LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_condenseq.c
// Function: gt_condenseq_runner
static int gt_condenseq_runner(int argc, const char **argv, int parsed_args,
                               void *toolbox, GtError *err)
{
  GtToolbox *condenseq_toolbox = toolbox;
  GtTool *tool;
  int had_err = 0;
  char **nargv = NULL;

  gt_error_check(err);
  gt_assert(condenseq_toolbox);

  /* get condenseq tools */
  tool = gt_toolbox_get_tool(condenseq_toolbox, argv[parsed_args]);
  if (!tool) {
    gt_error_set(err, "condenseq tool '%s' not found; option -help lists "
                      "possible tools", argv[parsed_args]);
    had_err = -1;
  }

  /* call condenseq tool */
  if (!had_err) {
    gt_assert(tool);
    nargv = gt_cstr_array_prefix_first(argv + parsed_args,
                                       gt_error_get_progname(err));
    gt_error_set_progname(err, nargv[0]);
    had_err = gt_tool_run(tool, argc - parsed_args, (const char**) nargv, err);
  }

  /* free */
  gt_cstr_array_delete(nargv);

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r8, %rbx
movq %rcx, %r15
movl %edx, %r14d
movq %rsi, %r12
movl %edi, %ebp
testq %r8, %r8
je 0x9eced
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0x9ed84
testq %r15, %r15
je 0x9ed7f
movslq %r14d, %rax
leaq (%r12,%rax,8), %r13
movq (%r13), %rsi
movq %r15, %rdi
callq 0x1239f1
testq %rax, %rax
je 0x9ed49
movq %rax, %r12
movq %rbx, %rdi
callq 0x101b22
movq %r13, %rdi
movq %rax, %rsi
callq 0xe8b1a
movq %rax, %r15
movq (%rax), %rsi
movq %rbx, %rdi
callq 0x101ada
subl %r14d, %ebp
movq %r12, %rdi
movl %ebp, %esi
movq %r15, %rdx
movq %rbx, %rcx
callq 0x123470
movl %eax, %ebx
jmp 0x9ed66
movq (%r13), %rdx
leaq 0x2b1f6c(%rip), %rsi    # 0x350cc0
xorl %r15d, %r15d
movq %rbx, %rdi
xorl %eax, %eax
callq 0x1019cf
movl $0xffffffff, %ebx       # imm = 0xFFFFFFFF
movq %r15, %rdi
callq 0xe8d46
movl %ebx, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x18e6f
callq 0x18e38
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_condenseq_blast.c
// Function: gt_condenseq_blast_arguments_new
static void* gt_condenseq_blast_arguments_new(void)
{
  GtCondenseqBlastArguments *arguments =
    gt_calloc((size_t) 1, sizeof *arguments);
  arguments->csa = gt_condenseq_search_arguments_new();
  arguments->extraopts = gt_str_new();
  arguments->gff = gt_str_new();
  arguments->ofi = gt_output_file_info_new();
  arguments->querypath = gt_str_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2b1f6c(%rip), %rdx    # 0x350d28
movl $0x1, %edi
movl $0x50, %esi
movl $0x6b, %ecx
callq 0x1093ef
movq %rax, %rbx
callq 0x136f60
movq %rax, 0x10(%rbx)
callq 0x1208f8
movq %rax, 0x28(%rbx)
callq 0x1208f8
movq %rax, 0x20(%rbx)
callq 0x10ff7c
movq %rax, 0x8(%rbx)
callq 0x1208f8
movq %rax, 0x18(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_condenseq_blast.c
// Function: gt_condenseq_blast_arguments_delete
static void gt_condenseq_blast_arguments_delete(void *tool_arguments)
{
  GtCondenseqBlastArguments *arguments = tool_arguments;
  if (arguments != NULL) {
    gt_condenseq_search_arguments_delete(arguments->csa);
    gt_file_delete(arguments->outfp);
    gt_output_file_info_delete(arguments->ofi);
    gt_str_delete(arguments->extraopts);
    gt_str_delete(arguments->gff);
    gt_str_delete(arguments->querypath);
    gt_free(arguments);
  }
}

// Assembly:
testq %rdi, %rdi
je 0x9ee58
pushq %rbx
movq %rdi, %rbx
movq 0x10(%rdi), %rdi
callq 0x136f87
movq (%rbx), %rdi
callq 0x1040fc
movq 0x8(%rbx), %rdi
callq 0x110231
movq 0x28(%rbx), %rdi
callq 0x121b03
movq 0x20(%rbx), %rdi
callq 0x121b03
movq 0x18(%rbx), %rdi
callq 0x121b03
leaq 0x2b1ede(%rip), %rsi    # 0x350d28
movq %rbx, %rdi
movl $0x7e, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_condenseq_blast.c
// Function: gt_condenseq_blast_arguments_check
static int gt_condenseq_blast_arguments_check(GT_UNUSED int rest_argc,
                                              void *tool_arguments,
                                              GT_UNUSED GtError *err)
{
  GtCondenseqBlastArguments *arguments = tool_arguments;
  int had_err = 0;
  if (!(arguments->blastn || arguments->blastp)) {
    gt_error_set(err, "no other searches then blast implemented yet, please "
                 "provide either -blastn or -blastp");
    had_err = -1;
  }
  gt_error_check(err);
  gt_assert(arguments);

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
movq %rdx, %r14
movq %rsi, %rbx
xorl %ebp, %ebp
cmpb $0x0, 0x4d(%rsi)
jne 0x9f0d4
cmpb $0x0, 0x4c(%rbx)
jne 0x9f0d4
leaq 0x2b1f33(%rip), %rsi    # 0x350ff8
movq %r14, %rdi
xorl %eax, %eax
callq 0x1019cf
movl $0xffffffff, %ebp       # imm = 0xFFFFFFFF
testq %r14, %r14
je 0x9f0e5
movq %r14, %rdi
callq 0x101a9a
testb %al, %al
jne 0x9f0f6
testq %rbx, %rbx
je 0x9f0f1
movl %ebp, %eax
popq %rbx
popq %r14
popq %rbp
retq
callq 0x18f18
callq 0x18edf
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_condenseq_blast.c
// Function: gt_ces_blast_range_compare
static int gt_ces_blast_range_compare(const void *a, const void *b,
                                      GT_UNUSED void* data)
{
  const HitRange *rangeA = a,
        *rangeB = b;
  gt_assert(data == NULL);

  if (rangeA->seqid < rangeB->seqid)
    return -1;
  if (rangeA->seqid > rangeB->seqid)
    return 1;
  if (rangeA->range.start < rangeB->range.start)
    return -1;
  if (rangeA->range.start > rangeB->range.start)
    return 1;
  if (rangeA->range.end < rangeB->range.end)
    return -1;
  if (rangeA->range.end > rangeB->range.end)
    return 1;
  return 0;
}

// Assembly:
testq %rdx, %rdx
jne 0xa0865
movq 0x10(%rsi), %rax
cmpq %rax, 0x10(%rdi)
jae 0xa083d
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
retq
movl $0x1, %eax
jbe 0xa0845
retq
movq (%rsi), %rcx
cmpq %rcx, (%rdi)
jb 0xa0837
ja 0xa0844
movq 0x8(%rsi), %rcx
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
cmpq %rcx, 0x8(%rdi)
jb 0xa0844
seta %al
movzbl %al, %eax
retq
pushq %rax
callq 0x19152
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_condenseq_blast.c
// Function: gt_condenseq_blast_process_hit
static int gt_condenseq_blast_process_hit(void *data,
                                          GtUword seqid,
                                          GtRange seqrange,
                                          GT_UNUSED GtError *err)
{
  GtCondenseqBlastPrintHitInfo *info =
    (GtCondenseqBlastPrintHitInfo *) data;
  bool nodecreated;
  HitRange *key = gt_malloc(sizeof(*key));

  gt_error_check(err);

  key->range = seqrange;
  key->seqid = seqid;
  key = gt_rbtree_search(info->to_extract_rbt, key, &nodecreated);
  if (!nodecreated)
    gt_free(key);

  return 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r8, %rbp
movq %rcx, %rbx
movq %rdx, %r12
movq %rsi, %r15
movq %rdi, %r14
leaq 0x2b048b(%rip), %rsi    # 0x350d28
movl $0x18, %edi
movl $0x15d, %edx            # imm = 0x15D
callq 0x1092b2
movq %rax, %r13
testq %rbp, %rbp
je 0xa08c0
movq %rbp, %rdi
callq 0x101a9a
testb %al, %al
jne 0xa090a
movq %r12, (%r13)
movq %rbx, 0x8(%r13)
movq %r15, 0x10(%r13)
movq 0x20(%r14), %rdi
leaq 0x7(%rsp), %rbx
movq %r13, %rsi
movq %rbx, %rdx
callq 0x16e310
cmpb $0x0, (%rbx)
jne 0xa08f9
leaq 0x2b043c(%rip), %rsi    # 0x350d28
movq %rax, %rdi
movl $0x165, %edx            # imm = 0x165
callq 0x109670
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x1918b
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_condenseq_blast.c
// Function: gt_condenseq_avg_helper
static inline int gt_condenseq_avg_helper(GtUword current_len,
                                          void *data,
                                          GT_UNUSED GtError *err)
{
  GtCondenseqBlastQInfo *qinfo = (GtCondenseqBlastQInfo *) data;
  qinfo->avg += current_len;
  qinfo->count++;
  gt_assert(qinfo->avg >= current_len);
  qinfo->max = qinfo->max < current_len ? current_len : qinfo->max;
  return 0;
}

// Assembly:
incq 0x10(%rsi)
addq %rdi, (%rsi)
jb 0xa092a
movq 0x8(%rsi), %rax
cmpq %rdi, %rax
cmovaq %rax, %rdi
movq %rdi, 0x8(%rsi)
xorl %eax, %eax
retq
pushq %rax
callq 0x191c4
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_condenseq_compress.c
// Function: gt_condenseq_compress_arguments_new
static void* gt_condenseq_compress_arguments_new(void)
{
  GtCondenseqCompressArguments *arguments = gt_calloc((size_t) 1,
                                                      sizeof *arguments);
  arguments->indexname = gt_str_new();
  arguments->input_es = NULL;
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2b0c18(%rip), %rdx    # 0x351578
movl $0x1, %edi
movl $0x60, %esi
movl $0x39, %ecx
callq 0x1093ef
movq %rax, %rbx
callq 0x1208f8
movq %rax, 0x8(%rbx)
movq $0x0, (%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_condenseq_compress.c
// Function: gt_condenseq_compress_arguments_delete
static void gt_condenseq_compress_arguments_delete(void *tool_arguments)
{
  GtCondenseqCompressArguments *arguments = tool_arguments;
  if (arguments != NULL) {
    gt_str_delete(arguments->indexname);
    gt_encseq_delete(arguments->input_es);
    gt_free(arguments);
  }
}

// Assembly:
testq %rdi, %rdi
je 0xa09bb
pushq %rbx
movq %rdi, %rbx
movq 0x8(%rdi), %rdi
callq 0x121b03
movq (%rbx), %rdi
callq 0xee90c
leaq 0x2b0bcb(%rip), %rsi    # 0x351578
movq %rbx, %rdi
movl $0x45, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_condenseq_compress.c
// Function: gt_condenseq_compress_arguments_check
static int gt_condenseq_compress_arguments_check(int rest_argc,
                                                 void *tool_arguments,
                                                 GtError *err)
{
  GT_UNUSED GtCondenseqCompressArguments *arguments = tool_arguments;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(arguments);

  if (rest_argc != 1) {
    gt_error_set(err, "give the basename of an encseq as minimum arguments");
    had_err = -1;
  }
  if (arguments->clean_percent != GT_UNDEF_UINT &&
      arguments->clean_percent > 100U) {
    gt_error_set(err, "'-diags_clean' expects an integer argument between 0 "
                 "and 100 ");
    had_err = -1;
  }
  if (arguments->brute && (arguments->diags || arguments->full_diags)) {
    gt_error_set(err, "'-brute_force' is not compatible with '-diagonals' or "
                 "'-full_diags'");
    had_err = -1;
  }
  if (arguments->cutoff_value == 0 && arguments->prune) {
    gt_error_set(err, "'-cutoff 0' disables cutoffs, so '-disable_prune' should"
                 " not be set.");
    had_err = -1;
  }

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
movq %rdx, %rbx
movq %rsi, %r14
movl %edi, %ebp
testq %rdx, %rdx
je 0xa0d89
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xa0e2a
testq %r14, %r14
je 0xa0e25
xorl %eax, %eax
cmpl $0x1, %ebp
je 0xa0daf
leaq 0x2b0f03(%rip), %rsi    # 0x351ca3
movq %rbx, %rdi
xorl %eax, %eax
callq 0x1019cf
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
movl 0x50(%r14), %ecx
addl $-0x65, %ecx
cmpl $-0x67, %ecx
ja 0xa0dd1
leaq 0x2b0f15(%rip), %rsi    # 0x351cd7
movq %rbx, %rdi
xorl %eax, %eax
callq 0x1019cf
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
cmpb $0x1, 0x56(%r14)
jne 0xa0dfc
cmpb $0x0, 0x54(%r14)
jne 0xa0de6
cmpb $0x1, 0x55(%r14)
jne 0xa0dfc
leaq 0x2b0f28(%rip), %rsi    # 0x351d15
movq %rbx, %rdi
xorl %eax, %eax
callq 0x1019cf
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
cmpq $0x0, 0x28(%r14)
jne 0xa0e20
cmpb $0x1, 0x59(%r14)
jne 0xa0e20
leaq 0x2b0f48(%rip), %rsi    # 0x351d59
movq %rbx, %rdi
xorl %eax, %eax
callq 0x1019cf
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
popq %rbx
popq %r14
popq %rbp
retq
callq 0x1926d
callq 0x19234
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_condenseq_extract.c
// Function: gt_condenseq_extract_arguments_new
static void* gt_condenseq_extract_arguments_new(void)
{
  GtCondenserExtractArguments *arguments = gt_calloc((size_t) 1,
                                                     sizeof *arguments);
  arguments->range.start =
    arguments->range.end = GT_UNDEF_UWORD;
  arguments->seqrange.start =
    arguments->seqrange.end = GT_UNDEF_UWORD;
  arguments->ofi = gt_output_file_info_new();
  arguments->mode = gt_str_new();
  arguments->sepchar = gt_str_new();
  arguments->sepchar_opt = NULL;
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2b0c97(%rip), %rdx    # 0x351e93
movl $0x1, %edi
movl $0x60, %esi
movl $0x33, %ecx
callq 0x1093ef
movq %rax, %rbx
pcmpeqd %xmm0, %xmm0
movdqu %xmm0, 0x28(%rax)
movdqu %xmm0, 0x38(%rax)
callq 0x10ff7c
movq %rax, 0x8(%rbx)
callq 0x1208f8
movq %rax, 0x10(%rbx)
callq 0x1208f8
movq %rax, 0x18(%rbx)
movq $0x0, 0x20(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_condenseq_extract.c
// Function: gt_condenseq_extract_arguments_delete
static void gt_condenseq_extract_arguments_delete(void *tool_arguments)
{
  GtCondenserExtractArguments *arguments = tool_arguments;
  if (arguments != NULL) {
    gt_file_delete(arguments->outfp);
    gt_output_file_info_delete(arguments->ofi);
    gt_str_delete(arguments->mode);
    gt_str_delete(arguments->sepchar);
    gt_option_delete(arguments->sepchar_opt);
    gt_free(arguments);
  }
}

// Assembly:
testq %rdi, %rdi
je 0xa1293
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x1040fc
movq 0x8(%rbx), %rdi
callq 0x110231
movq 0x10(%rbx), %rdi
callq 0x121b03
movq 0x18(%rbx), %rdi
callq 0x121b03
movq 0x20(%rbx), %rdi
callq 0x10f386
leaq 0x2b0c0e(%rip), %rsi    # 0x351e93
movq %rbx, %rdi
movl $0x48, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_condenseq_extract.c
// Function: gt_condenseq_extract_arguments_check
static int gt_condenseq_extract_arguments_check(int rest_argc,
                                                void *tool_arguments,
                                                GtError *err)
{
  GtCondenserExtractArguments *arguments = tool_arguments;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(arguments);

  if (rest_argc != 1) {
    had_err = -1;
    gt_error_set(err, "archive parameter is mandatory, use -help for usage");
  }
  if (!had_err &&
      arguments->range.start != GT_UNDEF_UWORD) {
    if (arguments->range.start > arguments->range.end) {
      had_err = -1;
      gt_error_set(err, "give range of positions in the form 'a b' with a "
                   "<= b");
    }
    if (!had_err &&
        strcmp(gt_str_get(arguments->mode), "fasta") == 0) {
      had_err = -1;
      gt_error_set(err, "-range is incompatible to fasta output");
    }
  }
  if (!had_err &&
      arguments->seqrange.start != GT_UNDEF_UWORD) {
    if (arguments->seqrange.start > arguments->seqrange.end) {
      had_err = -1;
      gt_error_set(err, "give range of positions in the form 'a b' with a "
                   "<= b");
    }
  }

  if (!had_err &&
      gt_option_is_set(arguments->sepchar_opt)) {
    if (strcmp(gt_str_get(arguments->mode), "fasta") == 0) {
      had_err = -1;
      gt_error_set(err, "-sepchar is incompatible with -output fasta");
    }
    if (!had_err &&
        gt_str_length(arguments->sepchar) != (GtUword) 1) {
      had_err = -1;
      gt_error_set(err, "sepchar (\"%s\" given) has to be a single character",
                   gt_str_get(arguments->sepchar));
    }
  }

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
movq %rdx, %rbx
movq %rsi, %r14
movl %edi, %ebp
testq %rdx, %rdx
je 0xa1458
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xa153f
testq %r14, %r14
je 0xa153a
cmpl $0x1, %ebp
jne 0xa14af
movq 0x28(%r14), %rax
cmpq $-0x1, %rax
je 0xa1496
cmpq 0x30(%r14), %rax
ja 0xa14a6
movq 0x10(%r14), %rdi
callq 0x120d23
leaq 0x2e19a8(%rip), %rsi    # 0x382e2e
movq %rax, %rdi
callq 0x17a40
testl %eax, %eax
je 0xa1525
movq 0x38(%r14), %rax
cmpq $-0x1, %rax
je 0xa14cc
cmpq 0x40(%r14), %rax
jbe 0xa14cc
leaq 0x2b0c4b(%rip), %rsi    # 0x3520f8
jmp 0xa14b6
leaq 0x2b0c0e(%rip), %rsi    # 0x3520c4
movq %rbx, %rdi
xorl %eax, %eax
callq 0x1019cf
movl $0xffffffff, %ebp       # imm = 0xFFFFFFFF
movl %ebp, %eax
popq %rbx
popq %r14
popq %rbp
retq
movq 0x20(%r14), %rdi
callq 0x10fe52
xorl %ebp, %ebp
testb %al, %al
je 0xa14c5
movq 0x10(%r14), %rdi
callq 0x120d23
leaq 0x2e1943(%rip), %rsi    # 0x382e2e
movq %rax, %rdi
callq 0x17a40
testl %eax, %eax
je 0xa152e
movq 0x18(%r14), %rdi
callq 0x120d4c
cmpq $0x1, %rax
je 0xa14c5
movq 0x18(%r14), %rdi
callq 0x120d23
leaq 0x2b0c6b(%rip), %rsi    # 0x352181
movq %rbx, %rdi
movq %rax, %rdx
xorl %eax, %eax
callq 0x1019cf
jmp 0xa14c0
leaq 0x2b0c02(%rip), %rsi    # 0x35212e
jmp 0xa14b6
leaq 0x2b0c20(%rip), %rsi    # 0x352155
jmp 0xa14b6
callq 0x193b5
callq 0x1937c
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_condenseq_hmmsearch.c
// Function: gt_condenseq_hmmsearch_arguments_new
static void* gt_condenseq_hmmsearch_arguments_new(void)
{
  GtCondenseqHmmsearchArguments *arguments =
    gt_calloc((size_t) 1, sizeof *arguments);
  arguments->csa = gt_condenseq_search_arguments_new();
  arguments->hmm = gt_str_new();
  arguments->hmmsearch_path = gt_str_new();
  arguments->outtable_filename = gt_str_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2b08ec(%rip), %rdx    # 0x3522cc
movl $0x1, %edi
movl $0x30, %esi
movl $0x3c, %ecx
callq 0x1093ef
movq %rax, %rbx
callq 0x136f60
movq %rax, (%rbx)
callq 0x1208f8
movq %rax, 0x8(%rbx)
callq 0x1208f8
movq %rax, 0x10(%rbx)
callq 0x1208f8
movq %rax, 0x18(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_condenseq_hmmsearch.c
// Function: gt_condenseq_hmmsearch_arguments_delete
static void gt_condenseq_hmmsearch_arguments_delete(void *tool_arguments)
{
  GtCondenseqHmmsearchArguments *arguments = tool_arguments;
  if (arguments != NULL) {
    gt_condenseq_search_arguments_delete(arguments->csa);
    gt_str_delete(arguments->hmm);
    gt_str_delete(arguments->hmmsearch_path);
    gt_str_delete(arguments->outtable_filename);
    gt_free(arguments);
  }
}

// Assembly:
testq %rdi, %rdi
je 0xa1a60
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x136f87
movq 0x8(%rbx), %rdi
callq 0x121b03
movq 0x10(%rbx), %rdi
callq 0x121b03
movq 0x18(%rbx), %rdi
callq 0x121b03
leaq 0x2b087a(%rip), %rsi    # 0x3522cc
movq %rbx, %rdi
movl $0x4c, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_condenseq_hmmsearch.c
// Function: gt_condenseq_hmmsearch_arguments_check
static int gt_condenseq_hmmsearch_arguments_check(int rest_argc,
                                                  void *tool_arguments,
                                                  GtError *err)
{
  GtCondenseqHmmsearchArguments GT_UNUSED *arguments = tool_arguments;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(arguments);

  if (rest_argc != 0) {
    gt_error_set(err, "to many arguments use -help for options");
    had_err = -1;
  }
  if (!had_err) {
    struct stat buf;
    if (stat(gt_str_get(arguments->hmmsearch_path), &buf) != 0) {
      gt_error_set(err, "error with %s: %s",
                   gt_str_get(arguments->hmmsearch_path),
                   strerror(errno));
      had_err = -1;
    }
    if (!had_err) {
      mode_t mode = buf.st_mode & S_IRWXU;
      if (!(mode & S_IXUSR)    /* owner executable */
#ifndef _WIN32
          && !(mode & S_IXGRP) /* group ~ */
          && !(mode & S_IXOTH) /* other ~ */
#endif
         ) {
        gt_error_set(err, "%s is not executable",
                     gt_str_get(arguments->hmmsearch_path));
        had_err = -1;
      }
    }
  }
  return had_err;
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
subq $0x90, %rsp
movq %rdx, %rbx
movq %rsi, %r14
movl %edi, %ebp
testq %rdx, %rdx
je 0xa1bba
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xa1c5f
testq %r14, %r14
je 0xa1c5a
testl %ebp, %ebp
je 0xa1bda
leaq 0x2b09ba(%rip), %rsi    # 0x352588
movq %rbx, %rdi
xorl %eax, %eax
callq 0x1019cf
jmp 0xa1c49
movq 0x10(%r14), %rdi
callq 0x120d23
movq %rsp, %rsi
movq %rax, %rdi
callq 0x18000
testl %eax, %eax
je 0xa1c23
movq 0x10(%r14), %rdi
callq 0x120d23
movq %rax, %r14
callq 0x17060
movl (%rax), %edi
callq 0x17240
leaq 0x2b099f(%rip), %rsi    # 0x3525b0
movq %rbx, %rdi
movq %r14, %rdx
movq %rax, %rcx
xorl %eax, %eax
callq 0x1019cf
jmp 0xa1c49
xorl %eax, %eax
testb $0x40, 0x18(%rsp)
jne 0xa1c4e
movq 0x10(%r14), %rdi
callq 0x120d23
leaq 0x2b0986(%rip), %rsi    # 0x3525c2
movq %rbx, %rdi
movq %rax, %rdx
xorl %eax, %eax
callq 0x1019cf
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
addq $0x90, %rsp
popq %rbx
popq %r14
popq %rbp
retq
callq 0x19542
callq 0x19509
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_condenseq_hmmsearch.c
// Function: hmmsearch_create_fine_fas
static void hmmsearch_create_fine_fas(GtStr *fine_fasta_filename,
                                      GtRBTree *seqnums,
                                      GtCondenseq *ces) {
  GtRBTreeIter *tree_iter;
  GtUword *seqnum;
  GtFile *gt_outfp;
  FILE *outfp;

  tree_iter = gt_rbtree_iter_new_from_first(seqnums);
  outfp = gt_xtmpfp_generic(fine_fasta_filename, GT_TMPFP_USETEMPLATE);
  gt_outfp = gt_file_new_from_fileptr(outfp);
  seqnum = gt_rbtree_iter_data(tree_iter);
  while (seqnum != NULL) {
    const char *seq, *desc;
    GtUword seqlen, desclen;
    seq = gt_condenseq_extract_decoded(ces, &seqlen, *seqnum);
    desc = gt_condenseq_description(ces, &desclen, *seqnum);
    gt_fasta_show_entry_nt(desc, desclen, seq, seqlen,
                           GT_FASTA_DEFAULT_WIDTH, gt_outfp);
    seqnum = gt_rbtree_iter_next(tree_iter);
  }
  gt_file_delete(gt_outfp);
  gt_rbtree_iter_delete(tree_iter);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %rdx, %rbx
movq %rdi, %r15
movq %rsi, %rdi
callq 0x16ecc4
movq %rax, %r14
leaq 0x2afc6a(%rip), %rdx    # 0x3522cc
movq %r15, %rdi
movl $0x2, %esi
movl $0xdb, %ecx
callq 0x1021c2
movq %rax, %rdi
callq 0x103c55
movq %rax, %r15
movq %r14, %rdi
callq 0x16efa2
testq %rax, %rax
je 0xa26e5
movq %rax, %rbp
leaq 0x8(%rsp), %r13
movq (%rbp), %rdx
movq %rbx, %rdi
leaq 0x10(%rsp), %rsi
callq 0x13368e
movq %rax, %r12
movq (%rbp), %rdx
movq %rbx, %rdi
movq %r13, %rsi
callq 0x131be9
movq 0x8(%rsp), %rsi
movq 0x10(%rsp), %rcx
movl $0x50, %r8d
movq %rax, %rdi
movq %r12, %rdx
movq %r15, %r9
callq 0x102f8a
movq %r14, %rdi
callq 0x16ee3e
movq %rax, %rbp
testq %rax, %rax
jne 0xa2694
movq %r15, %rdi
callq 0x1040fc
movq %r14, %rdi
callq 0x16efbe
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_condenseq_hmmsearch.c
// Function: hmmsearch_process_seq
static int hmmsearch_process_seq(void *data,
                                 GtUword seqnum,
                                 GT_UNUSED GtError *err)
{
  int had_err = 0;
  bool nodecreated = false;
  GtUword *seqnum_p = gt_malloc(sizeof (*seqnum_p));
  GtRBTree *tree = data;
  *seqnum_p = seqnum;
  (void) gt_rbtree_search(tree,
                          seqnum_p,
                          &nodecreated);
  if (!nodecreated)
    gt_free(seqnum_p);
  return had_err;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, %r14
movq %rdi, %r15
leaq 0x7(%rsp), %r12
movb $0x0, (%r12)
leaq 0x2afa25(%rip), %rsi    # 0x3522cc
movl $0x8, %edi
movl $0xbb, %edx
callq 0x1092b2
movq %rax, %rbx
movq %r14, (%rax)
movq %r15, %rdi
movq %rax, %rsi
movq %r12, %rdx
callq 0x16e310
cmpb $0x0, (%r12)
jne 0xa28e5
leaq 0x2af9f4(%rip), %rsi    # 0x3522cc
movq %rbx, %rdi
movl $0xc2, %edx
callq 0x109670
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
nop
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_condenseq_search.c
// Function: gt_condenseq_search_toolbox_new
static void* gt_condenseq_search_toolbox_new(void)
{
  GtToolbox *condenseq_search_toolbox = gt_toolbox_new();
  gt_toolbox_add_tool(condenseq_search_toolbox,
                      "blast", gt_condenseq_blast());
  gt_toolbox_add_tool(condenseq_search_toolbox,
                      "hmmsearch", gt_condenseq_hmmsearch());
  return condenseq_search_toolbox;
}

// Assembly:
pushq %rbx
callq 0x12391a
movq %rax, %rbx
callq 0x9ed8c
leaq 0x2edc35(%rip), %rsi    # 0x390b49
movq %rbx, %rdi
movq %rax, %rdx
callq 0x12394f
callq 0xa19b0
leaq 0x2af7d5(%rip), %rsi    # 0x352700
movq %rbx, %rdi
movq %rax, %rdx
callq 0x12394f
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_condenseq_search.c
// Function: gt_condenseq_search_option_parser_new
static GtOptionParser*
  gt_condenseq_search_option_parser_new(void *toolbox)
{
  GtToolbox *search_toolbox = toolbox;
  GtOptionParser *option_parser;
  gt_assert(search_toolbox);

  /* init */
  option_parser = gt_option_parser_new("tool [option ...]",
                            "Call one of the CONDENSER search tools to query "
                            "redundancy compressed genomic data.");
  gt_option_parser_set_comment_func(option_parser, gt_toolbox_show,
                                    search_toolbox);
  gt_option_parser_set_min_args(option_parser, 1U);
  return option_parser;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xa2f8c
movq %rdi, %rbx
leaq 0x2adcea(%rip), %rdi    # 0x350c3d
leaq 0x2afcc7(%rip), %rsi    # 0x352c21
callq 0x10cc4e
movq %rax, %r14
leaq 0x80b45(%rip), %rsi     # 0x123aae
movq %rax, %rdi
movq %rbx, %rdx
callq 0x10cd8d
movq %r14, %rdi
movl $0x1, %esi
callq 0x10d766
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x1973f
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_condenseq_search.c
// Function: gt_condenseq_search_runner
static int gt_condenseq_search_runner(GT_UNUSED int argc,
                                      GT_UNUSED const char **argv,
                                      GT_UNUSED int parsed_args,
                                      void *toolbox,
                                      GtError *err)
{
  GtToolbox *search_toolbox = toolbox;
  GtTool *tool;
  int had_err = 0;
  char **nargv = NULL;

  gt_error_check(err);
  gt_assert(search_toolbox);

  /* get search tools */
  tool = gt_toolbox_get_tool(search_toolbox, argv[parsed_args]);
  if (!tool) {
    gt_error_set(err,
                 "condenseq search tool '%s' not found; option -help lists "
                 "possible tools", argv[parsed_args]);
    had_err = -1;
  }
  /* call search tool */
  if (!had_err) {
    gt_assert(tool);
    nargv = gt_cstr_array_prefix_first(argv + parsed_args,
                                       gt_error_get_progname(err));
    gt_error_set_progname(err, nargv[0]);
    had_err = gt_tool_run(tool, argc - parsed_args, (const char**) nargv, err);
  }

  /* free */
  gt_cstr_array_delete(nargv);

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r8, %rbx
movq %rcx, %r15
movl %edx, %r14d
movq %rsi, %r12
movl %edi, %ebp
testq %r8, %r8
je 0xa2fbf
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xa3056
testq %r15, %r15
je 0xa3051
movslq %r14d, %rax
leaq (%r12,%rax,8), %r13
movq (%r13), %rsi
movq %r15, %rdi
callq 0x1239f1
testq %rax, %rax
je 0xa301b
movq %rax, %r12
movq %rbx, %rdi
callq 0x101b22
movq %r13, %rdi
movq %rax, %rsi
callq 0xe8b1a
movq %rax, %r15
movq (%rax), %rsi
movq %rbx, %rdi
callq 0x101ada
subl %r14d, %ebp
movq %r12, %rdi
movl %ebp, %esi
movq %r15, %rdx
movq %rbx, %rcx
callq 0x123470
movl %eax, %ebx
jmp 0xa3038
movq (%r13), %rdx
leaq 0x2afc6a(%rip), %rsi    # 0x352c90
xorl %r15d, %r15d
movq %rbx, %rdi
xorl %eax, %eax
callq 0x1019cf
movl $0xffffffff, %ebx       # imm = 0xFFFFFFFF
movq %r15, %rdi
callq 0xe8d46
movl %ebx, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x197ad
callq 0x19776
nop
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_congruence.c
// Function: gt_cge_option_parser_new
static GtOptionParser* gt_cge_option_parser_new(void *tool_arguments)
{
  GtToolbox *index_toolbox = tool_arguments;
  GtOptionParser *op;

  gt_assert(index_toolbox != NULL);
  op = gt_option_parser_new(
                    "[option ...] congruence_tool [argument ...]",
                    "Call a congruence subtool and pass argument(s) to it.");
  gt_option_parser_set_comment_func(op, gt_toolbox_show, index_toolbox);
  gt_option_parser_set_min_args(op, 1U);
  gt_option_parser_refer_to_manual(op);
  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xa3145
movq %rdi, %rbx
leaq 0x2afd85(%rip), %rdi    # 0x352e89
leaq 0x2afdaa(%rip), %rsi    # 0x352eb5
callq 0x10cc4e
movq %rax, %r14
leaq 0x80994(%rip), %rsi     # 0x123aae
movq %rax, %rdi
movq %rbx, %rdx
callq 0x10cd8d
movq %r14, %rdi
movl $0x1, %esi
callq 0x10d766
movq %r14, %rdi
callq 0x10cd7d
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x197e4
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_congruence.c
// Function: gt_cge_runner
static int gt_cge_runner(int argc, const char **argv, int parsed_args,
                                 void *tool_arguments, GtError *err)
{
  GtToolbox *index_toolbox = tool_arguments;
  GtToolfunc toolfunc;
  GtTool *tool = NULL;
  char **nargv = NULL;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(index_toolbox != NULL);

  /* determine tool */
  if (!gt_toolbox_has_tool(index_toolbox, argv[parsed_args]))
  {
    gt_error_set(err, "congruence tool '%s' not found; option -help lists "
                   "possible tools", argv[parsed_args]);
    had_err = -1;
  }

  /* call sub-tool */
  if (!had_err)
  {
    if (!(toolfunc = gt_toolbox_get(index_toolbox, argv[parsed_args])))
    {
      tool = gt_toolbox_get_tool(index_toolbox, argv[parsed_args]);
      gt_assert(tool != NULL);
    }
    nargv = gt_cstr_array_prefix_first(argv + parsed_args,
                                       gt_error_get_progname(err));
    gt_error_set_progname(err, nargv[0]);
    if (toolfunc != NULL)
      had_err = toolfunc(argc - parsed_args, (const char**) nargv, err);
    else
      had_err = gt_tool_run(tool, argc - parsed_args, (const char**) nargv,
                            err);
  }
  gt_cstr_array_delete(nargv);
  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r8, %rbx
movq %rcx, %r15
movl %edx, %r14d
movq %rsi, %r12
movl %edi, %ebp
testq %r8, %r8
je 0xa3178
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xa3250
testq %r15, %r15
je 0xa324b
movslq %r14d, %r13
movq (%r12,%r13,8), %rsi
movq %r15, %rdi
callq 0x123a17
movq (%r12,%r13,8), %rdx
testb %al, %al
je 0xa31b9
leaq (%r12,%r13,8), %r13
movq %r15, %rdi
movq %rdx, %rsi
callq 0x123a87
movq %rax, %r12
testq %rax, %rax
je 0xa31d4
movq $0x0, (%rsp)
jmp 0xa31e9
leaq 0x2afd39(%rip), %rsi    # 0x352ef9
xorl %r15d, %r15d
movq %rbx, %rdi
xorl %eax, %eax
callq 0x1019cf
movl $0xffffffff, %ebx       # imm = 0xFFFFFFFF
jmp 0xa3232
movq (%r13), %rsi
movq %r15, %rdi
callq 0x1239f1
movq %rax, (%rsp)
testq %rax, %rax
je 0xa3255
movq %rbx, %rdi
callq 0x101b22
movq %r13, %rdi
movq %rax, %rsi
callq 0xe8b1a
movq %rax, %r15
movq (%rax), %rsi
movq %rbx, %rdi
callq 0x101ada
subl %r14d, %ebp
testq %r12, %r12
je 0xa321f
movl %ebp, %edi
movq %r15, %rsi
movq %rbx, %rdx
callq *%r12
jmp 0xa3230
movq (%rsp), %rdi
movl %ebp, %esi
movq %r15, %rdx
movq %rbx, %rcx
callq 0x123470
movl %eax, %ebx
movq %r15, %rdi
callq 0xe8d46
movl %ebx, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x1988f
callq 0x1981d
callq 0x19856
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_congruence.c
// Function: gt_cge_spacedseed_arguments_new
static void *gt_cge_spacedseed_arguments_new(void)
{
  Cge_spacedseed_options *arguments
    = gt_malloc(sizeof (Cge_spacedseed_options));
  arguments->str_inputindex = gt_str_new();
  arguments->queryfilenames = gt_str_array_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2afa76(%rip), %rsi    # 0x352cd8
movl $0x28, %edi
movl $0x2a, %edx
callq 0x1092b2
movq %rax, %rbx
callq 0x1208f8
movq %rax, 0x8(%rbx)
callq 0x121b54
movq %rax, 0x10(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_congruence.c
// Function: gt_cge_spacedseed_arguments_delete
static void gt_cge_spacedseed_arguments_delete(void *tool_arguments)
{
  Cge_spacedseed_options *arguments = tool_arguments;

  if (!arguments)
  {
    return;
  }
  gt_str_delete(arguments->str_inputindex);
  gt_str_array_delete(arguments->queryfilenames);
  gt_option_delete(arguments->refoptionpckindex);
  gt_option_delete(arguments->refoptionesaindex);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xa32cd
pushq %rbx
movq %rdi, %rbx
movq 0x8(%rdi), %rdi
callq 0x121b03
movq 0x10(%rbx), %rdi
callq 0x121e8b
movq 0x20(%rbx), %rdi
callq 0x10f386
movq 0x18(%rbx), %rdi
callq 0x10f386
leaq 0x2afa19(%rip), %rsi    # 0x352cd8
movq %rbx, %rdi
movl $0x3c, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_congruence.c
// Function: gt_cge_spacedseed_arguments_check
static int gt_cge_spacedseed_arguments_check(int rest_argc,
                                             void *tool_arguments,
                                             GtError *err)
{
  Cge_spacedseed_options *arguments = tool_arguments;

  if (gt_str_length(arguments->str_inputindex) == 0)
  {
    gt_error_set(err,"missing indexname");
    return -1;
  }
  if (gt_option_is_set(arguments->refoptionesaindex))
  {
    arguments->withesa = true;
  } else
  {
    gt_assert(gt_option_is_set(arguments->refoptionpckindex));
    arguments->withesa = false;
  }
  if (rest_argc != 0)
  {
    gt_error_set(err,"superfluous file arguments");
    return -1;
  }
  return 0;
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
movq %rdx, %rbx
movq %rsi, %r14
movl %edi, %ebp
movq 0x8(%rsi), %rdi
callq 0x120d4c
testq %rax, %rax
je 0xa3444
movq 0x18(%r14), %rdi
callq 0x10fe52
movb $0x1, %cl
testb %al, %al
jne 0xa3434
movq 0x20(%r14), %rdi
callq 0x10fe52
testb %al, %al
je 0xa3463
xorl %ecx, %ecx
movb %cl, (%r14)
testl %ebp, %ebp
je 0xa345c
leaq 0x2af9c6(%rip), %rsi    # 0x352e08
jmp 0xa344b
leaq 0x2af95a(%rip), %rsi    # 0x352da5
movq %rbx, %rdi
xorl %eax, %eax
callq 0x1019cf
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
jmp 0xa345e
xorl %eax, %eax
popq %rbx
popq %r14
popq %rbp
retq
callq 0x198c8
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_congruence.c
// Function: gt_cge_spacedseed_runner
static int gt_cge_spacedseed_runner(GT_UNUSED int argc,
                                    GT_UNUSED const char **argv,
                                    GT_UNUSED int parsed_args,
                                    void *tool_arguments,
                                    GtError *err)
{
  Cge_spacedseed_options *arguments = tool_arguments;
  GtLogger *logger = NULL;
  bool haserr = false;

  gt_assert(parsed_args == argc);
  logger = gt_logger_new(arguments->verbose, GT_LOGGER_DEFLT_PREFIX, stdout);
  if (arguments->verbose)
  {
    GtUword idx;

    printf("# %sindex=%s\n",arguments->withesa ? "esa" : "pck",
                            gt_str_get(arguments->str_inputindex));
    for (idx = 0; idx < gt_str_array_size(arguments->queryfilenames); idx++)
    {
      printf("# queryfile=%s\n",
             gt_str_array_get(arguments->queryfilenames,idx));
    }
  }
  if (gt_matchspacedseed(arguments->withesa,
                      arguments->docompare,
                      gt_str_get(arguments->str_inputindex),
                      arguments->queryfilenames,
                      arguments->verbose,
                      err) != 0)
  {
    haserr = true;
  }
  gt_logger_delete(logger);
  return haserr ? - 1 : 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
cmpl %edi, %edx
jne 0xa3564
movq %r8, %rbx
movq %rcx, %r14
movzbl 0x2(%rcx), %edi
movq 0x420a5c(%rip), %rax    # 0x4c3ee8
movq (%rax), %rdx
leaq 0x2ac43e(%rip), %rsi    # 0x34f8d4
callq 0x108ed0
movq %rax, %r15
cmpb $0x1, 0x2(%r14)
jne 0xa351a
leaq 0x2bf7d6(%rip), %rax    # 0x362c82
cmpb $0x0, (%r14)
leaq 0x2b3327(%rip), %r12    # 0x3567de
cmovneq %rax, %r12
movq 0x8(%r14), %rdi
callq 0x120d23
leaq 0x2af971(%rip), %rdi    # 0x352e3c
movq %r12, %rsi
movq %rax, %rdx
xorl %eax, %eax
callq 0x17070
movq 0x10(%r14), %rdi
callq 0x121e78
testq %rax, %rax
je 0xa351a
leaq 0x2af95d(%rip), %r12    # 0x352e4a
xorl %r13d, %r13d
movq 0x10(%r14), %rdi
movq %r13, %rsi
callq 0x121cfa
movq %r12, %rdi
movq %rax, %rsi
xorl %eax, %eax
callq 0x17070
incq %r13
movq 0x10(%r14), %rdi
callq 0x121e78
cmpq %rax, %r13
jb 0xa34f0
movzbl (%r14), %ebp
movzbl 0x1(%r14), %r12d
movq 0x8(%r14), %rdi
callq 0x120d23
movq 0x10(%r14), %rcx
movzbl 0x2(%r14), %r8d
movl %ebp, %edi
movl %r12d, %esi
movq %rax, %rdx
movq %rbx, %r9
callq 0x194bb0
movl %eax, %ebx
movq %r15, %rdi
callq 0x10916a
xorl %eax, %eax
negl %ebx
sbbl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x198ff
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_consensus_sa.c
// Function: gt_consensus_sa_runner
static int gt_consensus_sa_runner(GT_UNUSED int argc, const char **argv,
                                  int parsed_args,
                                  GT_UNUSED void *tool_arguments, GtError *err)
{
  GtArray *spliced_alignments;
  GtSSplicedAlignment *sa;
  GtUword i;
  int had_err = 0;
  gt_error_check(err);

  /* parse input file and store resuilts in the spliced alignment array */
  spliced_alignments = gt_array_new(sizeof (GtSSplicedAlignment*));
  had_err = gt_sspliced_alignment_parse(spliced_alignments, argv[parsed_args],
                                     err);

  if (!had_err) {
    /* sort spliced alignments */
    qsort(gt_array_get_space(spliced_alignments),
          gt_array_size(spliced_alignments),
          gt_array_elem_size(spliced_alignments),
          (GtCompare) gt_sspliced_alignment_compare_ptr);

    /* compute the consensus spliced alignments */
    gt_consensus_sa(gt_array_get_space(spliced_alignments),
                    gt_array_size(spliced_alignments),
                    gt_array_elem_size(spliced_alignments), get_genomic_range,
                    get_strand, get_exons, process_splice_form, NULL);
  }

  /* free */
  for (i = 0; i < gt_array_size(spliced_alignments); i++) {
    sa = *(GtSSplicedAlignment**) gt_array_get(spliced_alignments, i);
    gt_sspliced_alignment_delete(sa);
  }
  gt_array_delete(spliced_alignments);

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movq %r8, %r14
movl %edx, %ebp
movq %rsi, %r15
testq %r8, %r8
je 0xa35d7
movq %r14, %rdi
callq 0x101a9a
testb %al, %al
jne 0xa36cb
movl $0x8, %edi
callq 0xd46fc
movq %rax, %rbx
movslq %ebp, %rax
movq (%r15,%rax,8), %rsi
movq %rbx, %rdi
movq %r14, %rdx
callq 0x1828e0
movl %eax, %ebp
testl %eax, %eax
jne 0xa3683
movq %rbx, %rdi
callq 0xd49a9
movq %rax, %r14
movq %rbx, %rdi
callq 0xd4a9a
movq %rax, %r15
movq %rbx, %rdi
callq 0xd4aa7
leaq 0xdf255(%rip), %rcx     # 0x18287a
movq %r14, %rdi
movq %r15, %rsi
movq %rax, %rdx
callq 0x17f60
movq %rbx, %rdi
callq 0xd49a9
movq %rax, %r14
movq %rbx, %rdi
callq 0xd4a9a
movq %rax, %r15
movq %rbx, %rdi
callq 0xd4aa7
leaq 0x10b(%rip), %r10       # 0xa3763
leaq 0x71(%rip), %rcx        # 0xa36d0
leaq 0x7c(%rip), %r8         # 0xa36e2
leaq 0x85(%rip), %r9         # 0xa36f2
movq %r14, %rdi
movq %r15, %rsi
movq %rax, %rdx
pushq $0x0
pushq %r10
callq 0x137064
addq $0x10, %rsp
movq %rbx, %rdi
callq 0xd4a9a
testq %rax, %rax
je 0xa36b6
xorl %r14d, %r14d
movq %rbx, %rdi
movq %r14, %rsi
callq 0xd47ba
movq (%rax), %rdi
callq 0x18277b
incq %r14
movq %rbx, %rdi
callq 0xd4a9a
cmpq %rax, %r14
jb 0xa3693
movq %rbx, %rdi
callq 0xd4ef4
movl %ebp, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
callq 0x19938
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_consensus_sa.c
// Function: get_exons
static void get_exons(GtArray *exon_ranges, const void *sa)
{
  GtSSplicedAlignment *alignment = *(GtSSplicedAlignment**) sa;
  GtRange exon;
  GtUword i;
  gt_assert(alignment);
  for (i = 0; i < gt_sspliced_alignment_num_of_exons(alignment); i++) {
    exon = gt_sspliced_alignment_get_exon(alignment, i);
    gt_array_add(exon_ranges, exon);
  }
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq (%rsi), %r14
testq %r14, %r14
je 0xa375e
movq %rdi, %rbx
movq %r14, %rdi
callq 0x1827fe
testq %rax, %rax
je 0xa3752
xorl %r15d, %r15d
leaq 0x8(%rsp), %r12
movq %r14, %rdi
movq %r15, %rsi
callq 0x182812
movq %rax, 0x8(%rsp)
movq %rdx, 0x10(%rsp)
movl $0x10, %edx
movq %rbx, %rdi
movq %r12, %rsi
callq 0xd49ce
incq %r15
movq %r14, %rdi
callq 0x1827fe
cmpq %rax, %r15
jb 0xa371d
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
callq 0x199a6
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_consensus_sa.c
// Function: process_splice_form
static void process_splice_form(GtArray *spliced_alignments_in_form,
                                GT_UNUSED const void *set_of_sas,
                                GT_UNUSED GtUword number_of_sas,
                                GT_UNUSED size_t size_of_sa,
                                GT_UNUSED void *userdata)
{
  GtUword i;

  printf("contains [");
  for (i = 0; i < gt_array_size(spliced_alignments_in_form); i++) {
    if (i)
      gt_xputchar(',');
    printf(""GT_WU"",
           *((GtUword*) gt_array_get(spliced_alignments_in_form, i)));
  }
  printf("]\n");
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %rdi, %rbx
leaq 0x2af89b(%rip), %rdi    # 0x35300d
xorl %eax, %eax
callq 0x17070
movq %rbx, %rdi
callq 0xd4a9a
testq %rax, %rax
je 0xa37c7
leaq 0x321e9f(%rip), %r14    # 0x3c562c
xorl %r15d, %r15d
testq %r15, %r15
je 0xa379f
movl $0x2c, %edi
callq 0x1256e8
movq %rbx, %rdi
movq %r15, %rsi
callq 0xd47ba
movq (%rax), %rsi
movq %r14, %rdi
xorl %eax, %eax
callq 0x17070
incq %r15
movq %rbx, %rdi
callq 0xd4a9a
cmpq %rax, %r15
jb 0xa3790
leaq 0x32dd3c(%rip), %rdi    # 0x3d150a
popq %rbx
popq %r14
popq %r15
jmp 0x17bd0
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_convertseq.c
// Function: gt_convertseq_arguments_new
static void* gt_convertseq_arguments_new(void)
{
  GtConvertseqArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->ofi = gt_output_file_info_new();
  arguments->outfp = NULL;
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2af815(%rip), %rdx    # 0x353018
movl $0x1, %edi
movl $0x20, %esi
movl $0x31, %ecx
callq 0x1093ef
movq %rax, %rbx
callq 0x10ff7c
movq %rax, 0x10(%rbx)
movq $0x0, 0x18(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_convertseq.c
// Function: gt_convertseq_arguments_delete
static void gt_convertseq_arguments_delete(void *tool_arguments)
{
  GtConvertseqArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xa3860
pushq %rbx
movq %rdi, %rbx
movq 0x18(%rdi), %rdi
callq 0x1040fc
movq 0x10(%rbx), %rdi
callq 0x110231
leaq 0x2af7c6(%rip), %rsi    # 0x353018
movq %rbx, %rdi
movl $0x3d, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_csa.c
// Function: gt_csa_arguments_delete
static void gt_csa_arguments_delete(void *tool_arguments)
{
  CSAArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xa3dfc
pushq %rbx
movq %rdi, %rbx
movq 0x18(%rdi), %rdi
callq 0x1040fc
movq 0x10(%rbx), %rdi
callq 0x110231
leaq 0x2af412(%rip), %rsi    # 0x353200
movq %rbx, %rdi
movl $0x31, %edx
popq %rbx
jmp 0x109670
retq
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_csa.c
// Function: gt_csa_option_parser_new
static GtOptionParser* gt_csa_option_parser_new(void *tool_arguments)
{
  CSAArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [GFF3_file]",
                            "Transform spliced alignments from GFF3 file into "
                            "consensus spliced alignments.");

  /* -join-length */
  option = gt_option_new_uword("join-length", "set join length for the spliced "
                               "alignment clustering", &arguments->join_length,
                               GT_DEFAULT_JOIN_LENGTH);
  gt_option_parser_add_option(op, option);

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  /* output file options */
  gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);

  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
  gt_option_parser_set_max_args(op, 1);

  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xa3e99
movq %rdi, %r14
leaq 0x2ab27b(%rip), %rdi    # 0x34f08f
leaq 0x2af411(%rip), %rsi    # 0x35322c
callq 0x10cc4e
movq %rax, %rbx
leaq 0x8(%r14), %rdx
leaq 0x2af44d(%rip), %rdi    # 0x35327b
leaq 0x2af452(%rip), %rsi    # 0x353287
movl $0x12c, %ecx            # imm = 0x12C
callq 0x10f4c7
movq %rbx, %rdi
movq %rax, %rsi
callq 0x10cd10
movq %r14, %rdi
callq 0x10f473
movq %rbx, %rdi
movq %rax, %rsi
callq 0x10cd10
movq 0x10(%r14), %rdi
addq $0x18, %r14
movq %rbx, %rsi
movq %r14, %rdx
callq 0x10ffa3
leaq 0xb0025(%rip), %rsi     # 0x153e9c
movq %rbx, %rdi
xorl %edx, %edx
callq 0x10cd8d
movq %rbx, %rdi
movl $0x1, %esi
callq 0x10d775
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x19af4
// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_csa.c
// Function: gt_csa_runner
static int gt_csa_runner(GT_UNUSED int argc, const char **argv, int parsed_args,
                         void *tool_arguments, GtError *err)
{
  GtNodeStream *gff3_in_stream, *csa_stream, *gff3_out_stream;
  CSAArguments *arguments = tool_arguments;
  int had_err;

  gt_error_check(err);
  gt_assert(arguments);

  /* create the streams */
  gff3_in_stream  = gt_gff3_in_stream_new_sorted(argv[parsed_args]);
  if (arguments->verbose && arguments->outfp)
    gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) gff3_in_stream);
  csa_stream      = gt_csa_stream_new(gff3_in_stream, arguments->join_length);
  gff3_out_stream = gt_gff3_out_stream_new(csa_stream, arguments->outfp);

  /* pull the features through the stream and free them afterwards */
  had_err = gt_node_stream_pull(gff3_out_stream, err);

  /* free */
  gt_node_stream_delete(gff3_out_stream);
  gt_node_stream_delete(csa_stream);
  gt_node_stream_delete(gff3_in_stream);

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movq %r8, %rbx
movq %rcx, %r14
movl %edx, %ebp
movq %rsi, %r15
testq %r8, %r8
je 0xa3ec2
movq %rbx, %rdi
callq 0x101a9a
testb %al, %al
jne 0xa3f3e
testq %r14, %r14
je 0xa3f39
movslq %ebp, %rax
movq (%r15,%rax,8), %rdi
callq 0x14d0a8
movq %rax, %r15
cmpb $0x1, (%r14)
jne 0xa3eeb
cmpq $0x0, 0x18(%r14)
je 0xa3eeb
movq %r15, %rdi
callq 0x14ce62
movq 0x8(%r14), %rsi
movq %r15, %rdi
callq 0x137fcf
movq %rax, %r12
movq 0x18(%r14), %rsi
movq %rax, %rdi
callq 0x14e310
movq %rax, %r14
movq %rax, %rdi
movq %rbx, %rsi
callq 0x16adca
movl %eax, %ebx
movq %r14, %rdi
callq 0x16ac6e
movq %r12, %rdi
callq 0x16ac6e
movq %r15, %rdi
callq 0x16ac6e
movl %ebx, %eax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
callq 0x19b62
callq 0x19b2b
nop