LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/tools/gt_compreads_refcompress.c
// Function: gt_compreads_refcompress_arguments_new
static void* gt_compreads_refcompress_arguments_new(void)
{
  GtCsrRcrEncodeArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->name = gt_str_new();
  arguments->ref = gt_str_new();
  arguments->align = gt_str_new();
  arguments->qrng.start = GT_UNDEF_UWORD;
  arguments->qrng.end = GT_UNDEF_UWORD;

  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2caa82(%rip), %rdx    # 0x2e73c1
pushq $0x1
popq %rdi
pushq $0x38
popq %rsi
pushq $0x35
popq %rcx
callq 0x9334a
movq %rax, %rbx
callq 0xacb84
movq %rax, 0x8(%rbx)
callq 0xacb84
movq %rax, 0x10(%rbx)
callq 0xacb84
movq %rax, 0x18(%rbx)
pcmpeqd %xmm0, %xmm0
movdqu %xmm0, 0x28(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/tools/gt_compreads_refcompress.c
// Function: gt_compreads_refcompress_arguments_delete
static void gt_compreads_refcompress_arguments_delete(void *tool_arguments)
{
  GtCsrRcrEncodeArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->name);
  gt_str_delete(arguments->ref);
  gt_str_delete(arguments->align);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0x1c9b0
pushq %rbx
movq %rdi, %rbx
movq 0x8(%rdi), %rdi
callq 0xae103
movq 0x10(%rbx), %rdi
callq 0xae103
movq 0x18(%rbx), %rdi
callq 0xae103
leaq 0x2caa1d(%rip), %rsi    # 0x2e73c1
pushq $0x46
popq %rdx
movq %rbx, %rdi
popq %rbx
jmp 0x936f9
retq
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/tools/gt_compreads_refdecompress.c
// Function: gt_compreads_refdecompress_arguments_new
static void* gt_compreads_refdecompress_arguments_new(void)
{
  GtCsrRcrDecodeArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->file = gt_str_new();
  arguments->ref = gt_str_new();
  arguments->name = gt_str_new();

  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2ca87f(%rip), %rdx    # 0x2e774e
pushq $0x1
popq %rdi
pushq $0x20
popq %rsi
pushq $0x2c
popq %rcx
callq 0x9334a
movq %rax, %rbx
callq 0xacb84
movq %rax, (%rbx)
callq 0xacb84
movq %rax, 0x8(%rbx)
callq 0xacb84
movq %rax, 0x10(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/tools/gt_compreads_refdecompress.c
// Function: gt_compreads_refdecompress_arguments_delete
static void gt_compreads_refdecompress_arguments_delete(void *tool_arguments)
{
  GtCsrRcrDecodeArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->file);
  gt_str_delete(arguments->name);
  gt_str_delete(arguments->ref);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0x1cf35
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0xae103
movq 0x10(%rbx), %rdi
callq 0xae103
movq 0x8(%rbx), %rdi
callq 0xae103
leaq 0x2ca825(%rip), %rsi    # 0x2e774e
pushq $0x3b
popq %rdx
movq %rbx, %rdi
popq %rbx
jmp 0x936f9
retq
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/tools/gt_condenseq.c
// Function: gt_condenseq_toolbox_new
static void* gt_condenseq_toolbox_new(void)
{
  GtToolbox *condenseq_toolbox = gt_toolbox_new();
  gt_toolbox_add_tool(condenseq_toolbox, "compress", gt_condenseq_compress());
  gt_toolbox_add_tool(condenseq_toolbox, "search", gt_condenseq_search());
  gt_toolbox_add_tool(condenseq_toolbox, "extract", gt_condenseq_extract());
  gt_toolbox_add_tool(condenseq_toolbox, "info", gt_condenseq_info());
  return condenseq_toolbox;
}

// Assembly:
pushq %rbx
callq 0xb0c26
movq %rax, %rbx
callq 0x1f948
leaq 0x2c909f(%rip), %rsi    # 0x2e6a9f
movq %rbx, %rdi
movq %rax, %rdx
callq 0xb0c55
callq 0x221c4
leaq 0x2ca6f1(%rip), %rsi    # 0x2e8108
movq %rbx, %rdi
movq %rax, %rdx
callq 0xb0c55
callq 0x202e8
leaq 0x2ce8d6(%rip), %rsi    # 0x2ec304
movq %rbx, %rdi
movq %rax, %rdx
callq 0xb0c55
callq 0x21ba8
leaq 0x316091(%rip), %rsi    # 0x333ad6
movq %rbx, %rdi
movq %rax, %rdx
callq 0xb0c55
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/tools/gt_condenseq.c
// Function: gt_condenseq_option_parser_new
static GtOptionParser* gt_condenseq_option_parser_new(void *tool_arguments)
{
  GtToolbox *condenseq_toolbox = tool_arguments;
  GtOptionParser *op;
  gt_assert(condenseq_toolbox);

  /* init */
  op = gt_option_parser_new("tool [option ...]",
                            "Call one of the CONDENSER tools to prepare "
                            "or manipulate redundancy compressed genomic data."
                            );
  gt_option_parser_set_comment_func(op, gt_toolbox_show, condenseq_toolbox);
  gt_option_parser_set_min_args(op, 1U);
  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x1daa4
movq %rdi, %rbx
leaq 0x2ca1d0(%rip), %rdi    # 0x2e7c3d
leaq 0x2ca1db(%rip), %rsi    # 0x2e7c4f
callq 0x97df5
movq %rax, %r14
leaq 0x93415(%rip), %rsi     # 0xb0e98
movq %rax, %rdi
movq %rbx, %rdx
callq 0x98045
pushq $0x1
popq %rsi
movq %r14, %rdi
callq 0x98be7
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
movq 0x41a4bd(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2c755e(%rip), %rsi    # 0x2e5013
leaq 0x2ca137(%rip), %rdx    # 0x2e7bf3
leaq 0x2ca142(%rip), %rcx    # 0x2e7c05
leaq 0x2ca15a(%rip), %r8     # 0x2e7c24
pushq $0x31
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x1db08
movq %rbx, %rdi
callq 0x89eb7
testb %al, %al
jne 0x1dbc2
testq %r15, %r15
je 0x1db98
movslq %r14d, %rax
leaq (%r12,%rax,8), %r13
movq (%r13), %rsi
movq %r15, %rdi
callq 0xb0d2d
testq %rax, %rax
je 0x1db64
movq %rax, %r12
movq %rbx, %rdi
callq 0x8a001
movq %r13, %rdi
movq %rax, %rsi
callq 0x6c7c9
movq %rax, %r15
movq (%rax), %rsi
movq %rbx, %rdi
callq 0x89f8a
subl %r14d, %ebp
movq %r12, %rdi
movl %ebp, %esi
movq %r15, %rdx
movq %rbx, %rcx
callq 0xb05a1
movl %eax, %ebx
jmp 0x1db7f
movq (%r13), %rdx
leaq 0x2ca151(%rip), %rsi    # 0x2e7cc0
xorl %r15d, %r15d
movq %rbx, %rdi
xorl %eax, %eax
callq 0x89dbb
pushq $-0x1
popq %rbx
movq %r15, %rdi
callq 0x6ca1b
movl %ebx, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x41a3c9(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2c746a(%rip), %rsi    # 0x2e5013
leaq 0x2ca043(%rip), %rdx    # 0x2e7bf3
leaq 0x2ca0f5(%rip), %rcx    # 0x2e7cac
leaq 0x2ca066(%rip), %r8     # 0x2e7c24
pushq $0x46
jmp 0x1dbea
movq 0x41a39f(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2c7440(%rip), %rsi    # 0x2e5013
leaq 0x2c75e5(%rip), %rdx    # 0x2e51bf
leaq 0x2ca0cb(%rip), %rcx    # 0x2e7cac
leaq 0x2ca03c(%rip), %r8     # 0x2e7c24
pushq $0x45
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x2ca100(%rip), %rdx    # 0x2e7d28
pushq $0x1
popq %rdi
pushq $0x50
popq %rsi
pushq $0x6b
popq %rcx
callq 0x9334a
movq %rax, %rbx
callq 0xc6d38
movq %rax, 0x10(%rbx)
callq 0xacb84
movq %rax, 0x28(%rbx)
callq 0xacb84
movq %rax, 0x20(%rbx)
callq 0x9b6b4
movq %rax, 0x8(%rbx)
callq 0xacb84
movq %rax, 0x18(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x1dcbc
pushq %rbx
movq %rdi, %rbx
movq 0x10(%rdi), %rdi
callq 0xc6d5b
movq (%rbx), %rdi
callq 0x8da06
movq 0x8(%rbx), %rdi
callq 0x9ba24
movq 0x28(%rbx), %rdi
callq 0xae103
movq 0x20(%rbx), %rdi
callq 0xae103
movq 0x18(%rbx), %rdi
callq 0xae103
leaq 0x2ca078(%rip), %rsi    # 0x2e7d28
pushq $0x7e
popq %rdx
movq %rbx, %rdi
popq %rbx
jmp 0x936f9
retq
// File: /workspace/github_c_makefile_star2_O2/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 %rbx
pushq %rax
movq %rdx, %rbx
xorl %ebp, %ebp
cmpb $0x0, 0x4d(%rsi)
jne 0x1df5e
cmpb $0x0, 0x4c(%rsi)
jne 0x1df5e
leaq 0x2ca0a7(%rip), %rsi    # 0x2e7ff8
movq %rbx, %rdi
xorl %eax, %eax
callq 0x89dbb
pushq $-0x1
popq %rbp
testq %rbx, %rbx
je 0x1df6f
movq %rbx, %rdi
callq 0x89eb7
testb %al, %al
jne 0x1df78
movl %ebp, %eax
addq $0x8, %rsp
popq %rbx
popq %rbp
retq
movq 0x419fe9(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2c708a(%rip), %rsi    # 0x2e5013
leaq 0x2c722f(%rip), %rdx    # 0x2e51bf
leaq 0x2ca0b8(%rip), %rcx    # 0x2e804f
leaq 0x2c9d8a(%rip), %r8     # 0x2e7d28
movl $0xe1, %r9d
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x1f7e6
movq 0x10(%rsi), %rax
pushq $-0x1
popq %rcx
cmpq %rax, 0x10(%rdi)
jae 0x1f7c3
movl %ecx, %eax
retq
pushq $0x1
popq %rax
jbe 0x1f7c9
retq
movq (%rsi), %rdx
cmpq %rdx, (%rdi)
jb 0x1f7c0
ja 0x1f7c8
movq 0x8(%rsi), %rdx
movl %ecx, %eax
cmpq %rdx, 0x8(%rdi)
jb 0x1f7c8
seta %al
movzbl %al, %eax
retq
pushq %rax
movq 0x41877a(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2c581b(%rip), %rsi    # 0x2e5013
leaq 0x32ef1c(%rip), %rdx    # 0x34e71b
leaq 0x2c8cf9(%rip), %rcx    # 0x2e84ff
leaq 0x2c851b(%rip), %r8     # 0x2e7d28
movl $0x144, %r9d            # imm = 0x144
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x2c84d7(%rip), %rsi    # 0x2e7d28
pushq $0x18
popq %rdi
movl $0x15d, %edx            # imm = 0x15D
callq 0x93160
movq %rax, %r13
testq %rbp, %rbp
je 0x1f872
movq %rbp, %rdi
callq 0x89eb7
testb %al, %al
jne 0x1f8bc
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 0x106b2f
cmpb $0x0, (%rbx)
jne 0x1f8ab
leaq 0x2c848a(%rip), %rsi    # 0x2e7d28
movq %rax, %rdi
movl $0x165, %edx            # imm = 0x165
callq 0x936f9
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x4186a5(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2c5746(%rip), %rsi    # 0x2e5013
leaq 0x2c58eb(%rip), %rdx    # 0x2e51bf
leaq 0x2c8c3f(%rip), %rcx    # 0x2e851a
leaq 0x2c8446(%rip), %r8     # 0x2e7d28
movl $0x15f, %r9d            # imm = 0x15F
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x1f90f
movq 0x8(%rsi), %rax
cmpq %rdi, %rax
cmovaq %rax, %rdi
movq %rdi, 0x8(%rsi)
xorl %eax, %eax
retq
pushq %rax
movq 0x418651(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2c56f2(%rip), %rsi    # 0x2e5013
leaq 0x2c89d5(%rip), %rdx    # 0x2e82fd
leaq 0x2c89e8(%rip), %rcx    # 0x2e8317
leaq 0x2c83f2(%rip), %r8     # 0x2e7d28
movl $0x12a, %r9d            # imm = 0x12A
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x2c8bf0(%rip), %rdx    # 0x2e8568
pushq $0x1
popq %rdi
pushq $0x60
popq %rsi
pushq $0x39
popq %rcx
callq 0x9334a
movq %rax, %rbx
callq 0xacb84
movq %rax, 0x8(%rbx)
andq $0x0, (%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x1f9c8
pushq %rbx
movq %rdi, %rbx
movq 0x8(%rdi), %rdi
callq 0xae103
movq (%rbx), %rdi
callq 0x735fd
leaq 0x2c8bac(%rip), %rsi    # 0x2e8568
pushq $0x45
popq %rdx
movq %rbx, %rdi
popq %rbx
jmp 0x936f9
retq
// File: /workspace/github_c_makefile_star2_O2/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 %r15
pushq %r14
pushq %rbx
pushq %rax
movq %rdx, %rbx
movq %rsi, %r14
movl %edi, %r15d
testq %rdx, %rdx
je 0x1fdbb
movq %rbx, %rdi
callq 0x89eb7
testb %al, %al
jne 0x1fe86
testq %r14, %r14
je 0x1fe58
xorl %ebp, %ebp
cmpl $0x1, %r15d
je 0x1fde0
pushq $-0x1
popq %rbp
leaq 0x2c8ebd(%rip), %rsi    # 0x2e8c93
movq %rbx, %rdi
xorl %eax, %eax
callq 0x89dbb
movl 0x50(%r14), %eax
addl $-0x65, %eax
cmpl $-0x67, %eax
ja 0x1fe00
leaq 0x2c8ed4(%rip), %rsi    # 0x2e8cc7
movq %rbx, %rdi
xorl %eax, %eax
callq 0x89dbb
pushq $-0x1
popq %rbp
cmpb $0x1, 0x56(%r14)
jne 0x1fe29
cmpb $0x0, 0x54(%r14)
jne 0x1fe15
cmpb $0x1, 0x55(%r14)
jne 0x1fe29
leaq 0x2c8ee9(%rip), %rsi    # 0x2e8d05
movq %rbx, %rdi
xorl %eax, %eax
callq 0x89dbb
pushq $-0x1
popq %rbp
cmpq $0x0, 0x28(%r14)
jne 0x1fe4b
cmpb $0x1, 0x59(%r14)
jne 0x1fe4b
leaq 0x2c8f0b(%rip), %rsi    # 0x2e8d49
movq %rbx, %rdi
xorl %eax, %eax
callq 0x89dbb
pushq $-0x1
popq %rbp
movl %ebp, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
movq 0x418109(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2c51aa(%rip), %rsi    # 0x2e5013
leaq 0x3287e3(%rip), %rdx    # 0x348653
leaq 0x2c8df6(%rip), %rcx    # 0x2e8c6d
leaq 0x2c86ea(%rip), %r8     # 0x2e8568
movl $0xf8, %r9d
jmp 0x1feb2
movq 0x4180db(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2c517c(%rip), %rsi    # 0x2e5013
leaq 0x2c5321(%rip), %rdx    # 0x2e51bf
leaq 0x2c8dc8(%rip), %rcx    # 0x2e8c6d
leaq 0x2c86bc(%rip), %r8     # 0x2e8568
movl $0xf7, %r9d
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x2c8b6b(%rip), %rdx    # 0x2e8e83
pushq $0x1
popq %rdi
pushq $0x60
popq %rsi
pushq $0x33
popq %rcx
callq 0x9334a
movq %rax, %rbx
pcmpeqd %xmm0, %xmm0
movdqu %xmm0, 0x28(%rax)
movdqu %xmm0, 0x38(%rax)
callq 0x9b6b4
movq %rax, 0x8(%rbx)
callq 0xacb84
movq %rax, 0x10(%rbx)
callq 0xacb84
movq %rax, 0x18(%rbx)
andq $0x0, 0x20(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x203a4
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x8da06
movq 0x8(%rbx), %rdi
callq 0x9ba24
movq 0x10(%rbx), %rdi
callq 0xae103
movq 0x18(%rbx), %rdi
callq 0xae103
movq 0x20(%rbx), %rdi
callq 0x9a8ea
leaq 0x2c8aeb(%rip), %rsi    # 0x2e8e83
pushq $0x48
popq %rdx
movq %rbx, %rdi
popq %rbx
jmp 0x936f9
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x2c870c(%rip), %rdx    # 0x2e92bc
pushq $0x1
popq %rdi
pushq $0x30
popq %rsi
pushq $0x3c
popq %rcx
callq 0x9334a
movq %rax, %rbx
callq 0xc6d38
movq %rax, (%rbx)
callq 0xacb84
movq %rax, 0x8(%rbx)
callq 0xacb84
movq %rax, 0x10(%rbx)
callq 0xacb84
movq %rax, 0x18(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x20c28
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0xc6d5b
movq 0x8(%rbx), %rdi
callq 0xae103
movq 0x10(%rbx), %rdi
callq 0xae103
movq 0x18(%rbx), %rdi
callq 0xae103
leaq 0x2c86a0(%rip), %rsi    # 0x2e92bc
pushq $0x4c
popq %rdx
movq %rbx, %rdi
popq %rbx
jmp 0x936f9
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x20daf
movq %rbx, %rdi
callq 0x89eb7
testb %al, %al
jne 0x20e7b
testq %r14, %r14
je 0x20e4d
testl %ebp, %ebp
je 0x20dcf
leaq 0x2c87b5(%rip), %rsi    # 0x2e9578
movq %rbx, %rdi
xorl %eax, %eax
callq 0x89dbb
jmp 0x20e3e
movq 0x10(%r14), %rdi
callq 0xad1fa
movq %rsp, %rsi
movq %rax, %rdi
callq 0x17f60
testl %eax, %eax
je 0x20e18
movq 0x10(%r14), %rdi
callq 0xad1fa
movq %rax, %r14
callq 0x17060
movl (%rax), %edi
callq 0x17220
leaq 0x2c879a(%rip), %rsi    # 0x2e95a0
movq %rbx, %rdi
movq %r14, %rdx
movq %rax, %rcx
xorl %eax, %eax
callq 0x89dbb
jmp 0x20e3e
xorl %eax, %eax
testb $0x40, 0x18(%rsp)
jne 0x20e41
movq 0x10(%r14), %rdi
callq 0xad1fa
leaq 0x2c8781(%rip), %rsi    # 0x2e95b2
movq %rbx, %rdi
movq %rax, %rdx
xorl %eax, %eax
callq 0x89dbb
pushq $-0x1
popq %rax
addq $0x90, %rsp
popq %rbx
popq %r14
popq %rbp
retq
movq 0x417114(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2c41b5(%rip), %rsi    # 0x2e5013
leaq 0x3277ee(%rip), %rdx    # 0x348653
leaq 0x2c86e5(%rip), %rcx    # 0x2e9551
leaq 0x2c8449(%rip), %r8     # 0x2e92bc
movl $0x90, %r9d
jmp 0x20ea7
movq 0x4170e6(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2c4187(%rip), %rsi    # 0x2e5013
leaq 0x2c432c(%rip), %rdx    # 0x2e51bf
leaq 0x2c86b7(%rip), %rcx    # 0x2e9551
leaq 0x2c841b(%rip), %r8     # 0x2e92bc
movl $0x8f, %r9d
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x107a70
movq %rax, %r14
leaq 0x2c79be(%rip), %rdx    # 0x2e92bc
pushq $0x2
popq %rsi
movq %r15, %rdi
movl $0xdb, %ecx
callq 0x8abea
movq %rax, %rdi
callq 0x8d2a4
movq %rax, %r15
movq %r14, %rdi
callq 0x107d59
movq %rax, %r12
pushq $0x50
popq %rbp
testq %r12, %r12
je 0x21979
movq (%r12), %rdx
movq %rbx, %rdi
leaq 0x10(%rsp), %rsi
callq 0xc2ebc
movq %rax, %r13
movq (%r12), %rdx
movq %rbx, %rdi
leaq 0x8(%rsp), %rsi
callq 0xc11fb
movq 0x8(%rsp), %rsi
movq 0x10(%rsp), %rcx
movq %rax, %rdi
movq %r13, %rdx
movq %rbp, %r8
movq %r15, %r9
callq 0x8c186
movq %r14, %rdi
callq 0x107c2f
movq %rax, %r12
jmp 0x21927
movq %r15, %rdi
callq 0x8da06
movq %r14, %rdi
callq 0x107da8
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/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 0x2c7761(%rip), %rsi    # 0x2e92bc
pushq $0x8
popq %rdi
movl $0xbb, %edx
callq 0x93160
movq %rax, %rbx
movq %r14, (%rax)
movq %r15, %rdi
movq %rax, %rsi
movq %r12, %rdx
callq 0x106b2f
cmpb $0x0, (%r12)
jne 0x21b97
leaq 0x2c7732(%rip), %rsi    # 0x2e92bc
movq %rbx, %rdi
movl $0xc2, %edx
callq 0x936f9
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O2/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 0xb0c26
movq %rax, %rbx
callq 0x1dbf8
leaq 0x305969(%rip), %rsi    # 0x327b65
movq %rbx, %rdi
movq %rax, %rdx
callq 0xb0c55
callq 0x20b80
leaq 0x2c74dd(%rip), %rsi    # 0x2e96f0
movq %rbx, %rdi
movq %rax, %rdx
callq 0xb0c55
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x22272
movq %rdi, %rbx
leaq 0x2c5a02(%rip), %rdi    # 0x2e7c3d
leaq 0x2c79cf(%rip), %rsi    # 0x2e9c11
callq 0x97df5
movq %rax, %r14
leaq 0x8ec47(%rip), %rsi     # 0xb0e98
movq %rax, %rdi
movq %rbx, %rdx
callq 0x98045
pushq $0x1
popq %rsi
movq %r14, %rdi
callq 0x98be7
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
movq 0x415cef(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2c2d90(%rip), %rsi    # 0x2e5013
leaq 0x2c7932(%rip), %rdx    # 0x2e9bbc
leaq 0x2c793a(%rip), %rcx    # 0x2e9bcb
leaq 0x2c7959(%rip), %r8     # 0x2e9bf1
pushq $0x3c
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x222d6
movq %rbx, %rdi
callq 0x89eb7
testb %al, %al
jne 0x22390
testq %r15, %r15
je 0x22366
movslq %r14d, %rax
leaq (%r12,%rax,8), %r13
movq (%r13), %rsi
movq %r15, %rdi
callq 0xb0d2d
testq %rax, %rax
je 0x22332
movq %rax, %r12
movq %rbx, %rdi
callq 0x8a001
movq %r13, %rdi
movq %rax, %rsi
callq 0x6c7c9
movq %rax, %r15
movq (%rax), %rsi
movq %rbx, %rdi
callq 0x89f8a
subl %r14d, %ebp
movq %r12, %rdi
movl %ebp, %esi
movq %r15, %rdx
movq %rbx, %rcx
callq 0xb05a1
movl %eax, %ebx
jmp 0x2234d
movq (%r13), %rdx
leaq 0x2c7943(%rip), %rsi    # 0x2e9c80
xorl %r15d, %r15d
movq %rbx, %rdi
xorl %eax, %eax
callq 0x89dbb
pushq $-0x1
popq %rbx
movq %r15, %rdi
callq 0x6ca1b
movl %ebx, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x415bfb(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2c2c9c(%rip), %rsi    # 0x2e5013
leaq 0x2c783e(%rip), %rdx    # 0x2e9bbc
leaq 0x2c78e0(%rip), %rcx    # 0x2e9c65
leaq 0x2c7865(%rip), %r8     # 0x2e9bf1
pushq $0x54
jmp 0x223b8
movq 0x415bd1(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2c2c72(%rip), %rsi    # 0x2e5013
leaq 0x2c2e17(%rip), %rdx    # 0x2e51bf
leaq 0x2c78b6(%rip), %rcx    # 0x2e9c65
leaq 0x2c783b(%rip), %r8     # 0x2e9bf1
pushq $0x53
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
nop
// File: /workspace/github_c_makefile_star2_O2/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 0x224af
movq %rdi, %rbx
leaq 0x2c7a09(%rip), %rdi    # 0x2e9e79
leaq 0x2c7a2e(%rip), %rsi    # 0x2e9ea5
callq 0x97df5
movq %rax, %r14
leaq 0x8ea12(%rip), %rsi     # 0xb0e98
movq %rax, %rdi
movq %rbx, %rdx
callq 0x98045
pushq $0x1
popq %rsi
movq %r14, %rdi
callq 0x98be7
movq %r14, %rdi
callq 0x98002
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
movq 0x415ab2(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2c2b53(%rip), %rsi    # 0x2e5013
leaq 0x2c7983(%rip), %rdx    # 0x2e9e4a
leaq 0x2c7992(%rip), %rcx    # 0x2e9e60
leaq 0x2c77f3(%rip), %r8     # 0x2e9cc8
movl $0xc8, %r9d
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x2c7642(%rip), %rsi    # 0x2e9cc8
pushq $0x28
popq %rdi
pushq $0x2a
popq %rdx
callq 0x93160
movq %rax, %rbx
callq 0xacb84
movq %rax, 0x8(%rbx)
callq 0xae154
movq %rax, 0x10(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x226eb
pushq %rbx
movq %rdi, %rbx
movq 0x8(%rdi), %rdi
callq 0xae103
movq 0x10(%rbx), %rdi
callq 0xae662
movq 0x20(%rbx), %rdi
callq 0x9a8ea
movq 0x18(%rbx), %rdi
callq 0x9a8ea
leaq 0x2c75e9(%rip), %rsi    # 0x2e9cc8
pushq $0x3c
popq %rdx
movq %rbx, %rdi
popq %rbx
jmp 0x936f9
retq
// File: /workspace/github_c_makefile_star2_O2/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 0xad289
testq %rax, %rax
je 0x22862
movq 0x18(%r14), %rdi
callq 0x9b4cb
movb $0x1, %cl
testb %al, %al
jne 0x22852
movq 0x20(%r14), %rdi
callq 0x9b4cb
testb %al, %al
je 0x2287f
xorl %ecx, %ecx
movb %cl, (%r14)
testl %ebp, %ebp
je 0x22878
leaq 0x2c7598(%rip), %rsi    # 0x2e9df8
jmp 0x22869
leaq 0x2c752c(%rip), %rsi    # 0x2e9d95
movq %rbx, %rdi
xorl %eax, %eax
callq 0x89dbb
pushq $-0x1
popq %rax
jmp 0x2287a
xorl %eax, %eax
popq %rbx
popq %r14
popq %rbp
retq
movq 0x4156e2(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2c2783(%rip), %rsi    # 0x2e5013
leaq 0x2c7510(%rip), %rdx    # 0x2e9da7
leaq 0x2c7538(%rip), %rcx    # 0x2e9dd6
leaq 0x2c7423(%rip), %r8     # 0x2e9cc8
pushq $0x7c
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 0x229a5
movq %r8, %rbx
movq %rcx, %r14
movzbl 0x2(%rcx), %edi
movq 0x4155d7(%rip), %rax    # 0x437eb0
movq (%rax), %rdx
leaq 0x2c3ff1(%rip), %rsi    # 0x2e68d4
callq 0x92b50
movq %rax, %r15
cmpb $0x1, 0x2(%r14)
jne 0x2295b
leaq 0x2d7304(%rip), %rax    # 0x2f9bfd
cmpb $0x0, (%r14)
leaq 0x2caeaa(%rip), %r12    # 0x2ed7ae
cmovneq %rax, %r12
movq 0x8(%r14), %rdi
callq 0xad1fa
leaq 0x2c7514(%rip), %rdi    # 0x2e9e2c
movq %r12, %rsi
movq %rax, %rdx
xorl %eax, %eax
callq 0x17070
leaq 0x2c750e(%rip), %r12    # 0x2e9e3a
xorl %r13d, %r13d
movq 0x10(%r14), %rdi
callq 0xae61c
cmpq %rax, %r13
jae 0x2295b
movq 0x10(%r14), %rdi
movq %r13, %rsi
callq 0xae386
movq %r12, %rdi
movq %rax, %rsi
xorl %eax, %eax
callq 0x17070
incq %r13
jmp 0x2292f
movzbl (%r14), %ebp
movzbl 0x1(%r14), %r12d
movq 0x8(%r14), %rdi
callq 0xad1fa
movq 0x10(%r14), %rcx
movzbl 0x2(%r14), %r8d
movl %ebp, %edi
movl %r12d, %esi
movq %rax, %rdx
movq %rbx, %r9
callq 0x135cb0
movl %eax, %ebx
movq %r15, %rdi
callq 0x92fd0
xorl %eax, %eax
negl %ebx
sbbl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x4155bc(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2c265d(%rip), %rsi    # 0x2e5013
leaq 0x2c3f03(%rip), %rdx    # 0x2e68c0
leaq 0x2c744f(%rip), %rcx    # 0x2e9e13
leaq 0x2c72fd(%rip), %r8     # 0x2e9cc8
movl $0x91, %r9d
xorl %eax, %eax
callq 0x17a50
callq 0x17390
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O2/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 0x22a46
movq %r14, %rdi
callq 0x89eb7
testb %al, %al
jne 0x22b2b
pushq $0x8
popq %rdi
callq 0x5809c
movq %rax, %rbx
movslq %ebp, %rax
movq (%r15,%rax,8), %rsi
movq %rbx, %rdi
movq %r14, %rdx
callq 0x11f930
movl %eax, %ebp
testl %eax, %eax
jne 0x22aee
movq %rbx, %rdi
callq 0x584c7
movq %rax, %r14
movq %rbx, %rdi
callq 0x586a4
movq %rax, %r15
movq %rbx, %rdi
callq 0x586b1
leaq 0xfce07(%rip), %rcx     # 0x11f899
movq %r14, %rdi
movq %r15, %rsi
movq %rax, %rdx
callq 0x17ed0
movq %rbx, %rdi
callq 0x584c7
movq %rax, %r14
movq %rbx, %rdi
callq 0x586a4
movq %rax, %r15
movq %rbx, %rdi
callq 0x586b1
leaq 0x189(%rip), %r10       # 0x22c4e
leaq 0x95(%rip), %rcx        # 0x22b61
leaq 0xd1(%rip), %r8         # 0x22ba4
leaq 0xda(%rip), %r9         # 0x22bb4
movq %r14, %rdi
movq %r15, %rsi
movq %rax, %rdx
pushq $0x0
pushq %r10
callq 0xc6e38
popq %rax
popq %rcx
xorl %r14d, %r14d
movq %rbx, %rdi
callq 0x586a4
cmpq %rax, %r14
jae 0x22b16
movq %rbx, %rdi
movq %r14, %rsi
callq 0x581aa
movq (%rax), %rdi
callq 0x11f686
incq %r14
jmp 0x22af1
movq %rbx, %rdi
callq 0x58eb9
movl %ebp, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
movq 0x415436(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2c24d7(%rip), %rsi    # 0x2e5013
leaq 0x2c267c(%rip), %rdx    # 0x2e51bf
leaq 0x2c746e(%rip), %rcx    # 0x2e9fb8
leaq 0x2c747e(%rip), %r8     # 0x2e9fcf
pushq $0x5a
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 %r13
pushq %r12
pushq %rbx
subq $0x10, %rsp
movq (%rsi), %r14
testq %r14, %r14
je 0x22c18
movq %rdi, %rbx
xorl %r15d, %r15d
movq %rsp, %r12
pushq $0x10
popq %r13
movq %r14, %rdi
callq 0x11f765
cmpq %rax, %r15
jae 0x22c0a
movq %r14, %rdi
movq %r15, %rsi
callq 0x11f7aa
movq %rax, (%rsp)
movq %rdx, 0x8(%rsp)
movq %rbx, %rdi
movq %r12, %rsi
movq %r13, %rdx
callq 0x5851d
incq %r15
jmp 0x22bd6
addq $0x10, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
movq 0x415349(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2c23ea(%rip), %rsi    # 0x2e5013
leaq 0x2ccf55(%rip), %rdx    # 0x2efb85
leaq 0x2f7b87(%rip), %rcx    # 0x31a7be
leaq 0x2c7391(%rip), %r8     # 0x2e9fcf
pushq $0x2e
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/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 %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
leaq 0x2c739e(%rip), %rdi    # 0x2e9ffd
xorl %eax, %eax
callq 0x17070
leaq 0x3397a1(%rip), %r14    # 0x35c40e
pushq $0x2c
popq %rbp
xorl %r15d, %r15d
movq %rbx, %rdi
callq 0x586a4
cmpq %rax, %r15
jae 0x22ca9
testq %r15, %r15
je 0x22c8c
movl %ebp, %edi
callq 0xb30c7
movq %rbx, %rdi
movq %r15, %rsi
callq 0x581aa
movq (%rax), %rsi
movq %r14, %rdi
xorl %eax, %eax
callq 0x17070
incq %r15
jmp 0x22c73
leaq 0x345532(%rip), %rdi    # 0x3681e2
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
jmp 0x17b60
nop
// File: /workspace/github_c_makefile_star2_O2/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 0x2c731d(%rip), %rdx    # 0x2ea008
pushq $0x1
popq %rdi
pushq $0x20
popq %rsi
pushq $0x31
popq %rcx
callq 0x9334a
movq %rax, %rbx
callq 0x9b6b4
movq %rax, 0x10(%rbx)
andq $0x0, 0x18(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/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 0x22d3d
pushq %rbx
movq %rdi, %rbx
movq 0x18(%rdi), %rdi
callq 0x8da06
movq 0x10(%rbx), %rdi
callq 0x9ba24
leaq 0x2c72d7(%rip), %rsi    # 0x2ea008
pushq $0x3d
popq %rdx
movq %rbx, %rdi
popq %rbx
jmp 0x936f9
retq