %r15, %rdi
movl $0x3cd, %edx            # imm = 0x3CD
callq 0x936f9
movq %rbx, %rdi
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x2c1a84
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/match/rdj-contigpaths.c
// Function: gt_contigpaths_get_file
static GtFile* gt_contigpaths_get_file(const char *indexname,
    const char *suffix, const char* mode, GtError *err)
{
  GtStr *path;
  GtFile *file;

  path = gt_str_new_cstr(indexname);
  gt_str_append_cstr(path, suffix);
  file = gt_file_new(gt_str_get(path), mode, err);
  gt_str_delete(path);
  return file;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rcx, %rbx
movq %rdx, %r14
movq %rsi, %r15
callq 0xacbd1
movq %rax, %r12
movq %rax, %rdi
movq %r15, %rsi
callq 0xacbfb
movq %r12, %rdi
callq 0xad1fa
movq %rax, %rdi
movq %r14, %rsi
movq %rbx, %rdx
callq 0x8ce05
movq %rax, %rbx
movq %r12, %rdi
callq 0xae103
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
nop
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/match/rdj-contigs-graph.c
// Function: gt_contigs_graph_delete
void gt_contigs_graph_delete(GtContigsGraph *cg)
{
  if (cg != NULL)
  {
    gt_free(cg->v_spm[0]);
    gt_free(cg->v_spm[1]);
    gt_free(cg->v_scf);
    gt_free(cg->v_d);
    gt_free(cg->v_m);
    gt_free(cg->e_spm[0]);
    gt_free(cg->e_spm[1]);
    gt_free(cg->e_scf);
    gt_free(cg->v_cmp);
    gt_free(cg->units);
    gt_reads_libraries_table_delete(cg->rlt);
    gt_free(cg);
  }
}

// Assembly:
testq %rdi, %rdi
je 0x17716f
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq 0x18(%rdi), %rdi
leaq 0x1d64f4(%rip), %r14    # 0x34d591
movq %r14, %rsi
movl $0x4c3, %edx            # imm = 0x4C3
callq 0x936f9
movq 0x20(%rbx), %rdi
movq %r14, %rsi
movl $0x4c4, %edx            # imm = 0x4C4
callq 0x936f9
movq 0x28(%rbx), %rdi
movq %r14, %rsi
movl $0x4c5, %edx            # imm = 0x4C5
callq 0x936f9
movq 0x30(%rbx), %rdi
movq %r14, %rsi
movl $0x4c6, %edx            # imm = 0x4C6
callq 0x936f9
movq 0x38(%rbx), %rdi
movq %r14, %rsi
movl $0x4c7, %edx            # imm = 0x4C7
callq 0x936f9
movq 0x80(%rbx), %rdi
movq %r14, %rsi
movl $0x4c8, %edx            # imm = 0x4C8
callq 0x936f9
movq 0x88(%rbx), %rdi
movq %r14, %rsi
movl $0x4c9, %edx            # imm = 0x4C9
callq 0x936f9
movq 0x98(%rbx), %rdi
movq %r14, %rsi
movl $0x4ca, %edx            # imm = 0x4CA
callq 0x936f9
movq 0x40(%rbx), %rdi
movq %r14, %rsi
movl $0x4cb, %edx            # imm = 0x4CB
callq 0x936f9
movq 0x58(%rbx), %rdi
movq %r14, %rsi
movl $0x4cc, %edx            # imm = 0x4CC
callq 0x936f9
movq 0xa0(%rbx), %rdi
callq 0x18d518
movq %rbx, %rdi
movq %r14, %rsi
movl $0x4ce, %edx            # imm = 0x4CE
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x936f9
retq
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/match/rdj-contigs-graph.c
// Function: gt_contigs_graph_rm_vertex
void gt_contigs_graph_rm_vertex(GtContigsGraph *cg, GtUword cnum)
{
  GtContigsGraphSpmEdge *edge;
  unsigned int incoming;
  gt_log_log("rm vertex "GT_WU"", cnum);
  for (incoming = 0; incoming < 2U; incoming++)
  {
    for (GT_CONTIGS_GRAPH_EACH_SPM_EDGE(cg, cnum, incoming, edge))
    {
      if (edge->deleted)
        continue;
      gt_contigs_graph_rm_spm_edge(cg, cnum, incoming, edge);
    }
  }
  cg->v_m[cnum].deleted = true;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
leaq 0x1d6172(%rip), %rdi    # 0x34d8bc
xorl %r15d, %r15d
xorl %eax, %eax
callq 0x92a82
cmpq $0x2, %r15
je 0x1777b6
movq 0x18(%r14,%r15,8), %rax
movq 0x80(%r14,%r15,8), %rcx
movq (%rax,%rbx,8), %rdx
shrq $0x10, %rdx
leaq (%rcx,%rdx,8), %r12
movq 0x8(%rax,%rbx,8), %rdx
shrq $0x10, %rdx
leaq (%rcx,%rdx,8), %rdx
cmpq %rdx, %r12
jae 0x1777b1
testb $0x40, 0x7(%r12)
jne 0x1777ab
movq %r14, %rdi
movq %rbx, %rsi
movl %r15d, %edx
movq %r12, %rcx
callq 0x1775b3
movq 0x18(%r14,%r15,8), %rax
movq 0x80(%r14,%r15,8), %rcx
addq $0x8, %r12
jmp 0x177773
incq %r15
jmp 0x177754
movq 0x38(%r14), %rax
orb $0x1, (%rax,%rbx)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/match/rdj-contigs-graph.c
// Function: gt_contigs_graph_nof_optional_neighbours
uint64_t gt_contigs_graph_nof_optional_neighbours(GtContigsGraph *cg,
    GtUword cnum, unsigned int incoming)
{
  uint64_t n = 0;
  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))
      n++;
  }
  return n;
}

// Assembly:
movl %edx, %eax
movq 0x18(%rdi,%rax,8), %rcx
movq 0x80(%rdi,%rax,8), %rax
movq (%rcx,%rsi,8), %rdx
movq 0x8(%rcx,%rsi,8), %rsi
shrq $0x10, %rdx
leaq (%rax,%rdx,8), %rcx
shrq $0x10, %rsi
leaq (%rax,%rsi,8), %rdx
xorl %eax, %eax
cmpq %rdx, %rcx
jae 0x177819
testb $0x40, 0x7(%rcx)
jne 0x177813
movq 0x38(%rdi), %rsi
movl (%rcx), %r8d
movzbl (%rsi,%r8), %esi
btl $0x1, %esi
adcq $0x0, %rax
addq $0x8, %rcx
jmp 0x1777f4
retq
// File: /workspace/github_c_makefile_star2_O2/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
movq %rsi, %r14
movq %rdi, %r15
movl %edx, %r13d
movq 0x18(%rdi,%r13,8), %rcx
movq 0x80(%rdi,%r13,8), %rax
movq (%rcx,%rsi,8), %rdx
shrq $0x10, %rdx
leaq (%rax,%rdx,8), %r12
movq 0x8(%rcx,%r14,8), %rcx
shrq $0x10, %rcx
leaq (%rax,%rcx,8), %rax
cmpq %rax, %r12
jae 0x1778b4
testb $0x40, 0x7(%r12)
jne 0x1778a1
movq 0x38(%r15), %rax
movl (%r12), %ecx
testb $0x2, (%rax,%rcx)
je 0x1778a1
movq %r15, %rdi
movq %r14, %rsi
movl %ebx, %edx
movq %r12, %rcx
callq 0x1775b3
movq 0x18(%r15), %rax
movl (%r12), %esi
cmpw $0x0, (%rax,%rsi,8)
je 0x177899
movq 0x20(%r15), %rax
cmpw $0x0, (%rax,%rsi,8)
jne 0x1778a1
movq %r15, %rdi
callq 0x177735
addq $0x8, %r12
movq 0x18(%r15,%r13,8), %rcx
movq 0x80(%r15,%r13,8), %rax
jmp 0x177847
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O2/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 %r12
pushq %rbx
testq %rdi, %rdi
je 0x177aee
movq %rdi, %rbx
xorl %ecx, %ecx
movq (%rbx), %rax
cmpq %rax, %rcx
jae 0x177a77
movq 0x38(%rbx), %rax
andb $-0x41, (%rax,%rcx)
movq 0x38(%rbx), %rax
andb $0x7f, (%rax,%rcx)
movq 0x38(%rbx), %rax
andb $-0x11, (%rax,%rcx)
incq %rcx
jmp 0x177a52
pushq $0x1c
popq %r12
xorl %r14d, %r14d
movzbl %sil, %ebp
pushq $0x1
popq %r15
cmpq %rax, %r14
jae 0x177ae5
movq 0x38(%rbx), %rax
movb (%rax,%r14), %al
testb $0x1, %al
jne 0x177ad9
movq 0x30(%rbx), %rcx
movss (%rcx,%r12), %xmm0
ucomiss 0x1d5abc(%rip), %xmm0   # 0x34d564
jb 0x177ad9
testb $0x40, %al
jne 0x177ac5
movq %rbx, %rdi
movq %r14, %rsi
xorl %edx, %edx
movl %ebp, %ecx
callq 0x1778be
movq 0x38(%rbx), %rax
movb (%rax,%r14), %al
testb %al, %al
js 0x177ad9
movq %rbx, %rdi
movq %r14, %rsi
movl %r15d, %edx
movl %ebp, %ecx
callq 0x1778be
incq %r14
movq (%rbx), %rax
addq $0x20, %r12
jmp 0x177a86
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
movq 0x2c0473(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x16d514(%rip), %rsi    # 0x2e5013
leaq 0x1d5a62(%rip), %rdx    # 0x34d568
leaq 0x1d5dbd(%rip), %rcx    # 0x34d8ca
leaq 0x1d5a7d(%rip), %r8     # 0x34d591
movl $0x32e, %r9d            # imm = 0x32E
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x1787df
movq %rsi, %r15
movq %rdi, %rbx
leaq 0x1d5ad3(%rip), %rsi    # 0x34e21a
pushq $0x34
popq %rdx
movl $0xa8, %edi
callq 0x93160
movq %rax, %r14
movq %rbx, (%rax)
movq %r15, 0x8(%rax)
xorl %r15d, %r15d
movb %r15b, 0x10(%rax)
movq %rbx, %rdi
callq 0x705a1
movq %rax, 0x60(%r14)
andq $0x0, 0x50(%r14)
movaps 0x1d5a73(%rip), %xmm0   # 0x34e1f0
movups %xmm0, 0x88(%r14)
xorps %xmm0, %xmm0
movups %xmm0, 0x68(%r14)
movb %r15b, 0x11(%r14)
movups %xmm0, 0x28(%r14)
andq $0x0, 0x38(%r14)
movups %xmm0, 0x78(%r14)
callq 0xacb84
movq %rax, 0x40(%r14)
callq 0xacb84
movq %rax, 0x48(%r14)
callq 0xba9f0
movq %rax, 0x18(%r14)
movq %rbx, %rdi
xorl %esi, %esi
xorl %edx, %edx
callq 0x72260
movq %rax, 0x20(%r14)
xorps %xmm0, %xmm0
movups %xmm0, 0x98(%r14)
movq %r14, %rax
popq %rbx
popq %r14
popq %r15
retq
movq 0x2bf782(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x16c823(%rip), %rsi    # 0x2e5013
leaq 0x1d481a(%rip), %rdx    # 0x34d011
leaq 0x1d5a06(%rip), %rcx    # 0x34e204
leaq 0x1d5a15(%rip), %r8     # 0x34e21a
pushq $0x32
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x81d17
movq (%r15), %rdi
cmpl $0x2, %eax
jne 0x17884b
callq 0x81d1a
jmp 0x178866
callq 0x7055e
movq %rax, %r12
movq (%r15), %rdi
callq 0x705a1
movq %rax, %rcx
movq %r12, %rax
xorl %edx, %edx
divq %rcx
movq %rax, %xmm0
punpckldq 0x16f06d(%rip), %xmm0 # xmm0 = xmm0[0],mem[0],xmm0[1],mem[1]
movq %rax, 0x68(%r15)
subpd 0x16f071(%rip), %xmm0   # 0x2e78f0
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 0x1d5998(%rip), %rdi    # 0x34e239
movb $0x1, %al
callq 0x92a82
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_O2/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 0x178933
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq 0x28(%rdi), %rdi
testq %rdi, %rdi
je 0x1788f6
leaq 0x28(%rbx), %r14
leaq 0x1d5938(%rip), %rsi    # 0x34e21a
pushq $0x68
popq %rdx
callq 0x936f9
xorps %xmm0, %xmm0
movups %xmm0, (%r14)
andq $0x0, 0x10(%r14)
movq 0x40(%rbx), %rdi
callq 0xae103
movq 0x48(%rbx), %rdi
callq 0xae103
movq 0x18(%rbx), %rdi
callq 0xbaa2f
movq 0x20(%rbx), %rdi
callq 0x722ae
leaq 0x1d58f9(%rip), %rsi    # 0x34e21a
pushq $0x6d
popq %rdx
movq %rbx, %rdi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x936f9
retq
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/match/rdj-contigs-writer.c
// Function: gt_contigs_writer_reset_buffers
static void gt_contigs_writer_reset_buffers(GtContigsWriter *contigs_writer)
{
  gt_assert(contigs_writer != NULL);
  contigs_writer->contig.nextfreechar = 0;
  gt_str_reset(contigs_writer->contig_desc);
  gt_str_reset(contigs_writer->path_desc);
  contigs_writer->depthinfo.firstread_copynum = (float)0;
  contigs_writer->depthinfo.internal_copynum = (float)0;
  contigs_writer->depthinfo.lastread_copynum = (float)0;
  contigs_writer->depthinfo.depth = 0;
  contigs_writer->depthinfo.length = 0;
  contigs_writer->depthinfo.astat = (float)0;
}

// Assembly:
pushq %rbx
movq %rdi, %rbx
andq $0x0, 0x38(%rdi)
movq 0x40(%rdi), %rdi
callq 0xad357
movq 0x48(%rbx), %rdi
callq 0xad357
xorps %xmm0, %xmm0
movups %xmm0, 0x88(%rbx)
movups %xmm0, 0x78(%rbx)
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x17904b
cmpq $0x0, 0x50(%rdi)
je 0x179037
movq 0x18(%rdi), %rdi
jmp 0xbae5e
leaq 0x1d5307(%rip), %rax    # 0x34e345
movq %rsi, %rdi
movq %rax, %rsi
xorl %eax, %eax
jmp 0x92e71
pushq %rax
movq 0x2bef15(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x16bfb6(%rip), %rsi    # 0x2e5013
leaq 0x1d51e9(%rip), %rdx    # 0x34e24d
leaq 0x1d52bd(%rip), %rcx    # 0x34e328
leaq 0x1d51a8(%rip), %r8     # 0x34e21a
movl $0x132, %r9d            # imm = 0x132
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/match/rdj-errfind.c
// Function: gt_errfind_reset
static inline void gt_errfind_reset(GtBUstate_errfind *state)
{
  unsigned int i;
  state->currentchar = 0;
  for (i = 0; i < state->alphasize; i++)
    state->count[i] = 0;
  state->seprange = false;
}

// Assembly:
andl $0x0, 0x1c(%rdi)
movl 0x18(%rdi), %eax
xorl %ecx, %ecx
cmpq %rax, %rcx
jae 0x179b4d
movq 0x38(%rdi), %rdx
andq $0x0, (%rdx,%rcx,8)
incq %rcx
jmp 0x179b3a
movb $0x0, 0x40(%rdi)
retq
// File: /workspace/github_c_makefile_star2_O2/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), %rcx
decq %rcx
cmpq %rdi, %rcx
jbe 0x179c10
movq %rbx, %rdi
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
jmp 0x179b31
movb 0x40(%rbx), %al
testb %al, %al
jne 0x179cba
movq %rsi, %r15
movq %rdi, %r14
cmpq %rdi, %rcx
jne 0x179c53
leaq (%r15,%r14), %r12
movq 0x10(%rbx), %rdi
callq 0x7055e
cmpq %rax, %r12
je 0x179c4a
movq 0x10(%rbx), %rdi
movq %r12, %rsi
xorl %edx, %edx
callq 0x70e8f
testb %al, %al
je 0x179c50
movb $0x1, 0x40(%rbx)
jmp 0x179cba
movb 0x40(%rbx), %al
testb $0x1, %al
jne 0x179cba
movl 0x1c(%rbx), %eax
cmpl 0x18(%rbx), %eax
jae 0x179cba
movq 0x38(%rbx), %rcx
movq (%rcx,%rax,8), %r12
leaq 0x1(%r12), %rdx
movq %rdx, (%rcx,%rax,8)
cmpq 0x28(%rbx), %rdx
ja 0x179ca9
decq %r15
movq 0x20(%rbx), %r13
addq %r15, %r13
movq 0x10(%rbx), %rdi
callq 0x7055e
cmpq %rax, %r13
jae 0x179cc4
addq 0x20(%rbx), %r15
movl 0x1c(%rbx), %eax
movq %rax, %rcx
imulq 0x28(%rbx), %rcx
shlq $0x3, %rcx
addq 0x30(%rbx), %rcx
movq %r15, (%rcx,%r12,8)
movq 0x20(%rbx), %rcx
decq %rcx
cmpq %r14, %rcx
jne 0x179cba
incl %eax
movl %eax, 0x1c(%rbx)
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
movq 0x2be29d(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x16b33e(%rip), %rsi    # 0x2e5013
leaq 0x1d4743(%rip), %rdx    # 0x34e41f
leaq 0x1d477e(%rip), %rcx    # 0x34e461
leaq 0x1d46ed(%rip), %r8     # 0x34e3d7
pushq $0x56
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x179e2d
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, %rbx
movl 0x18(%rsi), %eax
movb $0x1, %dl
xorl %ecx, %ecx
cmpq %rax, %rcx
jae 0x179d3d
testb $0x1, %dl
je 0x179d3d
movq 0x38(%rbx), %rdx
movq (%rdx,%rcx,8), %rdx
cmpq 0x28(%rbx), %rdx
setae %dl
incq %rcx
jmp 0x179d1f
testb $0x1, %dl
jne 0x179e1f
movb $-0x1, %bpl
xorl %r14d, %r14d
movl %eax, %ecx
cmpq %rcx, %r14
jae 0x179d9b
cmpb $-0x1, %bpl
jne 0x179d9b
movq 0x28(%rbx), %rcx
movq 0x38(%rbx), %rdx
movq (%rdx,%r14,8), %rdx
cmpq %rcx, %rdx
setb %sil
testq %rdx, %rdx
sete %dl
orb %sil, %dl
movb $-0x1, %bpl
jne 0x179d96
movq 0x10(%rbx), %rdi
movq 0x30(%rbx), %rax
imulq %r14, %rcx
movq (%rax,%rcx,8), %rsi
xorl %edx, %edx
callq 0x70bf6
movl %eax, %ebp
movl 0x18(%rbx), %eax
incq %r14
jmp 0x179d4c
cmpb $-0x1, %bpl
je 0x179e1f
movb $0x3, %r14b
subb %bpl, %r14b
xorl %r15d, %r15d
cmpl %eax, %r15d
jae 0x179e1f
movl %r15d, %r15d
movq 0x38(%rbx), %rcx
movq (%rcx,%r15,8), %rcx
testq %rcx, %rcx
je 0x179e1f
cmpq 0x28(%rbx), %rcx
jae 0x179e1a
leaq (,%r15,8), %r12
xorl %r13d, %r13d
cmpq %rcx, %r13
jae 0x179e17
movq 0x28(%rbx), %rax
imulq %r12, %rax
addq 0x30(%rbx), %rax
movq (%rax,%r13,8), %rsi
cmpq 0x58(%rbx), %rsi
jae 0x179def
movl %ebp, %eax
jmp 0x179df9
notq %rsi
addq 0x60(%rbx), %rsi
movl %r14d, %eax
movq 0x68(%rbx), %rdi
testq %rdi, %rdi
je 0x179e12
movzbl %al, %edx
callq 0x1885e3
movq 0x38(%rbx), %rax
movq (%rax,%r15,8), %rcx
incq %r13
jmp 0x179dd0
movl 0x18(%rbx), %eax
incl %r15d
jmp 0x179daa
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x7055e
cmpq %rbx, %rax
jb 0x17ab7a
movq 0x60(%r14), %rax
movzbl (%rax,%rbx), %eax
cmpq $0xff, %rax
jne 0x17ab3a
cmpb $0x0, 0x8(%r14)
je 0x17aba8
movq 0x10(%r14), %rdx
movq 0x68(%r14), %rax
shlq $0x4, %rdx
addq %rax, %rdx
movq %rdx, %rcx
addq $-0x10, %rcx
cmpq %rcx, %rax
ja 0x17ab42
movq %rcx, %rsi
subq %rax, %rsi
sarq %rsi
andq $-0x10, %rsi
leaq (%rax,%rsi), %rdx
cmpq %rbx, (%rax,%rsi)
ja 0x17ab08
jae 0x17ab36
addq $0x10, %rdx
movq %rdx, %rax
jmp 0x17ab0f
movq 0x8(%rdx), %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
movq 0x2bd41f(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x16a4c0(%rip), %rsi    # 0x2e5013
leaq 0x1d3ae1(%rip), %rdx    # 0x34e63b
leaq 0x1d3a78(%rip), %rcx    # 0x34e5d9
leaq 0x1d3a7e(%rip), %r8     # 0x34e5e6
movl $0x8a, %r9d
xorl %eax, %eax
callq 0x17a50
callq 0x17390
movq 0x2bd3e7(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x16a488(%rip), %rsi    # 0x2e5013
leaq 0x1d3a14(%rip), %rdx    # 0x34e5a6
leaq 0x1d3a40(%rip), %rcx    # 0x34e5d9
leaq 0x1d3a46(%rip), %r8     # 0x34e5e6
movl $0x83, %r9d
jmp 0x17ab6e
movq 0x2bd3b9(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x16a45a(%rip), %rsi    # 0x2e5013
leaq 0x1d3a91(%rip), %rdx    # 0x34e651
leaq 0x1d3ab3(%rip), %rcx    # 0x34e67a
leaq 0x1d3a18(%rip), %r8     # 0x34e5e6
pushq $0x61
popq %r9
jmp 0x17ab6e
// File: /workspace/github_c_makefile_star2_O2/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 0x17ad1b
testq %rsi, %rsi
je 0x17ace9
testb $0x1, %dil
je 0x17acfb
movq 0x2bd2a9(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x16a34a(%rip), %rsi    # 0x2e5013
leaq 0x20a680(%rip), %rdx    # 0x385350
leaq 0x1d3a0f(%rip), %rcx    # 0x34e6e6
leaq 0x1d39ad(%rip), %r8     # 0x34e68b
movl $0x13b, %r9d            # imm = 0x13B
jmp 0x17add4
cmpl $0x1, %edi
jne 0x17ad7a
testq %rdx, %rdx
jne 0x17ada8
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 0x17ad4c
popq %rax
retq
movq 0x2bd246(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x16a2e7(%rip), %rsi    # 0x2e5013
leaq 0x1d3971(%rip), %rdx    # 0x34e6a4
leaq 0x1d39ac(%rip), %rcx    # 0x34e6e6
leaq 0x1d394a(%rip), %r8     # 0x34e68b
movl $0x134, %r9d            # imm = 0x134
jmp 0x17add4
movq 0x2bd215(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x16a2b6(%rip), %rsi    # 0x2e5013
leaq 0x1d39c4(%rip), %rdx    # 0x34e728
leaq 0x1d397b(%rip), %rcx    # 0x34e6e6
leaq 0x1d3919(%rip), %r8     # 0x34e68b
movl $0x13f, %r9d            # imm = 0x13F
jmp 0x17add4
movq 0x2bd1e7(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x16a288(%rip), %rsi    # 0x2e5013
leaq 0x1d3971(%rip), %rdx    # 0x34e703
leaq 0x1d394d(%rip), %rcx    # 0x34e6e6
leaq 0x1d38eb(%rip), %r8     # 0x34e68b
movl $0x137, %r9d            # imm = 0x137
jmp 0x17add4
movq 0x2bd1b9(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x16a25a(%rip), %rsi    # 0x2e5013
leaq 0x1d3957(%rip), %rdx    # 0x34e717
leaq 0x1d391f(%rip), %rcx    # 0x34e6e6
leaq 0x1d38bd(%rip), %r8     # 0x34e68b
movl $0x138, %r9d            # imm = 0x138
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/match/rdj-pairwise.c
// Function: gt_rdj_pairwise_approx
void gt_rdj_pairwise_approx(GtOvlfindMode m,  GtEncseq *encseq, bool revcompl,
    bool show_progressbar, double max_error, GtUword min_length,
    bool find_nonmaximal, GtSpmprocA proc, void* procdata, bool cntfilter,
    GtBitsequence *cntreads_in, GtBitsequence **cntreads_out,
    GtUword *nofreads)
{
  gt_assert(rdj_pairwise_check_arguments(m, proc, procdata, cntreads_in,
                            cntreads_out, cntfilter));
  rdj_pairwise_generic(true, m, encseq, revcompl, show_progressbar, false,
      max_error, min_length, find_nonmaximal, NULL, proc, procdata,
      cntfilter, cntreads_in, cntreads_out, nofreads);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x68, %rsp
movl %r9d, %r15d
movq %r8, %r12
movsd %xmm0, 0x60(%rsp)
movl %ecx, 0x54(%rsp)
movl %edx, 0x50(%rsp)
movq %rsi, 0x58(%rsp)
movl %edi, %r13d
movq 0xa0(%rsp), %rsi
movq 0xa8(%rsp), %rdx
movq 0xb8(%rsp), %rbx
movq 0xc0(%rsp), %rbp
movzbl 0xb0(%rsp), %r14d
movq %rbx, %rcx
movq %rbp, %r8
movl %r14d, %r9d
callq 0x17aca5
movq 0xc8(%rsp), %rax
movq %rax, 0x40(%rsp)
movq %rbp, 0x38(%rsp)
movq %rbx, 0x30(%rsp)
movl %r14d, 0x28(%rsp)
movq 0xa8(%rsp), %rax
movq %rax, 0x20(%rsp)
movq 0xa0(%rsp), %rax
movq %rax, 0x18(%rsp)
movl %r15d, 0x8(%rsp)
movq %r12, (%rsp)
andq $0x0, 0x10(%rsp)
pushq $0x1
popq %rdi
movl %r13d, %esi
movq 0x58(%rsp), %rdx
movl 0x50(%rsp), %ecx
movl 0x54(%rsp), %r8d
xorl %r9d, %r9d
movsd 0x60(%rsp), %xmm0
callq 0x17ade0
addq $0x68, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/match/rdj-pairwise.c
// Function: find_approx_overlaps
static inline GtContfind find_approx_overlaps(struct Data *d, double max_error,
    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;
    retval = gt_ovlfind_dp(d->u->seq, d->u->len, NULL, 0, max_error, d->mode,
        min_length, find_nonmaximal, call_spmproc_a, d);
  }
  else
  {
    retval = gt_ovlfind_dp(d->u->seq, d->u->len, d->v->seq, d->v->len,
        max_error, d->mode, min_length, find_nonmaximal, call_spmproc_a, d);
  }
  return retval;
}

// Assembly:
pushq %rbx
movq %rsi, %r9
movq %rdi, %rax
movq 0x18(%rdi), %rcx
movq 0x20(%rdi), %r8
movq 0x10(%rcx), %rsi
cmpq 0x10(%r8), %rsi
jne 0x17b68c
cmpb $0x1, 0x18(%r8)
jne 0x17b68c
movl 0x28(%rax), %r8d
testl $0xfffffffd, %r8d       # imm = 0xFFFFFFFD
jne 0x17b6be
movq (%rcx), %rdi
movq 0x8(%rcx), %rsi
subq $0x8, %rsp
leaq 0x1cc(%rip), %r10       # 0x17b849
movzbl %dl, %r11d
xorl %edx, %edx
xorl %ecx, %ecx
pushq %rax
pushq %r10
pushq %r11
jmp 0x17b6b3
movq (%rcx), %rdi
movq 0x8(%rcx), %rsi
movq (%r8), %r10
movq 0x8(%r8), %rcx
movl 0x28(%rax), %r8d
subq $0x8, %rsp
leaq 0x1a0(%rip), %r11       # 0x17b849
movzbl %dl, %ebx
movq %r10, %rdx
pushq %rax
pushq %r11
pushq %rbx
callq 0x2c7918
addq $0x20, %rsp
popq %rbx
retq
pushq $0x2
popq %rax
jmp 0x17b6bc
// File: /workspace/github_c_makefile_star2_O2/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 0x17b733
cmpb $0x1, 0x18(%r9)
jne 0x17b733
movl 0x28(%r10), %r11d
testl $0xfffffffd, %r11d      # imm = 0xFFFFFFFD
jne 0x17b7b4
movq (%rdx), %rdi
movq 0x8(%rdx), %r8
testb %sil, %sil
je 0x17b7bd
movq 0x20(%rdx), %rdx
subq $0x8, %rsp
leaq 0x19c(%rip), %rbx       # 0x17b8b6
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 0x17b770
movq (%rdx), %rdi
movq 0x8(%rdx), %r11
testb %sil, %sil
je 0x17b77b
movq 0x20(%rdx), %rdx
movq (%r9), %rbx
movq 0x8(%r9), %r8
movq 0x20(%r9), %r9
movl 0x28(%r10), %r14d
subq $0x8, %rsp
leaq 0x159(%rip), %r15       # 0x17b8b6
movzbl %cl, %r12d
movq %r11, %rsi
movq %rbx, %rcx
pushq %r10
pushq %r15
pushq %r12
pushq %rax
pushq %r14
callq 0x2c9597
addq $0x38, %rsp
jmp 0x17b7ac
movq (%r9), %rdx
movq 0x8(%r9), %r9
movl 0x28(%r10), %r8d
subq $0x8, %rsp
leaq 0x125(%rip), %rbx       # 0x17b8b6
movzbl %cl, %r14d
movq %r11, %rsi
movq %r9, %rcx
movq %rax, %r9
pushq %r10
pushq %rbx
pushq %r14
callq 0x2c6514
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
pushq $0x2
popq %rax
addq $0x8, %rsp
jmp 0x17b7ac
subq $0x8, %rsp
leaq 0xee(%rip), %rbx        # 0x17b8b6
movzbl %cl, %r14d
movq %r8, %rsi
xorl %edx, %edx
xorl %ecx, %ecx
movl %r11d, %r8d
jmp 0x17b79b
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/match/rdj-pairwise.c
// Function: mark_contained
static inline void mark_contained(GtContfind c, GtUword u_seqnum,
    GtUword v_seqnum, GtBitsequence *cntreads)
{
  gt_assert(cntreads != NULL);
  switch (c)
  {
    case GT_CONTFIND_U:
      GT_SETIBIT(cntreads, u_seqnum);
      break;
    case GT_CONTFIND_EQ:
      /* convention: skip one with higher seqnum (which is v) */
      if (v_seqnum != u_seqnum)
        GT_SETIBIT(cntreads, v_seqnum);
      break;
    case GT_CONTFIND_V:
      GT_SETIBIT(cntreads, v_seqnum);
      break;
    default:
      /* nothing to do */
      break;
  }
}

// Assembly:
testq %rcx, %rcx
je 0x17b810
movq %rcx, %rax
cmpl $0x4, %edi
je 0x17b7f8
cmpl $0x3, %edi
je 0x17b7f5
cmpl $0x2, %edi
jne 0x17b7f4
cmpq %rsi, %rdx
jne 0x17b7f8
retq
movq %rsi, %rdx
movabsq $-0x8000000000000000, %rsi # imm = 0x8000000000000000
movl %edx, %ecx
shrq %cl, %rsi
shrq $0x6, %rdx
orq %rsi, (%rax,%rdx,8)
retq
pushq %rax
movq 0x2bc750(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x1697f1(%rip), %rsi    # 0x2e5013
leaq 0x1d2f6f(%rip), %rdx    # 0x34e798
leaq 0x1d2fc1(%rip), %rcx    # 0x34e7f1
leaq 0x1d2e54(%rip), %r8     # 0x34e68b
movl $0xa3, %r9d
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x17b885
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 0x17b8a5
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
popq %rax
popq %rcx
popq %rbx
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/match/rdj-spmfind.c
// Function: processleafedge_spmeq
static inline int processleafedge_spmeq(bool firstsucc,
    GtUword fatherdepth,
    GtBUinfo_spmeq *father, GtUword seqnum, GtUword relpos,
    GtBUstate_spmeq *state, GT_UNUSED GtError *err)
{
  if (fatherdepth >= state->minmatchlength)
  {
    if (firstsucc)
    {
      gt_assert(father != NULL);
      father->w_left = state->w_nextfree;
    }
    if (relpos == 0)
      appendtowset_spm(seqnum, state);
    gt_assert(fatherdepth != state->read_length);
    if (relpos + fatherdepth == state->read_length)
      combine_terminal_with_wset(seqnum, seqnum * (state->read_length + 1),
         state->read_length, father->w_left, fatherdepth, state);
  }
  else
  {
#ifdef GT_READJOINER_STATISTICS
    reset_subtree_stats(state);
#endif
    state->w_nextfree = 0;
  }
  return 0;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
movq %r9, %rbx
cmpq %rsi, 0x20(%r9)
jbe 0x17b908
andq $0x0, 0x80(%rbx)
jmp 0x17b971
movq %r8, %r13
movq %rcx, %r15
movq %rdx, %r12
movq %rsi, %r14
testb %dil, %dil
je 0x17b92d
testq %r12, %r12
je 0x17b9a9
movq 0x80(%rbx), %rax
movq %rax, (%r12)
testq %r13, %r13
jne 0x17b93d
movq %r15, %rdi
movq %rbx, %rsi
callq 0x17cf82
movq 0x48(%rbx), %rdx
cmpq %r14, %rdx
je 0x17b97b
addq %r14, %r13
cmpq %rdx, %r13
jne 0x17b971
leaq 0x1(%rdx), %rsi
imulq %r15, %rsi
movq (%r12), %rcx
movq %r15, %rdi
movq %r14, %r8
movq %rbx, %r9
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
jmp 0x17d0e3
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
movq 0x2bc5e6(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x169687(%rip), %rsi    # 0x2e5013
leaq 0x1d2f21(%rip), %rdx    # 0x34e8b4
leaq 0x1d2f04(%rip), %rcx    # 0x34e89e
leaq 0x1d2ecb(%rip), %r8     # 0x34e86c
movl $0x197, %r9d            # imm = 0x197
jmp 0x17b9d5
movq 0x2bc5b8(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x169659(%rip), %rsi    # 0x2e5013
leaq 0x1c9bf2(%rip), %rdx    # 0x3455b3
leaq 0x1d2ed6(%rip), %rcx    # 0x34e89e
leaq 0x1d2e9d(%rip), %r8     # 0x34e86c
movl $0x192, %r9d            # imm = 0x192
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x17ba53
andq $0x0, 0x80(%rbx)
jmp 0x17bb5f
movq %r8, %r15
movq %rcx, %r14
movq %rdx, %rbp
movq %rsi, %r12
movl %edi, %r13d
movq 0x38(%rbx), %rdi
movq %rcx, %rsi
callq 0x75173
testb %r13b, %r13b
je 0x17ba87
testq %rbp, %rbp
je 0x17bb6e
movq 0x80(%rbx), %rcx
movq %rcx, (%rbp)
testq %r15, %r15
jne 0x17badd
movq %r14, %rdi
movq %rbx, %rsi
movq %rax, %r13
callq 0x17cf82
movq %r13, %rax
cmpq %r12, %r13
jne 0x17badd
movq 0x58(%rbx), %rcx
decq %rcx
movq %r14, %rax
cmpq %r14, %rcx
jae 0x17babb
movq %r14, %rax
notq %rax
addq 0x50(%rbx), %rax
movq %rsp, %rdi
movq %rax, (%rdi)
movq 0xe0(%rbx), %rcx
pushq $0x8
popq %rsi
pushq $0x1
popq %rdx
callq 0x17f00
incq 0xe8(%rbx)
movq %r13, %rax
addq %r12, %r15
cmpq %rax, %r15
jne 0x17bb5f
movq 0x68(%rbx), %rcx
cmpq 0x70(%rbx), %rcx
jne 0x17bb53
leaq 0x400(%rcx), %rax
movq %rax, 0x70(%rbx)
movq 0x60(%rbx), %rdi
leaq 0x2000(,%rcx,8), %rsi
leaq 0x1d2d5f(%rip), %rdx    # 0x34e86c
movl $0xf7, %ecx
callq 0x93472
movq %rax, 0x60(%rbx)
movq 0x68(%rbx), %rcx
cmpq 0x70(%rbx), %rcx
jb 0x17bb57
movq 0x2bc43c(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x1694dd(%rip), %rsi    # 0x2e5013
leaq 0x1d2e55(%rip), %rdx    # 0x34e992
leaq 0x1d2e75(%rip), %rcx    # 0x34e9b9
leaq 0x1d2d21(%rip), %r8     # 0x34e86c
movl $0xf8, %r9d
jmp 0x17bb9a
movq 0x60(%rbx), %rax
movq %r14, (%rax,%rcx,8)
incq 0x68(%rbx)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x2bc3f3(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x169494(%rip), %rsi    # 0x2e5013
leaq 0x1c9a2d(%rip), %rdx    # 0x3455b3
leaq 0x1d2dee(%rip), %rcx    # 0x34e97b
leaq 0x1d2cd8(%rip), %r8     # 0x34e86c
movl $0x1b0, %r9d            # imm = 0x1B0
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/match/rdj-spmfind.c
// Function: resetwsetbt_spm
static inline void resetwsetbt_spm(GtBUstate_spm *state)
{
  GtUword i, bsize_sum = 0, nofbltries = 0;
  GtBlindtrie *b;
  printcurrentspace_spm("before resizing");
  for (i = 0; i < state->w_allocated; i++)
  {
    b = (state->w_set + i)->blindtrie;
    if (b != NULL)
    {
      bsize_sum += gt_blindtrie_current_size(b);
      gt_blindtrie_resize(b, 1U);
      nofbltries++;
    }
    else
      break;
  }
  gt_log_log("current number of blindtries: "GT_WU"", nofbltries);
  gt_log_log("total size of the blindtries: %.2f MB", GT_MEGABYTES(bsize_sum));
  printcurrentspace_spm("after resizing");
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rdi, %rbx
leaq 0x1d2294(%rip), %rdi    # 0x34eb1e
callq 0x17d375
pushq $0x8
popq %r13
xorl %r12d, %r12d
pushq $0x1
popq %rbp
xorl %r14d, %r14d
cmpq 0x88(%rbx), %r14
jae 0x17c8d0
movq 0x78(%rbx), %rax
movq (%rax,%r13), %r15
testq %r15, %r15
je 0x17c8d0
movq %r15, %rdi
callq 0x1952ed
addq %rax, %r12
movq %r15, %rdi
movl %ebp, %esi
callq 0x195270
incq %r14
addq $0x10, %r13
jmp 0x17c89c
leaq 0x1d2257(%rip), %rdi    # 0x34eb2e
movq %r14, %rsi
xorl %eax, %eax
callq 0x92a82
movq %r12, %xmm1
punpckldq 0x16aff2(%rip), %xmm1 # xmm1 = xmm1[0],mem[0],xmm1[1],mem[1]
subpd 0x16affa(%rip), %xmm1   # 0x2e78f0
movapd %xmm1, %xmm0
unpckhpd %xmm1, %xmm0            # xmm0 = xmm0[1],xmm1[1]
addsd %xmm1, %xmm0
mulsd 0x16aff6(%rip), %xmm0   # 0x2e7900
leaq 0x1d223f(%rip), %rdi    # 0x34eb50
movb $0x1, %al
callq 0x92a82
leaq 0x1d2257(%rip), %rdi    # 0x34eb76
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x17d375
// File: /workspace/github_c_makefile_star2_O2/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 %r12
pushq %rbx
subq $0x18, %rsp
movq 0x90(%rsi), %rax
movq 0x98(%rsi), %rcx
incq %rcx
movq %rcx, 0x98(%rsi)
cmpq %rax, %rcx
jbe 0x17d0d7
movq %rsi, %rbx
addq 0xa0(%rsi), %rax
cmpq %rax, %rcx
jbe 0x17cfc9
movb $0x1, 0xa8(%rbx)
jmp 0x17d0d7
movq %rdi, %r14
movq 0x80(%rbx), %r12
cmpq 0x88(%rbx), %r12
jne 0x17d07a
leaq 0x400(%r12), %rsi
movq %rsi, 0x88(%rbx)
movq 0x78(%rbx), %rdi
shlq $0x4, %rsi
leaq 0x1d186e(%rip), %rdx    # 0x34e86c
movl $0x8d, %ecx
callq 0x93472
movq %rax, %r15
movq %rax, 0x78(%rbx)
movq 0x88(%rbx), %rax
movq %r12, %rcx
shlq $0x4, %rcx
addq %r15, %rcx
addq $0x8, %rcx
cmpq %rax, %r12
jae 0x17d036
andq $0x0, (%rcx)
incq %r12
addq $0x10, %rcx
jmp 0x17d024
movq 0x80(%rbx), %r12
cmpq %rax, %r12
jb 0x17d07e
movq 0x2baf1f(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x167fc0(%rip), %rsi    # 0x2e5013
leaq 0x1d187c(%rip), %rdx    # 0x34e8d6
leaq 0x1d189c(%rip), %rcx    # 0x34e8fd
leaq 0x1d1804(%rip), %r8     # 0x34e86c
movl $0x90, %r9d
xorl %eax, %eax
callq 0x17a50
callq 0x17390
movq 0x78(%rbx), %r15
movq %r12, %rax
shlq $0x4, %rax
incq %r12
movq %r12, 0x80(%rbx)
movq %r14, (%r15,%rax)
movq 0x8(%r15,%rax), %rdi
testq %rdi, %rdi
je 0x17d0ad
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
jmp 0x1952fa
addq %rax, %r15
movq 0x38(%rbx), %rcx
andq $0x0, (%rsp)
movl $0x1, 0x8(%rsp)
pushq $0x40
popq %rdx
xorl %edi, %edi
xorl %esi, %esi
xorl %r8d, %r8d
xorl %r9d, %r9d
callq 0x1950ec
movq %rax, 0x8(%r15)
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/match/rdj-spmfind.c
// Function: printcurrentspace_spm
static inline void printcurrentspace_spm(const char *label)
{
  GtUword m, f;
  if (gt_ma_bookkeeping_enabled())
  {
    m = gt_ma_get_space_current();
    f = gt_fa_get_space_current();
    gt_log_log("used space %s: %.2f MB (ma: %.2f MB; fa: %.2f MB)", label,
        GT_MEGABYTES(m + f), GT_MEGABYTES(m), GT_MEGABYTES(f));
  }
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
callq 0x93b7c
testb %al, %al
je 0x17d421
callq 0x93934
movq %rax, %r14
callq 0x8bf8b
leaq (%rax,%r14), %rcx
movq %rcx, %xmm1
movq 0x16a539(%rip), %xmm2   # 0x2e78e0
punpckldq %xmm2, %xmm1    # xmm1 = xmm1[0],xmm2[0],xmm1[1],xmm2[1]
movapd 0x16a53d(%rip), %xmm3   # 0x2e78f0
subpd %xmm3, %xmm1
movapd %xmm1, %xmm0
unpckhpd %xmm1, %xmm0            # xmm0 = xmm0[1],xmm1[1]
addsd %xmm1, %xmm0
movsd 0x16a535(%rip), %xmm4   # 0x2e7900
mulsd %xmm4, %xmm0
movq %r14, %xmm5
punpckldq %xmm2, %xmm5    # xmm5 = xmm5[0],xmm2[0],xmm5[1],xmm2[1]
subpd %xmm3, %xmm5
movapd %xmm5, %xmm1
unpckhpd %xmm5, %xmm1            # xmm1 = xmm1[1],xmm5[1]
addsd %xmm5, %xmm1
mulsd %xmm4, %xmm1
movq %rax, %xmm5
punpckldq %xmm2, %xmm5    # xmm5 = xmm5[0],xmm2[0],xmm5[1],xmm2[1]
subpd %xmm3, %xmm5
movapd %xmm5, %xmm2
unpckhpd %xmm5, %xmm2            # xmm2 = xmm2[1],xmm5[1]
addsd %xmm5, %xmm2
mulsd %xmm4, %xmm2
leaq 0x175c9b(%rip), %rdi    # 0x2f30ab
movq %rbx, %rsi
movb $0x3, %al
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x92a82
addq $0x8, %rsp
popq %rbx
popq %r14
retq