LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/optionargmode.c
// Function: gt_getsetargmodekeywords
void gt_getsetargmodekeywords(const Optionargmodedesc *modedesc,
                              size_t numberofentries,
                              unsigned int bitfield)
{
  size_t modecount;

  for (modecount=0; modecount < numberofentries; modecount++)
  {
    if (bitfield & modedesc[modecount].bitmask)
    {
      printf("%s ",modedesc[modecount].name);
    }
  }
  printf("\n");
}

// Assembly:
testq %rsi, %rsi
je 0x1c0c01
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movl %edx, %ebx
movq %rsi, %r14
movq %rdi, %r15
addq $0x10, %r15
leaq 0x212aca(%rip), %r12    # 0x3d36a4
testl %ebx, (%r15)
je 0x1c0bed
movq -0x10(%r15), %rsi
movq %r12, %rdi
xorl %eax, %eax
callq 0x17070
addq $0x18, %r15
decq %r14
jne 0x1c0bda
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
movl $0xa, %edi
jmp 0x17a20
nop
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/pckbucket.c
// Function: gt_pckbuckettable_delete
void gt_pckbuckettable_delete(Pckbuckettable *pckbt)
{
  gt_assert(pckbt != NULL);
  if (pckbt->mapptr == NULL)
  {
    gt_free(pckbt->mbtab[0]);
  } else
  {
    gt_fa_xmunmap(pckbt->mapptr);
  }
  pckbt->mbtab[0] = NULL;
  gt_free(pckbt->mbtab);
  pckbt->mbtab = NULL;
  gt_free(pckbt->basepower);
  pckbt->basepower = NULL;
  gt_free(pckbt);
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0x1c0c91
movq %rdi, %rbx
movq 0x20(%rdi), %rdi
testq %rdi, %rdi
je 0x1c0c29
callq 0x102b12
jmp 0x1c0c41
movq 0x18(%rbx), %rax
movq (%rax), %rdi
leaq 0x1f21d2(%rip), %rsi    # 0x3b2e09
movl $0x62, %edx
callq 0x109670
movq 0x18(%rbx), %rax
xorl %r15d, %r15d
movq %r15, (%rax)
movq 0x18(%rbx), %rdi
leaq 0x1f21b3(%rip), %r14    # 0x3b2e09
movq %r14, %rsi
movl $0x68, %edx
callq 0x109670
movq %r15, 0x18(%rbx)
movq 0x28(%rbx), %rdi
movq %r14, %rsi
movl $0x6a, %edx
callq 0x109670
movq %r15, 0x28(%rbx)
movq %rbx, %rdi
movq %r14, %rsi
movl $0x6c, %edx
popq %rbx
popq %r14
popq %r15
jmp 0x109670
callq 0x685b5
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/pckbucket.c
// Function: pckbuckettable_allocandinittable
static Pckbuckettable *pckbuckettable_allocandinittable(unsigned int numofchars,
                                                        unsigned int maxdepth,
                                                        bool writemode)
{
  Mbtab *cptr;
  unsigned int idx;
  Pckbuckettable *pckbt;

  pckbt = gt_malloc(sizeof (Pckbuckettable));
  pckbt->basepower = gt_initbasepower(numofchars,maxdepth);
  pckbt->numofchars = numofchars;
  pckbt->maxdepth = maxdepth;
  pckbt->maxnumofvalues = pckbt->numofvalues = 0;
  for (idx=0; idx <= maxdepth; idx++)
  {
    /*printf("basepower[%u]="GT_WU"\n",idx,pckbt->basepower[idx]); */
    pckbt->maxnumofvalues += pckbt->basepower[idx];
  }
  pckbt->mbtab = gt_malloc(sizeof (Mbtab *) * (maxdepth+1));
  if (writemode)
  {
    pckbt->mapptr = NULL;
    pckbt->mbtab[0] = gt_malloc(sizeof (Mbtab) * pckbt->maxnumofvalues);
    /*
    printf("allocated = %u * "GT_WU"\n",sizeof (Mbtab),pckbt->maxnumofvalues);
    */
    for (cptr = pckbt->mbtab[0];
         cptr < pckbt->mbtab[0] + pckbt->maxnumofvalues; cptr++)
    {
      cptr->lowerbound = cptr->upperbound = 0;
    }
    pckbuckettable_settaboffsets(pckbt);
  }
  return pckbt;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movl %edx, %ebp
movl %esi, %r14d
movl %edi, %r15d
leaq 0x1f1def(%rip), %rsi    # 0x3b2e09
movl $0x30, %edi
movl $0x41, %edx
callq 0x1092b2
movq %rax, %rbx
movl %r15d, %edi
movl %r14d, %esi
callq 0x1bed47
movq %rax, 0x28(%rbx)
movl %r15d, (%rbx)
movl %r14d, 0x4(%rbx)
leal 0x1(%r14), %edi
cmpl $0x1, %edi
adcl $0x1, %r14d
xorps %xmm0, %xmm0
movups %xmm0, 0x8(%rbx)
xorl %ecx, %ecx
xorl %edx, %edx
addq (%rax,%rcx,8), %rdx
movq %rdx, 0x10(%rbx)
incq %rcx
cmpq %rcx, %r14
jne 0x1c1058
shlq $0x3, %rdi
leaq 0x1f1d96(%rip), %rsi    # 0x3b2e09
movl $0x4b, %edx
callq 0x1092b2
movq %rax, 0x18(%rbx)
testb %bpl, %bpl
je 0x1c1117
movq $0x0, 0x20(%rbx)
movq 0x10(%rbx), %rdi
shlq $0x4, %rdi
leaq 0x1f1d68(%rip), %rsi    # 0x3b2e09
movl $0x4f, %edx
callq 0x1092b2
movq 0x18(%rbx), %rcx
movq %rax, (%rcx)
movq 0x10(%rbx), %rax
testq %rax, %rax
jle 0x1c10ec
movq 0x18(%rbx), %rcx
movq (%rcx), %rdi
shlq $0x4, %rax
addq %rdi, %rax
leaq 0x10(%rdi), %rcx
cmpq %rcx, %rax
cmovbeq %rcx, %rax
movq %rdi, %rdx
notq %rdx
addq %rax, %rdx
andq $-0x10, %rdx
addq $0x10, %rdx
xorl %esi, %esi
callq 0x173a0
movl 0x4(%rbx), %eax
testq %rax, %rax
je 0x1c1117
xorl %ecx, %ecx
movq 0x18(%rbx), %rdx
movq 0x28(%rbx), %rsi
movq (%rsi,%rcx,8), %rsi
shlq $0x4, %rsi
addq (%rdx,%rcx,8), %rsi
movq %rsi, 0x8(%rdx,%rcx,8)
incq %rcx
cmpq %rcx, %rax
jne 0x1c10f6
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/pckbucket.c
// Function: pckbuckettable_storeBoundsatdepth
static void pckbuckettable_storeBoundsatdepth(Pckbuckettable *pckbt,
                                              const Pckbck_Boundsatdepth *bd)
{
  gt_assert(bd != NULL && pckbt != NULL);
  gt_assert(bd->depth <= pckbt->maxdepth);
  gt_assert(bd->code <= pckbt->basepower[bd->depth]);
  /*
  printf("bd->depth=%u,bd->code="GT_WU"\n",bd->depth,bd->code);
  */
  gt_assert(pckbt->mbtab[bd->depth][bd->code].lowerbound == 0 &&
            pckbt->mbtab[bd->depth][bd->code].upperbound == 0);
  gt_assert(pckbt->numofvalues < pckbt->maxnumofvalues);
  pckbt->numofvalues++;
  pckbt->mbtab[bd->depth][bd->code].lowerbound = bd->lowerbound;
  pckbt->mbtab[bd->depth][bd->code].upperbound = bd->upperbound;
}

// Assembly:
pushq %rax
testq %rdi, %rdi
je 0x1c1181
testq %rsi, %rsi
je 0x1c1181
movl 0x10(%rsi), %eax
cmpl 0x4(%rdi), %eax
ja 0x1c1186
movq 0x18(%rsi), %rcx
movq 0x28(%rdi), %rdx
cmpq (%rdx,%rax,8), %rcx
ja 0x1c118b
movq 0x18(%rdi), %rdx
movq (%rdx,%rax,8), %rax
shlq $0x4, %rcx
cmpq $0x0, (%rax,%rcx)
jne 0x1c117c
addq %rcx, %rax
cmpq $0x0, 0x8(%rax)
jne 0x1c117c
movq 0x8(%rdi), %rcx
cmpq 0x10(%rdi), %rcx
jae 0x1c1190
incq %rcx
movq %rcx, 0x8(%rdi)
movups (%rsi), %xmm0
movups %xmm0, (%rax)
popq %rax
retq
callq 0x68740
callq 0x68709
callq 0x687e5
callq 0x687ae
callq 0x68777
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/pckbucket.c
// Function: gt_pckbuckettable_2file
int gt_pckbuckettable_2file(const char *indexname,
                            const Pckbuckettable *pckbuckettable,
                            GtError *err)
{
  FILE *fp;
  GtUword seqposmaxdepth;

  gt_error_check(err);
  fp = gt_fa_fopen_with_suffix(indexname,PCKBUCKETTABLE,"wb",err);
  if (fp == NULL)
  {
    return -1;
  }
  seqposmaxdepth = (GtUword) pckbuckettable->maxdepth;
  gt_xfwrite(&seqposmaxdepth,sizeof (GtUword),(size_t) 1,fp);
  gt_xfwrite(pckbuckettable->mbtab[0],sizeof (Mbtab),
             (size_t) pckbuckettable->maxnumofvalues,fp);
  gt_fa_fclose(fp);
  return 0;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
subq $0x10, %rsp
movq %rdx, %r14
movq %rsi, %rbx
movq %rdi, %r15
testq %rdx, %rdx
je 0x1c11b8
movq %r14, %rdi
callq 0x101a9a
testb %al, %al
jne 0x1c1236
leaq 0x1f1d2e(%rip), %rsi    # 0x3b2eed
leaq 0x19d947(%rip), %rdx    # 0x35eb0d
leaq 0x1f1c3c(%rip), %rcx    # 0x3b2e09
movq %r15, %rdi
movl $0xe2, %r8d
movq %r14, %r9
callq 0x101dff
testq %rax, %rax
je 0x1c1227
movq %rax, %r14
movl 0x4(%rbx), %eax
leaq 0x8(%rsp), %rdi
movq %rax, (%rdi)
movl $0x8, %esi
movl $0x1, %edx
movq %r14, %rcx
callq 0x125658
movq 0x10(%rbx), %rdx
movq 0x18(%rbx), %rax
movq (%rax), %rdi
movl $0x10, %esi
movq %r14, %rcx
callq 0x125658
movq %r14, %rdi
callq 0x101e80
xorl %eax, %eax
jmp 0x1c122c
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
addq $0x10, %rsp
popq %rbx
popq %r14
popq %r15
retq
callq 0x6881c
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/pckbucket.c
// Function: gt_pckbuckettable_exists
bool gt_pckbuckettable_exists(const char *indexname)
{
  GtStr *tmpfilename;
  bool retval;

  tmpfilename = gt_str_new_cstr(indexname);
  gt_str_append_cstr(tmpfilename,PCKBUCKETTABLE);
  retval = gt_file_exists(gt_str_get(tmpfilename));
  gt_str_delete(tmpfilename);
  return retval;
}

// Assembly:
pushq %rbp
pushq %rbx
pushq %rax
callq 0x120955
movq %rax, %rbx
leaq 0x1f1ca0(%rip), %rsi    # 0x3b2eed
movq %rax, %rdi
callq 0x12097f
movq %rbx, %rdi
callq 0x120d23
movq %rax, %rdi
callq 0x10415c
movl %eax, %ebp
movq %rbx, %rdi
callq 0x121b03
movl %ebp, %eax
addq $0x8, %rsp
popq %rbx
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/pckbucket.c
// Function: gt_pckbuckettable_map
Pckbuckettable *gt_pckbuckettable_map(const char *indexname,
                                      unsigned int numofchars,
                                      GtError *err)
{
  size_t numofbytes;
  void *mapptr;
  unsigned int maxdepth;
  Pckbuckettable *pckbt;

  gt_error_check(err);
  mapptr = gt_fa_mmap_read_with_suffix(indexname,PCKBUCKETTABLE,
                                       &numofbytes,err);
  if (mapptr == NULL)
  {
    return NULL;
  }
  maxdepth = (unsigned int) ((GtUword *) mapptr)[0];
  pckbt = pckbuckettable_allocandinittable(numofchars,maxdepth,false);
  pckbt->mapptr = mapptr;
  pckbt->mbtab[0] = (Mbtab *) (((GtUword *) mapptr) + 1);
  pckbuckettable_settaboffsets(pckbt);
  gt_assert(numofbytes ==
            sizeof (GtUword) + sizeof (Mbtab) * pckbt->maxnumofvalues);
  return pckbt;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
subq $0x10, %rsp
movq %rdx, %r14
movl %esi, %ebx
movq %rdi, %r15
testq %rdx, %rdx
je 0x1c129e
movq %r14, %rdi
callq 0x101a9a
testb %al, %al
jne 0x1c1338
leaq 0x1f1c48(%rip), %rsi    # 0x3b2eed
leaq 0x1f1b5d(%rip), %rcx    # 0x3b2e09
leaq 0x8(%rsp), %rdx
movq %r15, %rdi
movl $0x106, %r8d            # imm = 0x106
movq %r14, %r9
callq 0x102bc0
testq %rax, %rax
je 0x1c132c
movq %rax, %r14
movl (%rax), %esi
movl %ebx, %edi
xorl %edx, %edx
callq 0x1c1004
movq %r14, 0x20(%rax)
addq $0x8, %r14
movq 0x18(%rax), %rcx
movq %r14, (%rcx)
testq %rax, %rax
je 0x1c133d
movl 0x4(%rax), %ecx
testq %rcx, %rcx
je 0x1c1314
xorl %edx, %edx
movq 0x18(%rax), %rsi
movq 0x28(%rax), %rdi
movq (%rdi,%rdx,8), %rdi
shlq $0x4, %rdi
addq (%rsi,%rdx,8), %rdi
movq %rdi, 0x8(%rsi,%rdx,8)
incq %rdx
cmpq %rdx, %rcx
jne 0x1c12f3
movq 0x10(%rax), %rcx
shlq $0x4, %rcx
orq $0x8, %rcx
cmpq %rcx, 0x8(%rsp)
je 0x1c132e
callq 0x6888e
xorl %eax, %eax
addq $0x10, %rsp
popq %rbx
popq %r14
popq %r15
retq
callq 0x68855
callq 0x688c7
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch-align.c
// Function: gt_querymatchoutoptions_delete
void gt_querymatchoutoptions_delete(
        GtQuerymatchoutoptions *querymatchoutoptions)
{
  if (querymatchoutoptions != NULL)
  {
    front_trace_delete(querymatchoutoptions->front_trace);
    gt_greedy_extend_matchinfo_delete(querymatchoutoptions->ggemi);
    if (querymatchoutoptions->useqbuffer_size > 0)
    {
      gt_free(querymatchoutoptions->useqbuffer);
    }
    if (querymatchoutoptions->vseqbuffer_size > 0)
    {
      gt_free(querymatchoutoptions->vseqbuffer);
    }
    gt_eoplist_delete(querymatchoutoptions->eoplist);
    gt_eoplist_reader_delete(querymatchoutoptions->eoplist_reader);
    gt_eoplist_reader_delete(querymatchoutoptions->eoplist_reader_verify);
    gt_encseq_reader_delete(querymatchoutoptions->db_esr_for_align_show);
    gt_encseq_reader_delete(querymatchoutoptions->query_esr_for_align_show);
    polishing_info_delete(querymatchoutoptions->pol_info);
    gt_encseq_metadata_delete(querymatchoutoptions->emd);
    gt_free(querymatchoutoptions);
  }
}

// Assembly:
testq %rdi, %rdi
je 0x1c20a7
pushq %rbx
movq %rdi, %rbx
movq 0x40(%rdi), %rdi
callq 0x3243c5
movq 0x48(%rbx), %rdi
callq 0x1ea424
cmpq $0x0, (%rbx)
je 0x1c2034
movq 0x18(%rbx), %rdi
leaq 0x1f1335(%rip), %rsi    # 0x3b335f
movl $0xcf, %edx
callq 0x109670
cmpq $0x0, 0x8(%rbx)
je 0x1c2050
movq 0x20(%rbx), %rdi
leaq 0x1f1319(%rip), %rsi    # 0x3b335f
movl $0xd3, %edx
callq 0x109670
movq 0x28(%rbx), %rdi
callq 0x3229a7
movq 0x30(%rbx), %rdi
callq 0x322500
movq 0x38(%rbx), %rdi
callq 0x322500
movq 0x58(%rbx), %rdi
callq 0xed7bf
movq 0x60(%rbx), %rdi
callq 0xed7bf
movq 0xb0(%rbx), %rdi
callq 0x1b85e9
movq 0x68(%rbx), %rdi
callq 0x100e07
leaq 0x1f12c6(%rip), %rsi    # 0x3b335f
movq %rbx, %rdi
movl $0xdc, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch-align.c
// Function: gt_querymtch_alignment_verification
static void gt_querymtch_alignment_verification(
            GtQuerymatchoutoptions *querymatchoutoptions,
            GtUword dbstart,
            GtUword dblen,
            GtUword abs_querystart,
            GtUword querylen,
            GtUword sumdist)
{
  if (querymatchoutoptions->eoplist_reader_verify == NULL)
  {
    querymatchoutoptions->eoplist_reader_verify = gt_eoplist_reader_new();
  }
  gt_eoplist_set_sequences(querymatchoutoptions->eoplist,NULL,
                           dbstart,
                           dblen,
                           NULL,
                           abs_querystart,
                           querylen);
  gt_eoplist_verify(querymatchoutoptions->eoplist,
                    querymatchoutoptions->eoplist_reader_verify,
                    sumdist);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r9, %rbx
movq %r8, %rbp
movq %rcx, %r15
movq %rdx, %r12
movq %rsi, %r13
movq %rdi, %r14
cmpq $0x0, 0x38(%rdi)
jne 0x1c24aa
callq 0x3222fa
movq %rax, 0x38(%r14)
movq 0x28(%r14), %rdi
movq %rbp, (%rsp)
xorl %esi, %esi
movq %r13, %rdx
movq %r12, %rcx
xorl %r8d, %r8d
movq %r15, %r9
callq 0x32308f
movq 0x28(%r14), %rdi
movq 0x38(%r14), %rsi
movq %rbx, %rdx
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x324124
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch-align.c
// Function: gt_querymatchoutoptions_cigar_show
void gt_querymatchoutoptions_cigar_show(const GtQuerymatchoutoptions
                                              *querymatchoutoptions,
                                        bool distinguish_mismatch_match,
                                        FILE *fp)
{
  gt_assert(querymatchoutoptions != NULL &&
            querymatchoutoptions->eoplist != NULL);
  gt_eoplist_reader_reset(querymatchoutoptions->eoplist_reader,
                          querymatchoutoptions->eoplist,true);
  gt_eoplist_show_cigar(querymatchoutoptions->eoplist_reader,
                        distinguish_mismatch_match,fp);
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0x1c28df
movl %esi, %ebp
movq %rdi, %r14
movq 0x28(%rdi), %rsi
testq %rsi, %rsi
je 0x1c28df
movq %rdx, %rbx
movq 0x30(%r14), %rdi
movl $0x1, %edx
callq 0x32236b
movq 0x30(%r14), %rdi
movzbl %bpl, %esi
movq %rbx, %rdx
popq %rbx
popq %r14
popq %rbp
jmp 0x323013
callq 0x68ec4
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch-align.c
// Function: gt_querymatchoutoptions_trace_show
void gt_querymatchoutoptions_trace_show(const GtQuerymatchoutoptions
                                              *querymatchoutoptions,
                                        bool dtrace,
                                        FILE *fp)
{
  GtEoplistSegment segment;
  bool first = true;

  gt_assert(querymatchoutoptions != NULL);
  gt_eoplist_reader_reset(querymatchoutoptions->eoplist_reader,
                          querymatchoutoptions->eoplist,true);
  while (gt_eoplist_reader_next_segment(&segment,
                                        querymatchoutoptions->eoplist_reader,
                                        querymatchoutoptions->trace_delta))
  {
    if (!first)
    {
      fputc(',',fp);
    } else
    {
      first = false;
    }
    fprintf(fp,"%d",dtrace ? ((int) querymatchoutoptions->trace_delta -
                              (int) segment.aligned_v)
                           : (int) segment.aligned_v);
  }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
testq %rdi, %rdi
je 0x1c2995
movq %rdx, %rbx
movl %esi, %ebp
movq %rdi, %r14
movq 0x28(%rdi), %rsi
movq 0x30(%rdi), %rdi
movl $0x1, %edx
callq 0x32236b
movq 0x10(%r14), %rdx
movq 0x30(%r14), %rsi
leaq 0x8(%rsp), %rdi
callq 0x322ad5
testb %al, %al
je 0x1c2986
movb $0x1, %r13b
leaq 0x210d75(%rip), %r15    # 0x3d36aa
leaq 0x8(%rsp), %r12
testb $0x1, %r13b
je 0x1c2945
xorl %r13d, %r13d
jmp 0x1c2952
movl $0x2c, %edi
movq %rbx, %rsi
callq 0x17980
testb %bpl, %bpl
je 0x1c2961
movl 0x10(%r14), %edx
subl 0x10(%rsp), %edx
jmp 0x1c2965
movl 0x10(%rsp), %edx
movq %rbx, %rdi
movq %r15, %rsi
xorl %eax, %eax
callq 0x17ab0
movq 0x10(%r14), %rdx
movq 0x30(%r14), %rsi
movq %r12, %rdi
callq 0x322ad5
testb %al, %al
jne 0x1c293a
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x68efd
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch-display.c
// Function: gt_querymatch_display_args_contain
static bool gt_querymatch_display_args_contain(const GtStrArray *display_args,
                                               const char *keyword)
{
  GtUword idx;

  for (idx = 0; idx < gt_str_array_size(display_args); idx++)
  {
    if (strcmp_ignore_ws(gt_str_array_get(display_args,idx),keyword) == 0)
    {
      return true;
    }
  }
  return false;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
callq 0x121e78
testq %rax, %rax
setne %bpl
je 0x1c33a3
movq %r14, %rdi
xorl %esi, %esi
callq 0x121cfa
movq %rax, %rdi
movq %rbx, %rsi
callq 0x1c36a2
testl %eax, %eax
je 0x1c33a3
movl $0x1, %r15d
movq %r14, %rdi
callq 0x121e78
cmpq %rax, %r15
setb %bpl
jae 0x1c33a3
movq %r14, %rdi
movq %r15, %rsi
callq 0x121cfa
movq %rax, %rdi
movq %rbx, %rsi
callq 0x1c36a2
incq %r15
testl %eax, %eax
jne 0x1c3375
movl %ebp, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch-display.c
// Function: gt_querymatch_Options_output
void gt_querymatch_Options_output(FILE *stream,int argc,const char **argv,
                                  bool idhistout,GtUword minidentity,
                                  GtUword historysize)
{
  int idx;
  bool minid_out = false, history_out = false;

  fprintf(stream,"# Options:");
  for (idx = 1; idx < argc; idx++) {
    if (strcmp(argv[idx],"-minidentity") == 0) {
      minid_out = true;
    }
    if (strcmp(argv[idx],"-history") == 0) {
      history_out = true;
    }
    fprintf(stream," %s", argv[idx]);
  }
  if (idhistout)
  {
    if (!minid_out)
    {
      fprintf(stream," -minidentity " GT_WU,minidentity);
    }
    if (!history_out)
    {
      fprintf(stream," -history " GT_WU,historysize);
    }
  }
  fputc('\n',stream);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq %r9, %r12
movq %r8, 0x18(%rsp)
movl %ecx, 0x4(%rsp)
movq %rdx, %r15
movl %esi, %ebp
movq %rdi, %rbx
leaq 0x1f1129(%rip), %rdi    # 0x3b4502
movl $0x1, %r14d
movl $0xa, %esi
movl $0x1, %edx
movq %rbx, %rcx
callq 0x17fa0
cmpl $0x2, %ebp
jl 0x1c347c
movq %r12, 0x10(%rsp)
movq %rbx, 0x8(%rsp)
movl %ebp, %eax
movq %rax, 0x20(%rsp)
xorl %r13d, %r13d
movl $0x1, %r12d
movq %r15, %rbx
xorl %r15d, %r15d
movq (%rbx,%r14,8), %rbp
movq %rbp, %rdi
leaq 0x1f10e5(%rip), %rsi    # 0x3b450d
callq 0x17a40
testl %eax, %eax
movzbl %r15b, %r15d
cmovel %r12d, %r15d
movq %rbp, %rdi
leaq 0x1f10d9(%rip), %rsi    # 0x3b451a
callq 0x17a40
testl %eax, %eax
movzbl %r13b, %r13d
cmovel %r12d, %r13d
movq 0x8(%rsp), %rdi
leaq 0x1f118a(%rip), %rsi    # 0x3b45e6
movq %rbp, %rdx
xorl %eax, %eax
callq 0x17ab0
incq %r14
cmpq %r14, 0x20(%rsp)
jne 0x1c341a
movq 0x8(%rsp), %rbx
movq 0x10(%rsp), %r12
jmp 0x1c3482
xorl %r15d, %r15d
xorl %r13d, %r13d
cmpb $0x0, 0x4(%rsp)
je 0x1c34bf
testb $0x1, %r15b
jne 0x1c34a5
leaq 0x1f108d(%rip), %rsi    # 0x3b4523
movq %rbx, %rdi
movq 0x18(%rsp), %rdx
xorl %eax, %eax
callq 0x17ab0
testb $0x1, %r13b
jne 0x1c34bf
leaq 0x1f1083(%rip), %rsi    # 0x3b4535
movq %rbx, %rdi
movq %r12, %rdx
xorl %eax, %eax
callq 0x17ab0
movl $0xa, %edi
movq %rbx, %rsi
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x17980
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch-display.c
// Function: gt_querymatch_Fields_output
void gt_querymatch_Fields_output(FILE *stream,
                                 const GtSeedExtendDisplayFlag *display_flag)
{
  const unsigned int *column_order;
  GtUword numcolumns, idx;

  gt_assert(display_flag != NULL);
  column_order = gt_querymatch_display_order(&numcolumns,display_flag);
  gt_assert(numcolumns > 0);
  fprintf(stream,"# Fields: ");
  gt_assert(numcolumns <= GT_DISPLAY_LARGEST_FLAG);
  for (idx = 0; idx < numcolumns; idx++)
  {
    unsigned int argnum, flag = column_order[idx];
    gt_assert(flag < sizeof gt_display_flag2index/
                     sizeof gt_display_flag2index[0]);
    argnum = gt_display_flag2index[flag];
    gt_assert(argnum < sizeof gt_display_arguments_table/
                       sizeof gt_display_arguments_table[0]);
    if (flag == Gt_Identity_display)
    {
      fprintf(stream,"%% %s",gt_display_arguments_table[argnum].name);
    } else
    {
      gt_querymatch_display_keyword_out(stream,
                                        gt_display_arguments_table[argnum].
                                          name);
    }
    fprintf(stream,"%s",idx < numcolumns - 1 ? ", " : "\n");
  }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
testq %rsi, %rsi
je 0x1c35f4
movq %rsi, %r13
movq 0xb8(%rsi), %rbx
testq %rbx, %rbx
je 0x1c35f9
movq %rdi, %r14
leaq 0x1f1063(%rip), %rdi    # 0x3b456e
movl $0xa, %esi
movl $0x1, %edx
movq %r14, %rcx
callq 0x17fa0
cmpq $0x26, %rbx
ja 0x1c35fe
movq %rbx, %r15
leaq -0x1(%rbx), %rax
movq %rax, (%rsp)
leaq 0x19cd40(%rip), %r12    # 0x360279
xorl %ebx, %ebx
movl 0x8(%r13,%rbx,4), %eax
cmpq $0x27, %rax
jae 0x1c35ef
movq %r13, %rbp
leaq 0x1f165c(%rip), %rcx    # 0x3b4bb0
movl (%rcx,%rax,4), %ecx
shlq $0x4, %rcx
leaq 0x301d7e(%rip), %rdx    # 0x4c52e0
movq (%rcx,%rdx), %r13
cmpq $0x1f, %rax
jne 0x1c35ab
movq %r14, %rdi
leaq 0x1f106e(%rip), %rsi    # 0x3b45e4
movq %r13, %rdx
xorl %eax, %eax
callq 0x17ab0
cmpq (%rsp), %rbx
leaq 0x206194(%rip), %rdi    # 0x3c971f
leaq 0x1eb611(%rip), %rax    # 0x3aeba3
cmovbq %rax, %rdi
movq %r14, %rsi
callq 0x178c0
incq %rbx
cmpq %r15, %rbx
movq %rbp, %r13
jne 0x1c353b
jmp 0x1c35e0
movzbl (%r13), %eax
cmpl $0x2e, %eax
je 0x1c35c6
testl %eax, %eax
je 0x1c3580
movsbl %al, %edi
movq %r14, %rsi
callq 0x17980
jmp 0x1c35db
movl $0x2, %esi
movl $0x1, %edx
movq %r12, %rdi
movq %r14, %rcx
callq 0x17fa0
incq %r13
jmp 0x1c35ab
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x69207
callq 0x69279
callq 0x69240
callq 0x691ce
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch-display.c
// Function: gt_querymatch_read_Fields_line
GtStrArray *gt_querymatch_read_Fields_line(const char *line_ptr)
{
  const char *header = "# Fields:", *ptr, *last_start;
  const size_t header_len = strlen(header);
  GtStrArray *fields;

  if (strncmp(header,line_ptr,header_len) != 0)
  {
    return NULL;
  }
  fields = gt_str_array_new();
  for (last_start = ptr = line_ptr + header_len + 1; /* Nothing */; ptr++)
  {
    if (*ptr == ',' || *ptr == '\0')
    {
      GtUword len_arg;

      if (*last_start == '%')
      {
        last_start += 2;
      }
      len_arg = (size_t) (ptr - last_start);
      gt_str_array_add_cstr_nt(fields, last_start, len_arg);
      last_start = ptr + 2;
    }
    if (*ptr == '\0')
    {
      break;
    }
  }
  return fields;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %rdi, %rbx
leaq 0x1f0fe9(%rip), %rdi    # 0x3b4622
movl $0x9, %edx
movq %rbx, %rsi
callq 0x17330
testl %eax, %eax
je 0x1c364f
xorl %r14d, %r14d
jmp 0x1c3699
callq 0x121b54
movq %rax, %r14
leaq 0xa(%rbx), %r15
addq $0xc, %rbx
movq %r15, %rax
movzbl -0x2(%rbx), %ecx
cmpl $0x2c, %ecx
je 0x1c366f
testl %ecx, %ecx
jne 0x1c368c
xorl %ecx, %ecx
cmpb $0x25, (%rax)
sete %cl
leaq (%rax,%rcx,2), %rsi
movq %r15, %rdx
subq %rsi, %rdx
movq %r14, %rdi
callq 0x121c6a
movq %rbx, %rax
incq %r15
cmpb $0x0, -0x2(%rbx)
leaq 0x1(%rbx), %rbx
jne 0x1c3662
movq %r14, %rax
popq %rbx
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch-display.c
// Function: strcmp_ignore_ws
static int strcmp_ignore_ws(const char *s,const char *t)
{
  const char *sptr = s, *tptr = t;
  while (true)
  {
    if (isspace(*sptr))
    {
      sptr++;
    } else
    {
      if (isspace(*tptr))
      {
        tptr++;
      } else
      {
        if (*sptr < *tptr)
        {
          return -1;
        }
        if (*sptr > *tptr)
        {
          return 1;
        }
        if (*sptr == '\0')
        {
          return 0;
        }
        sptr++;
        tptr++;
      }
    }
  }
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
callq 0x17870
movq (%rax), %rax
movsbq (%r14), %rcx
movzwl (%rax,%rcx,2), %edx
btl $0xd, %edx
jb 0x1c36e0
movsbq (%rbx), %rsi
testb $0x20, 0x1(%rax,%rsi,2)
je 0x1c36d2
incq %rbx
jmp 0x1c36bc
cmpb %sil, %cl
jl 0x1c36e5
jg 0x1c36ec
testb %cl, %cl
je 0x1c36f3
incq %rbx
incq %r14
jmp 0x1c36b4
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
jmp 0x1c36f5
movl $0x1, %eax
jmp 0x1c36f5
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch-display.c
// Function: gt_querymatch_display_flag_add
static void gt_querymatch_display_flag_add(GtSeedExtendDisplayFlag
                                            *display_flag,
                                           GtSeedExtendDisplay_enum flag)
{
  const uint64_t mask = gt_display_mask(flag);

  gt_assert(display_flag != NULL);
  if ((display_flag->flags & mask) == 0)
  {
    display_flag->flags |= mask;
    gt_assert(flag <= GT_DISPLAY_LARGEST_FLAG);
    if (gt_display_arguments_table[gt_display_flag2index[flag]].incolumn)
    {
      gt_assert(display_flag->nextfree <= GT_DISPLAY_LARGEST_FLAG);
      display_flag->order[display_flag->nextfree++] = flag;
    }
  }
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movl %esi, %ebx
movq %rdi, %r14
movl %esi, %edi
callq 0x1c3325
testq %r14, %r14
je 0x1c3768
movq (%r14), %rcx
testq %rax, %rcx
jne 0x1c3760
orq %rax, %rcx
movq %rcx, (%r14)
cmpl $0x27, %ebx
jae 0x1c376d
movl %ebx, %eax
leaq 0x1f1482(%rip), %rcx    # 0x3b4bb0
movl (%rcx,%rax,4), %eax
shlq $0x4, %rax
leaq 0x301ba4(%rip), %rcx    # 0x4c52e0
cmpb $0x1, 0xc(%rax,%rcx)
jne 0x1c3760
movq 0xb8(%r14), %rax
cmpq $0x27, %rax
jae 0x1c3772
leaq 0x1(%rax), %rcx
movq %rcx, 0xb8(%r14)
movl %ebx, 0x8(%r14,%rax,4)
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x6935d
callq 0x692eb
callq 0x69324
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch-display.c
// Function: gt_display_arg_get
static const GtSEdisplayStruct *gt_display_arg_get(char *copyspace,
                                                   const char *str,
                                                   size_t cmplen)
{
  char *copy = NULL;
  const GtSEdisplayStruct *left = gt_display_arguments_table,
                          *right = gt_display_arguments_table +
                                   sizeof gt_display_arguments_table/
                                   sizeof gt_display_arguments_table[0] - 1;

  if (cmplen > 0)
  {
    copy = copyspace;
    memcpy(copy,str,sizeof *copy * cmplen);
    copy[cmplen] = '\0';
  }
  while (left <= right)
  {
    const GtSEdisplayStruct *mid = left + (right - left + 1)/2;
    const int cmp = strcmp_ignore_ws(copy == NULL ? str : copy,mid->name);

    if (cmp < 0)
    {
      right = mid - 1;
    } else
    {
      if (cmp > 0)
      {
        left = mid + 1;
      } else
      {
        return mid;
      }
    }
  }
  return NULL;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
movq %rsi, %rbx
testq %rdx, %rdx
je 0x1c379d
movq %rdx, %r15
movq %rdi, %r14
movq %rbx, %rsi
callq 0x17660
movb $0x0, (%r14,%r15)
jmp 0x1c37a0
xorl %r14d, %r14d
testq %r14, %r14
cmovneq %r14, %rbx
leaq 0x301d92(%rip), %r12    # 0x4c5540
leaq 0x301b2b(%rip), %r15    # 0x4c52e0
cmpq %r12, %r15
ja 0x1c380d
movq %r12, %rax
subq %r15, %rax
sarq $0x4, %rax
leaq 0x1(%rax), %rcx
shrq $0x3f, %rcx
addq %rcx, %rax
incq %rax
andq $-0x2, %rax
leaq (%r15,%rax,8), %r13
movq (%r13), %rsi
movq %rbx, %rdi
callq 0x1c36a2
testl %eax, %eax
js 0x1c37f7
je 0x1c3802
addq $0x10, %r13
movb $0x1, %al
movq %r13, %r15
jmp 0x1c3807
addq $-0x10, %r13
movb $0x1, %al
movq %r13, %r12
jmp 0x1c3807
xorl %eax, %eax
movq %r13, %r14
testb %al, %al
jne 0x1c37b5
jmp 0x1c3810
xorl %r14d, %r14d
movq %r14, %rax
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch.c
// Function: gt_querymatch_new
GtQuerymatch *gt_querymatch_new(void)
{
  GtQuerymatch *querymatch = gt_malloc(sizeof *querymatch);

  gt_assert(querymatch != NULL);
  querymatch->ref_querymatchoutoptions = NULL;
  querymatch->verify_alignment = false;
  querymatch->query_readmode = GT_READMODE_FORWARD;
  querymatch->fp = stdout;
  querymatch->queryseqnum = GT_UWORD_MAX;
  querymatch->db_desc = NULL;
  querymatch->query_desc = NULL;
  return querymatch;
}

// Assembly:
pushq %rax
leaq 0x1f1520(%rip), %rsi    # 0x3b4d48
movl $0xb8, %edi
movl $0x3f, %edx
callq 0x1092b2
testq %rax, %rax
je 0x1c387d
movq $0x0, 0x90(%rax)
movb $0x0, 0x8d(%rax)
movl $0x0, 0x88(%rax)
movq 0x300689(%rip), %rcx    # 0x4c3ee8
movq (%rcx), %rcx
movq %rcx, 0x98(%rax)
movq $-0x1, 0x28(%rax)
xorps %xmm0, %xmm0
movups %xmm0, 0xa0(%rax)
popq %rcx
retq
callq 0x69396
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch.c
// Function: gt_querymatch_outoptions_set
void gt_querymatch_outoptions_set(GtQuerymatch *querymatch,
                GtQuerymatchoutoptions *querymatchoutoptions)
{
  gt_assert(querymatch != NULL && querymatchoutoptions != NULL);
  querymatch->ref_querymatchoutoptions = querymatchoutoptions;
  querymatch->ref_eoplist
    = gt_querymatchoutoptions_eoplist(querymatchoutoptions);
}

// Assembly:
pushq %rbx
testq %rdi, %rdi
je 0x1c3968
testq %rsi, %rsi
je 0x1c3968
movq %rdi, %rbx
movq %rsi, 0x90(%rdi)
movq %rsi, %rdi
callq 0x1c2aa1
movq %rax, 0xb0(%rbx)
popq %rbx
retq
callq 0x69404
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch.c
// Function: gt_querymatch_init
void gt_querymatch_init(GtQuerymatch *querymatch,
                        GtUword dblen,
                        GtUword dbseqnum,
                        GtUword dbstart_relative,
                        GtUword db_seqstart,
                        GtUword db_seqlen,
                        GtWord score,
                        GtUword distance,
                        GtUword mismatches,
                        bool selfmatch,
                        GtUword queryseqnum,
                        GtUword querylen,
                        GtUword querystart,
                        GtUword query_seqstart,
                        GtUword query_seqlen,
                        const char *db_desc,
                        const char *query_desc)
{
  gt_assert(querymatch != NULL);
  querymatch->dblen = dblen;
  querymatch->score = score;
  querymatch->distance = distance;
  querymatch->queryseqnum = queryseqnum;
  querymatch->querylen = querylen;
  querymatch->querystart = querystart;
  querymatch->dbseqnum = dbseqnum;
  querymatch->mismatches = mismatches;
  querymatch->dbstart_relative = dbstart_relative;
  gt_assert((int) querymatch->query_readmode < 4);
  querymatch->selfmatch = selfmatch;
  querymatch->query_seqlen = query_seqlen;
  querymatch->querystart_fwdstrand
    = gt_querymatch_position_convert(querymatch->query_readmode,
                                     querymatch->querylen,
                                     querymatch->query_seqlen,
                                     querymatch->querystart);
  querymatch->query_seqstart = query_seqstart;
  querymatch->db_seqstart = db_seqstart;
  querymatch->db_seqlen = db_seqlen;
  querymatch->db_desc = db_desc;
  querymatch->query_desc = query_desc;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x1c3b0e
movq %r9, %rbx
movq %r8, %r14
movq %rcx, %rax
movq %rsi, %r8
movq %rdi, %r15
movq 0x70(%rsp), %rcx
movq 0x68(%rsp), %rsi
movq 0x60(%rsp), %rdi
movq 0x50(%rsp), %r9
movq 0x48(%rsp), %r10
movq 0x40(%rsp), %r11
movq %r8, 0x10(%r15)
movq %r11, 0x80(%r15)
movq %r10, 0x70(%r15)
movq %rdi, 0x28(%r15)
movq %rsi, 0x40(%r15)
movq %rcx, 0x30(%r15)
movq %rdx, (%r15)
movq %r9, 0x78(%r15)
movq %rax, 0x8(%r15)
movl 0x88(%r15), %edi
cmpl $0x4, %edi
jge 0x1c3b13
movq 0x90(%rsp), %r12
movq 0x88(%rsp), %r13
movq 0x80(%rsp), %rdx
movq 0x78(%rsp), %rbp
movb 0x58(%rsp), %al
movb %al, 0x8c(%r15)
movq %rdx, 0x48(%r15)
callq 0x1c3b18
movq %rax, 0x38(%r15)
movq %rbp, 0x50(%r15)
movq %r14, 0x20(%r15)
movq %rbx, 0x18(%r15)
movq %r13, 0xa0(%r15)
movq %r12, 0xa8(%r15)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x694ab
callq 0x69472
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch.c
// Function: gt_querymatch_description_out
static int gt_non_white_space_prefix_length(const char *s)
{
  const char *sptr;

  gt_assert(s != NULL);
  for (sptr = s; !isspace(*sptr); sptr++)
  {
    /* Nothing */ ;
  }
  return (int) (sptr - s);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rsi, %rsi
je 0x1c43af
movq %rsi, %r14
movq %rdi, %rbx
callq 0x17870
movq (%rax), %rax
movabsq $-0x100000000, %rdx     # imm = 0xFFFFFFFF00000000
movabsq $0x100000000, %rcx      # imm = 0x100000000
movq %r14, %rsi
addq %rcx, %rdx
movsbq (%rsi), %rdi
incq %rsi
testb $0x20, 0x1(%rax,%rdi,2)
je 0x1c4383
sarq $0x20, %rdx
movl $0x1, %esi
movq %r14, %rdi
movq %rbx, %rcx
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x17fa0
callq 0x696af
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch.c
// Function: gt_querymatch_show_failed_seed
void gt_querymatch_show_failed_seed(const GtSeedExtendDisplayFlag
                                       *out_display_flag,
                                    const GtQuerymatch *querymatch)
{
  if (gt_querymatch_failed_seed_display(out_display_flag))
  {
    const char separator
      = (gt_querymatch_blast_display(out_display_flag) ||
         gt_querymatch_tabsep_display(out_display_flag)) ? '\t' : ' ';
    fprintf(querymatch->fp, "# failed_seed:%c" GT_WU "%c" GT_WU "%c"  GT_WU
                                   "%c%c%c" GT_WU "%c" GT_WU "\n",
            separator,
            querymatch->seedlen,
            separator,
            querymatch->dbseqnum,
            separator,
            querymatch->db_seedpos_rel,
            separator,
            gt_seed_extend_outflag[querymatch->query_readmode],
            separator,
            querymatch->queryseqnum,
            separator,
            querymatch->query_seedpos_rel);
  }
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
callq 0x1c2ae7
testb %al, %al
je 0x1c4435
movq %r14, %rdi
callq 0x1c2b17
movl $0x9, %edx
testb %al, %al
jne 0x1c43ef
movq %r14, %rdi
callq 0x1c2b07
testb %al, %al
movl $0x9, %eax
movl $0x20, %edx
cmovnel %eax, %edx
movq 0x98(%rbx), %rdi
movq 0x68(%rbx), %rcx
movl 0x88(%rbx), %eax
leaq 0x1f0e4e(%rip), %rsi    # 0x3b5255
movsbl (%rax,%rsi), %r10d
movq (%rbx), %r9
leaq 0x1f0ba2(%rip), %rsi    # 0x3b4fb8
movl %edx, %r8d
xorl %eax, %eax
pushq 0x60(%rbx)
pushq %rdx
pushq 0x28(%rbx)
pushq %rdx
pushq %r10
pushq %rdx
pushq 0x58(%rbx)
pushq %rdx
callq 0x17ab0
addq $0x48, %rsp
jmp 0x1c4439
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch.c
// Function: gt_querymatch_evalue_bit_score_generic
static void gt_querymatch_evalue_bit_score_generic(double *evalue_ptr,
                                                   double *bit_score_ptr,
                                                   const GtKarlinAltschulStat
                                                     *karlin_altschul_stat,
                                                   GtUword query_seqlen,
                                                   GtUword matches,
                                                   GtUword mismatches,
                                                   GtUword indels)
{
  if (karlin_altschul_stat != NULL)
  {
    GtUword evalue_searchspace
      = gt_evalue_searchspace(karlin_altschul_stat,query_seqlen);
    GtWord raw_score = gt_evalue_raw_score(karlin_altschul_stat,
                                           matches,
                                           mismatches,
                                           indels);
    *evalue_ptr = gt_evalue_from_raw_score(karlin_altschul_stat,
                                           raw_score,
                                           evalue_searchspace);
    *bit_score_ptr = gt_evalue_raw_score2bit_score(karlin_altschul_stat,
                                                   raw_score);
    gt_assert(*evalue_ptr != DBL_MAX && *bit_score_ptr != DBL_MAX);
  }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r9, %r15
movq %r8, %r12
movq %rdx, %r13
movq %rsi, %r14
movq %rdi, %rbx
movq %rdx, %rdi
movq %rcx, %rsi
callq 0x1bfd4a
movq %rax, %rbp
movq %r13, %rdi
movq %r12, %rsi
movq %r15, %rdx
movq 0x40(%rsp), %rcx
callq 0x1c032b
movq %rax, %r15
movq %r13, %rdi
movq %rax, %rsi
movq %rbp, %rdx
callq 0x1c03ae
movsd %xmm0, (%rbx)
movq %r13, %rdi
movq %r15, %rsi
callq 0x1c036a
movsd %xmm0, (%r14)
movsd (%rbx), %xmm1
ucomisd 0x18c73c(%rip), %xmm1   # 0x350d10
jne 0x1c45d8
jnp 0x1c45f3
ucomisd 0x18c730(%rip), %xmm0   # 0x350d10
jne 0x1c45e4
jnp 0x1c45f3
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x6975a
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch.c
// Function: gt_querymatch_check_final
bool gt_querymatch_check_final(double *evalue_ptr,
                               double *bit_score_ptr,
                               const GtKarlinAltschulStat *karlin_altschul_stat,
                               const GtQuerymatch *querymatch,
                               GtUword userdefinedleastlength,
                               GtUword errorpercentage,
                               double evalue_threshold)
{
  GtUword aligned_len;

  if (!gt_querymatch_ordered(querymatch))
  {
#ifdef SKDEBUG
    fprintf(querymatch->fp, "# !gt_querymatch_ordered => reject\n");
#endif
    return false;
  }
  aligned_len = gt_querymatch_aligned_len(querymatch);
  return gt_querymatch_check_final_generic(
                               evalue_ptr,
                               bit_score_ptr,
                               karlin_altschul_stat,
                               querymatch->query_seqlen,
                               aligned_len,
                               querymatch->distance,
                               querymatch->mismatches,
                               userdefinedleastlength,
                               errorpercentage,
                               evalue_threshold,
                               querymatch->fp);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movsd %xmm0, (%rsp)
movq %r9, %r15
movq %r8, %r14
movq %rcx, %rbx
movq %rdx, %r12
movq %rsi, %r13
movq %rdi, %rbp
movq %rcx, %rdi
callq 0x1c466c
testb %al, %al
je 0x1c465b
movq 0x40(%rbx), %r8
movq 0x48(%rbx), %rcx
addq 0x10(%rbx), %r8
movq 0x70(%rbx), %r9
subq $0x8, %rsp
movq %rbp, %rdi
movq %r13, %rsi
movq %r12, %rdx
movsd 0x8(%rsp), %xmm0
pushq %r15
pushq %r14
pushq 0x78(%rbx)
callq 0x1c443d
addq $0x28, %rsp
jmp 0x1c4661
xorl %eax, %eax
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/querymatch.c
// Function: gt_querymatch_ordered
static bool gt_querymatch_ordered(const GtQuerymatch *querymatch)
{
  return (!querymatch->selfmatch ||
          querymatch->dbseqnum < querymatch->queryseqnum ||
          (querymatch->dbseqnum == querymatch->queryseqnum &&
           (querymatch->dbstart_relative <
             (GT_ISDIRREVERSE(querymatch->query_readmode)
                ? (querymatch->querystart_fwdstrand + 1)
                : querymatch->querystart)))) ? true : false;
}

// Assembly:
movb $0x1, %al
cmpb $0x1, 0x8c(%rdi)
jne 0x1c46a2
movq (%rdi), %rcx
movq 0x28(%rdi), %rdx
cmpq %rdx, %rcx
jb 0x1c46a2
jne 0x1c46a0
movq 0x8(%rdi), %rax
movl 0x88(%rdi), %ecx
orl $0x2, %ecx
cmpl $0x3, %ecx
jne 0x1c46a3
movq 0x38(%rdi), %rcx
incq %rcx
jmp 0x1c46a7
xorl %eax, %eax
retq
movq 0x30(%rdi), %rcx
cmpq %rcx, %rax
setb %al
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch.c
// Function: gt_querymatch_table_sort
void gt_querymatch_table_sort(GtArrayGtQuerymatch *querymatch_table,
                              bool ascending)
{
  if (querymatch_table->nextfreeGtQuerymatch >= 2)
  {
    qsort(querymatch_table->spaceGtQuerymatch,
          querymatch_table->nextfreeGtQuerymatch,
          sizeof *querymatch_table->spaceGtQuerymatch,
          ascending ? gt_querymatch_compare_ascending
                    : gt_querymatch_compare_descending);
  }
}

// Assembly:
movl %esi, %eax
movq 0x10(%rdi), %rsi
cmpq $0x2, %rsi
jb 0x1c4fa4
movq (%rdi), %rdi
leaq 0x18(%rip), %rdx        # 0x1c4fa5
leaq 0x4d(%rip), %rcx        # 0x1c4fe1
testb %al, %al
cmovneq %rdx, %rcx
movl $0xb8, %edx
jmp 0x17f60
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch.c
// Function: gt_querymatch_compare_ascending
static int gt_querymatch_compare_ascending(const void *va,const void *vb)
{
  const GtQuerymatch *a = (const GtQuerymatch *) va;
  const GtQuerymatch *b = (const GtQuerymatch *) vb;

  gt_assert(a != NULL && b != NULL);
  if (a->queryseqnum < b->queryseqnum ||
       (a->queryseqnum == b->queryseqnum &&
        a->querystart_fwdstrand + gt_querymatch_querylen(a) <=
        b->querystart_fwdstrand + gt_querymatch_querylen(b)))
  {
    return -1;
  }
  return 1;
}

// Assembly:
testq %rdi, %rdi
je 0x1c4fdb
testq %rsi, %rsi
je 0x1c4fdb
movq 0x28(%rsi), %rcx
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
cmpq %rcx, 0x28(%rdi)
jb 0x1c4fda
jne 0x1c4fd5
movq 0x40(%rdi), %rcx
addq 0x38(%rdi), %rcx
movq 0x40(%rsi), %rdx
addq 0x38(%rsi), %rdx
cmpq %rdx, %rcx
jbe 0x1c4fda
movl $0x1, %eax
retq
pushq %rax
callq 0x69ab1
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch.c
// Function: gt_querymatch_compare_descending
static int gt_querymatch_compare_descending(const void *va,const void *vb)
{
  const GtQuerymatch *a = (const GtQuerymatch *) va;
  const GtQuerymatch *b = (const GtQuerymatch *) vb;

  gt_assert(a != NULL && b != NULL);
  if (a->queryseqnum < b->queryseqnum ||
       (a->queryseqnum == b->queryseqnum &&
        a->querystart_fwdstrand + gt_querymatch_querylen(a) <=
        b->querystart_fwdstrand + gt_querymatch_querylen(b)))
  {
    return 1;
  }
  return -1;
}

// Assembly:
testq %rdi, %rdi
je 0x1c5017
testq %rsi, %rsi
je 0x1c5017
movq 0x28(%rsi), %rcx
movl $0x1, %eax
cmpq %rcx, 0x28(%rdi)
jb 0x1c5016
jne 0x1c5011
movq 0x40(%rdi), %rcx
addq 0x38(%rdi), %rcx
movq 0x40(%rsi), %rdx
addq 0x38(%rsi), %rdx
cmpq %rdx, %rcx
jbe 0x1c5016
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
retq
pushq %rax
callq 0x69aea
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/match/querymatch.c
// Function: gt_querymatch_extract_sequence_pair
void gt_querymatch_extract_sequence_pair(GtSequencepairbuffer *seqpairbuf,
                                         const GtEncseq *db_encseq,
                                         const GtEncseq *query_encseq,
                                         const GtQuerymatch *querymatch)
{
  GtReadmode query_readmode = gt_querymatch_query_readmode(querymatch);
  const GtUword dblen = gt_querymatch_dblen(querymatch),
                querylen = gt_querymatch_querylen(querymatch),
                apos_ab = gt_querymatch_dbstart(querymatch),
                bpos_ab = querymatch->query_seqstart +
                          querymatch->querystart_fwdstrand;

  if (dblen >= seqpairbuf->a_allocated)
  {
    seqpairbuf->a_sequence = gt_realloc(seqpairbuf->a_sequence,
                                        sizeof *seqpairbuf->a_sequence * dblen);
    seqpairbuf->a_allocated = dblen;
  }
  if (querylen >= seqpairbuf->b_allocated)
  {
    seqpairbuf->b_sequence = gt_realloc(seqpairbuf->b_sequence,
                                        sizeof *seqpairbuf->b_sequence *
                                        querylen);
    seqpairbuf->b_allocated = querylen;
  }
  gt_encseq_extract_encoded(db_encseq, seqpairbuf->a_sequence, apos_ab,
                            apos_ab + dblen - 1);
  gt_encseq_extract_encoded(query_encseq, seqpairbuf->b_sequence, bpos_ab,
                            bpos_ab + querylen - 1);
  if (query_readmode == GT_READMODE_REVCOMPL)
  {
    gt_inplace_reverse_complement(seqpairbuf->b_sequence,querylen);
  }
  seqpairbuf->a_len = dblen;
  seqpairbuf->b_len = querylen;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %rdx, 0x10(%rsp)
movq %rsi, %rbp
movq %rdi, %rbx
movl 0x88(%rcx), %eax
movl %eax, 0xc(%rsp)
movq 0x8(%rcx), %r12
movq 0x10(%rcx), %r14
movq 0x40(%rcx), %r15
addq 0x20(%rcx), %r12
movq 0x38(%rcx), %r13
addq 0x50(%rcx), %r13
cmpq 0x10(%rdi), %r14
jb 0x1c5092
movq (%rbx), %rdi
leaq 0x1efcca(%rip), %rdx    # 0x3b4d48
movq %r14, %rsi
movl $0x4dd, %ecx            # imm = 0x4DD
callq 0x1094e6
movq %rax, (%rbx)
movq %r14, 0x10(%rbx)
cmpq 0x18(%rbx), %r15
jb 0x1c50b8
movq 0x8(%rbx), %rdi
leaq 0x1efca5(%rip), %rdx    # 0x3b4d48
movq %r15, %rsi
movl $0x4e4, %ecx            # imm = 0x4E4
callq 0x1094e6
movq %rax, 0x8(%rbx)
movq %r15, 0x18(%rbx)
movq (%rbx), %rsi
leaq (%r14,%r12), %rcx
decq %rcx
movq %rbp, %rdi
movq %r12, %rdx
callq 0xed6e0
movq 0x8(%rbx), %rsi
leaq (%r15,%r13), %rcx
decq %rcx
movq 0x10(%rsp), %rdi
movq %r13, %rdx
callq 0xed6e0
cmpl $0x3, 0xc(%rsp)
jne 0x1c50f8
movq 0x8(%rbx), %rdi
movq %r15, %rsi
callq 0x1e9170
movq %r14, 0x20(%rbx)
movq %r15, 0x28(%rbx)
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq