LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_gff3.c
// Function: gt_gff3_arguments_new
static void* gt_gff3_arguments_new(void)
{
  GFF3Arguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->newsource = gt_str_new();
  arguments->offsetfile = gt_str_new();
  arguments->tci = gt_typecheck_info_new();
  arguments->xci = gt_xrfcheck_info_new();
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2a35dd(%rip), %rdx    # 0x34d948
movl $0x1, %edi
movl $0x50, %esi
movl $0x44, %ecx
callq 0x10436a
movq %rax, %rbx
callq 0x11ac6c
movq %rax, 0x20(%rbx)
callq 0x11ac6c
movq %rax, 0x18(%rbx)
callq 0x1832ac
movq %rax, 0x30(%rbx)
callq 0x186028
movq %rax, 0x38(%rbx)
callq 0x10ad60
movq %rax, 0x40(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_gff3.c
// Function: gt_gff3_arguments_delete
static void gt_gff3_arguments_delete(void *tool_arguments)
{
  GFF3Arguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_str_delete(arguments->newsource);
  gt_output_file_info_delete(arguments->ofi);
  gt_typecheck_info_delete(arguments->tci);
  gt_xrfcheck_info_delete(arguments->xci);
  gt_str_delete(arguments->offsetfile);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xaa408
pushq %rbx
movq %rdi, %rbx
movq 0x48(%rdi), %rdi
callq 0xff22c
movq 0x20(%rbx), %rdi
callq 0x11bdbf
movq 0x40(%rbx), %rdi
callq 0x10b00c
movq 0x30(%rbx), %rdi
callq 0x1832d8
movq 0x38(%rbx), %rdi
callq 0x186054
movq 0x18(%rbx), %rdi
callq 0x11bdbf
leaq 0x2a354e(%rip), %rsi    # 0x34d948
movq %rbx, %rdi
movl $0x57, %edx
popq %rbx
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_gff3_to_gtf.c
// Function: gt_gff3_to_gtf_arguments_delete
static void gt_gff3_to_gtf_arguments_delete(void *tool_arguments)
{
  GFF3ToGTFArguments *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 0xaabde
pushq %rbx
movq %rdi, %rbx
movq 0x8(%rdi), %rdi
callq 0xff22c
movq (%rbx), %rdi
callq 0x10b00c
leaq 0x2a33e4(%rip), %rsi    # 0x34dfb4
movq %rbx, %rdi
movl $0x2c, %edx
popq %rbx
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_gff3_to_gtf.c
// Function: gt_gff3_to_gtf_runner
static int gt_gff3_to_gtf_runner(int argc, const char **argv, int parsed_args,
                                 void *tool_arguments, GtError *err)
{
  GFF3ToGTFArguments *arguments = tool_arguments;
  GtNodeStream *gff3_in_stream = NULL, *gtf_out_stream = NULL;
  int had_err;

  gt_error_check(err);
  gt_assert(arguments);

  /* create a gff3 input stream */
  gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
                                                  argv + parsed_args);

  /* create a gtf output stream */
  gtf_out_stream = gt_gtf_out_stream_new(gff3_in_stream, arguments->outfp);

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

  /* free */
  gt_node_stream_delete(gff3_in_stream);
  gt_node_stream_delete(gtf_out_stream);

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movq %r8, %rbx
movq %rcx, %r14
movl %edx, %r12d
movq %rsi, %r15
movl %edi, %ebp
testq %r8, %r8
je 0xaac40
movq %rbx, %rdi
callq 0xfcc32
testb %al, %al
jne 0xaac95
testq %r14, %r14
je 0xaac90
subl %r12d, %ebp
movslq %r12d, %rax
leaq (%r15,%rax,8), %rsi
movl %ebp, %edi
callq 0x145cdf
movq %rax, %r15
movq 0x8(%r14), %rsi
movq %rax, %rdi
callq 0x14cd20
movq %rax, %r14
movq %rax, %rdi
movq %rbx, %rsi
callq 0x162f5d
movl %eax, %ebx
movq %r15, %rdi
callq 0x162dee
movq %r14, %rdi
callq 0x162dee
movl %ebx, %eax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
callq 0x1b854
callq 0x1b81d
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_gff3validator.c
// Function: gt_gff3validator_arguments_new
static void* gt_gff3validator_arguments_new(void)
{
  GFF3ValidatorArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->tci = gt_typecheck_info_new();
  arguments->xci = gt_xrfcheck_info_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2a334a(%rip), %rdx    # 0x34e011
movl $0x1, %edi
movl $0x18, %esi
movl $0x23, %ecx
callq 0x10436a
movq %rax, %rbx
callq 0x1832ac
movq %rax, (%rbx)
callq 0x186028
movq %rax, 0x8(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_gff3validator.c
// Function: gt_gff3validator_arguments_delete
static void gt_gff3validator_arguments_delete(void *tool_arguments)
{
  GFF3ValidatorArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_typecheck_info_delete(arguments->tci);
  gt_xrfcheck_info_delete(arguments->xci);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xaad23
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x1832d8
movq 0x8(%rbx), %rdi
callq 0x186054
leaq 0x2a32fc(%rip), %rsi    # 0x34e011
movq %rbx, %rdi
movl $0x2f, %edx
popq %rbx
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_gff3validator.c
// Function: gt_gff3validator_option_parser_new
static GtOptionParser* gt_gff3validator_option_parser_new(void *tool_arguments)
{
  GFF3ValidatorArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [GFF3_file ...]",
                         "Strictly validate given GFF3 files.");

  /* typecheck options */
  gt_typecheck_info_register_options(arguments->tci, op);

  /* xrfcheck options */
  gt_xrfcheck_info_register_options(arguments->xci, op);

  /* -strict */
  option = gt_option_new_bool("strict", "be very strict during GFF3 parsing "
                              "(stricter than the specification requires)",
                              &arguments->strict, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xaad9a
movq %rdi, %r14
leaq 0x29f7c2(%rip), %rdi    # 0x34a4f9
leaq 0x2a3313(%rip), %rsi    # 0x34e051
callq 0x107bfe
movq %rax, %rbx
movq (%r14), %rdi
movq %rax, %rsi
callq 0x1833b7
movq 0x8(%r14), %rdi
movq %rbx, %rsi
callq 0x186084
addq $0x10, %r14
leaq 0x2d4d8d(%rip), %rdi    # 0x37faf5
leaq 0x2a2d50(%rip), %rsi    # 0x34dabf
movq %r14, %rdx
xorl %ecx, %ecx
callq 0x10a235
movq %rax, %r14
movq %rax, %rdi
callq 0x10a9d4
movq %rbx, %rdi
movq %r14, %rsi
callq 0x107cc0
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x1b88b
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_gtf_to_gff3.c
// Function: gt_gtf_to_gff3_arguments_delete
static void gt_gtf_to_gff3_arguments_delete(void *tool_arguments)
{
  GTFToGFF3Arguments *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 0xaaf88
pushq %rbx
movq %rdi, %rbx
movq 0x10(%rdi), %rdi
callq 0xff22c
movq 0x8(%rbx), %rdi
callq 0x10b00c
leaq 0x2a3127(%rip), %rsi    # 0x34e0a1
movq %rbx, %rdi
movl $0x2f, %edx
popq %rbx
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_gtf_to_gff3.c
// Function: gt_gtf_to_gff3_option_parser_new
static GtOptionParser* gt_gtf_to_gff3_option_parser_new(void *tool_arguments)
{
  GTFToGFF3Arguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  op = gt_option_parser_new("[GTF_file]",
                            "Parse GTF2.2 file and convert it to GFF3.");

  /* -tidy */
  option = gt_option_new_bool("tidy", "try to tidy the GTF file up during "
                              "parsing", &arguments->tidy, false);
  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_max_args(op, 1);

  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xaaff9
movq %rdi, %rbx
leaq 0x2a3141(%rip), %rdi    # 0x34e0dd
leaq 0x2a3145(%rip), %rsi    # 0x34e0e8
callq 0x107bfe
movq %rax, %r14
leaq 0x2d4b09(%rip), %rdi    # 0x37fabb
leaq 0x2a3159(%rip), %rsi    # 0x34e112
movq %rbx, %rdx
xorl %ecx, %ecx
callq 0x10a235
movq %r14, %rdi
movq %rax, %rsi
callq 0x107cc0
movq 0x8(%rbx), %rdi
addq $0x10, %rbx
movq %r14, %rsi
movq %rbx, %rdx
callq 0x10ad87
movq %r14, %rdi
movl $0x1, %esi
callq 0x10873c
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x1b930
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_gtf_to_gff3.c
// Function: gt_gtf_to_gff3_runner
static int gt_gtf_to_gff3_runner(GT_UNUSED int argc, const char **argv,
                                 int parsed_args, void *tool_arguments,
                                 GtError *err)
{
  GTFToGFF3Arguments *arguments = tool_arguments;
  GtNodeStream *gtf_in_stream = NULL, *gff3_out_stream = NULL;
  int had_err;

  gt_error_check(err);
  gt_assert(arguments);

  /* create a GTF input stream */
  gtf_in_stream = gt_gtf_in_stream_new(argv[parsed_args]);
  if (arguments->tidy)
    gt_gtf_in_stream_enable_tidy_mode(gtf_in_stream);

  /* create a GFF3 output stream */
  gff3_out_stream = gt_gff3_out_stream_new(gtf_in_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(gtf_in_stream);

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movq %r8, %rbx
movq %rcx, %r14
movl %edx, %ebp
movq %rsi, %r15
testq %r8, %r8
je 0xab021
movq %rbx, %rdi
callq 0xfcc32
testb %al, %al
jne 0xab081
testq %r14, %r14
je 0xab07c
movslq %ebp, %rax
movq (%r15,%rax,8), %rdi
callq 0x14cc96
movq %rax, %r15
cmpb $0x1, (%r14)
jne 0xab043
movq %r15, %rdi
callq 0x14cd03
movq 0x10(%r14), %rsi
movq %r15, %rdi
callq 0x146fc0
movq %rax, %r14
movq %rax, %rdi
movq %rbx, %rsi
callq 0x162f5d
movl %eax, %ebx
movq %r14, %rdi
callq 0x162dee
movq %r15, %rdi
callq 0x162dee
movl %ebx, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
callq 0x1b99e
callq 0x1b967
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_guessprot.c
// Function: gt_guessprot
int gt_guessprot(int argc, const char **argv, GtError *err)
{
  int i, parsed_args, retval;
  GtStrArray *filenametab;

  gt_error_check(err);

  switch (parse_options(&parsed_args, argc, argv, err)) {
    case GT_OPTION_PARSER_OK: break;
    case GT_OPTION_PARSER_ERROR: return -1;
    case GT_OPTION_PARSER_REQUESTS_EXIT: return 0;
  }

  filenametab = gt_str_array_new();
  for (i=parsed_args; i < argc; i++)
  {
    gt_str_array_add_cstr(filenametab,argv[i]);
  }
  retval = gt_files_guess_if_protein_sequences(filenametab,err);
  gt_str_array_delete(filenametab);
  if (retval < 0)
  {
    return -1;
  }
  if (retval == 1)
  {
    /*@ignore@*/
    exit(EXIT_FAILURE); /* guess it is a protein sequence */
    /*@end@*/

  } else
  {
    return 0;
  }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rdx, %rbx
movq %rsi, %r15
movl %edi, %r14d
testq %rdx, %rdx
je 0xab0c1
movq %rbx, %rdi
callq 0xfcc32
testb %al, %al
jne 0xab147
leaq 0x4(%rsp), %rdi
movl %r14d, %esi
movq %r15, %rdx
movq %rbx, %rcx
jmp 0xab0ce
leaq 0x4(%rsp), %rdi
movl %r14d, %esi
movq %r15, %rdx
xorl %ecx, %ecx
callq 0xab156
movl $0xffffffff, %ebp       # imm = 0xFFFFFFFF
cmpl $0x1, %eax
je 0xab136
cmpl $0x2, %eax
jne 0xab0e6
xorl %ebp, %ebp
jmp 0xab136
callq 0x11be10
movq %rax, %r12
movslq 0x4(%rsp), %rax
cmpl %eax, %r14d
jle 0xab116
leaq (%r15,%rax,8), %r15
subl %eax, %r14d
xorl %r13d, %r13d
movq (%r15,%r13,8), %rsi
movq %r12, %rdi
callq 0x11bee9
incq %r13
cmpl %r13d, %r14d
jne 0xab102
movq %r12, %rdi
movq %rbx, %rsi
callq 0xff8be
movl %eax, %ebx
movq %r12, %rdi
callq 0x11c144
testl %ebx, %ebx
js 0xab136
xorl %ebp, %ebp
cmpl $0x1, %ebx
je 0xab14c
movl %ebp, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x1b9d5
movl $0x1, %edi
callq 0x17940
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_guessprot.c
// Function: parse_options
static GtOPrval parse_options(int *parsed_args, int argc, const char **argv,
                              GtError *err)
{
  GtOptionParser *op;
  GtOPrval oprval;
  gt_error_check(err);
  op = gt_option_parser_new("filenames",
                         "Guess if sequence in filenames is protein or DNA.");
  gt_option_parser_set_min_args(op, 1U);
  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);
  gt_option_parser_delete(op);
  return oprval;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movq %rcx, %rbx
movq %rdx, %r14
movl %esi, %ebp
movq %rdi, %r15
testq %rcx, %rcx
je 0xab17a
movq %rbx, %rdi
callq 0xfcc32
testb %al, %al
jne 0xab1cc
leaq 0x2e508b(%rip), %rdi    # 0x39020c
leaq 0x2a2ff1(%rip), %rsi    # 0x34e179
callq 0x107bfe
movq %rax, %r12
movq %rax, %rdi
movl $0x1, %esi
callq 0x10872d
leaq 0x74468(%rip), %r8      # 0x11f60c
movq %r12, %rdi
movq %r15, %rsi
movl %ebp, %edx
movq %r14, %rcx
movq %rbx, %r9
callq 0x10875d
movl %eax, %ebx
movq %r12, %rdi
callq 0x10a0b4
movl %ebx, %eax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
callq 0x1ba0c
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_hop.c
// Function: gt_hop_arguments_check
int gt_hop_arguments_check(GT_UNUSED int rest_argc, void *tool_arguments,
    GtError* err)
{
  GtHopArguments *args = (GtHopArguments*) tool_arguments;
  int had_err = 0;

  if (!args->aggressive &&
      !args->moderate &&
      !args->conservative &&
      !args->expert &&
      !args->state_of_truth)
  {
    gt_error_set(err, "Select correction mode: "
        "-aggressive, -moderate, -conservative or -expert");
    had_err = -1;
  }
  else if (args->aggressive || args->state_of_truth)
  {
    args->hmin = 3UL;
    args->read_hmin = 1UL;
    args->qmax = 120UL;
    args->altmax = (double) 1.00;
    args->cogmin = (double) 0.00;
    args->mapqmin = 0UL;
    args->covmin = 1UL;
    args->clenmax = ULONG_MAX;
    args->allow_multiple = true;
  }
  else if (args->moderate)
  {
    args->hmin = 3UL;
    args->read_hmin = 1UL;
    args->qmax = 120UL;
    args->altmax = (double) 0.99;
    args->cogmin = (double) 0.00;
    args->mapqmin = 10UL;
    args->covmin = 1UL;
    args->clenmax = ULONG_MAX;
    args->allow_multiple = true;
  }
  else if (args->conservative)
  {
    args->hmin = 3UL;
    args->read_hmin = 2UL;
    args->qmax = 120UL;
    args->altmax = (double) 0.80;
    args->cogmin = (double) 0.10;
    args->mapqmin = 21UL;
    args->covmin = 1UL;
    args->clenmax = ULONG_MAX;
    args->allow_multiple = false;
  }

  if (gt_str_length(args->outprefix) == 0)
  {
    gt_error_set(err, "outprefix cannot be an empty string");
    had_err = -1;
  }
  return had_err;
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
movq %rdx, %rbx
movq %rsi, %r14
cmpb $0x0, 0x66(%rsi)
je 0xab250
movq $0x3, 0x30(%r14)
movl $0x1, %eax
movq %rax, 0x40(%r14)
movq $0x78, 0x58(%r14)
movsd 0x29b023(%rip), %xmm0   # 0x346228
movups %xmm0, 0x70(%r14)
movq $0x0, 0x50(%r14)
movq %rax, 0x48(%r14)
movq $-0x1, 0x38(%r14)
movb $0x1, 0x65(%r14)
xorl %ebp, %ebp
movq 0x28(%r14), %rdi
callq 0x11b0ca
testq %rax, %rax
jne 0xab249
leaq 0x2a2fe7(%rip), %rsi    # 0x34e221
movq %rbx, %rdi
xorl %eax, %eax
callq 0xfcb67
movl $0xffffffff, %ebp       # imm = 0xFFFFFFFF
movl %ebp, %eax
popq %rbx
popq %r14
popq %rbp
retq
movb 0x67(%r14), %al
testb %al, %al
je 0xab261
cmpb $0x1, 0x6a(%r14)
je 0xab1e4
jmp 0xab289
cmpb $0x0, 0x68(%r14)
jne 0xab27a
cmpb $0x0, 0x69(%r14)
jne 0xab27a
cmpb $0x0, 0x6a(%r14)
je 0xab30f
cmpb $0x0, 0x6a(%r14)
jne 0xab1e4
testb %al, %al
je 0xab2bc
movq $0x3, 0x30(%r14)
movl $0x1, %eax
movq %rax, 0x40(%r14)
movq $0x78, 0x58(%r14)
movsd 0x2a2f16(%rip), %xmm0   # 0x34e1c0
movups %xmm0, 0x70(%r14)
movq $0xa, 0x50(%r14)
jmp 0xab212
xorl %ebp, %ebp
cmpb $0x1, 0x68(%r14)
jne 0xab225
movq $0x3, 0x30(%r14)
movq $0x2, 0x40(%r14)
movq $0x78, 0x58(%r14)
movaps 0x2a2ec8(%rip), %xmm0   # 0x34e1b0
movups %xmm0, 0x70(%r14)
movq $0x15, 0x50(%r14)
movq $0x1, 0x48(%r14)
movq $-0x1, 0x38(%r14)
movb $0x0, 0x65(%r14)
jmp 0xab225
leaq 0x2a2ec2(%rip), %rsi    # 0x34e1d8
movq %rbx, %rdi
xorl %eax, %eax
callq 0xfcb67
movl $0xffffffff, %ebp       # imm = 0xFFFFFFFF
jmp 0xab225
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_hop.c
// Function: gt_hop_arguments_new
static void* gt_hop_arguments_new(void)
{
  GtHopArguments *arguments = gt_malloc(sizeof (*arguments));
  arguments->encseqinput = gt_str_new();
  arguments->annotation = gt_str_new();
  arguments->atype = gt_str_new();
  arguments->map = gt_str_new();
  arguments->outfilename = gt_str_new();
  arguments->outprefix = gt_str_new();
  arguments->readset = gt_str_array_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2a2eeb(%rip), %rsi    # 0x34e245
movl $0x88, %edi
movl $0x27, %edx
callq 0x104226
movq %rax, %rbx
callq 0x11ac6c
movq %rax, (%rbx)
callq 0x11ac6c
movq %rax, 0x8(%rbx)
callq 0x11ac6c
movq %rax, 0x20(%rbx)
callq 0x11ac6c
movq %rax, 0x10(%rbx)
callq 0x11ac6c
movq %rax, 0x18(%rbx)
callq 0x11ac6c
movq %rax, 0x28(%rbx)
callq 0x11be10
movq %rax, 0x80(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_hop.c
// Function: gt_hop_arguments_delete
static void gt_hop_arguments_delete(void *tool_arguments)
{
  GtHopArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->encseqinput);
  gt_str_delete(arguments->annotation);
  gt_str_delete(arguments->atype);
  gt_str_delete(arguments->map);
  gt_str_delete(arguments->outfilename);
  gt_str_delete(arguments->outprefix);
  gt_str_array_delete(arguments->readset);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xab411
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x11bdbf
movq 0x8(%rbx), %rdi
callq 0x11bdbf
movq 0x20(%rbx), %rdi
callq 0x11bdbf
movq 0x10(%rbx), %rdi
callq 0x11bdbf
movq 0x18(%rbx), %rdi
callq 0x11bdbf
movq 0x28(%rbx), %rdi
callq 0x11bdbf
movq 0x80(%rbx), %rdi
callq 0x11c144
leaq 0x2a2e42(%rip), %rsi    # 0x34e245
movq %rbx, %rdi
movl $0x3d, %edx
popq %rbx
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_id_to_md5.c
// Function: gt_id_to_md5_arguments_new
static void *gt_id_to_md5_arguments_new(void)
{
  SeqidsToMD5Arguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->s2fi = gt_seqid2file_info_new();
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2a2e32(%rip), %rdx    # 0x34f05d
movl $0x1, %edi
movl $0x20, %esi
movl $0x28, %ecx
callq 0x10436a
movq %rax, %rbx
callq 0x172c40
movq %rax, 0x8(%rbx)
callq 0x10ad60
movq %rax, 0x10(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_id_to_md5.c
// Function: gt_id_to_md5_arguments_delete
static void gt_id_to_md5_arguments_delete(void *tool_arguments)
{
  SeqidsToMD5Arguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_seqid2file_info_delete(arguments->s2fi);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xac292
pushq %rbx
movq %rdi, %rbx
movq 0x18(%rdi), %rdi
callq 0xff22c
movq 0x10(%rbx), %rdi
callq 0x10b00c
movq 0x8(%rbx), %rdi
callq 0x172c87
leaq 0x2a2dd9(%rip), %rsi    # 0x34f05d
movq %rbx, %rdi
movl $0x35, %edx
popq %rbx
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_id_to_md5.c
// Function: gt_id_to_md5_option_parser_new
static GtOptionParser* gt_id_to_md5_option_parser_new(void *tool_arguments)
{
  SeqidsToMD5Arguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  op = gt_option_parser_new("[option ...] [GFF3_file ...]",
                            "Change sequence IDs in given GFF3 files to MD5 "
                            "fingerprints of the corresponding sequences.");

  /* -seqfile, -matchdesc, -usedesc and -regionmapping */
  gt_seqid2file_register_options(op, arguments->s2fi);

  /* -subtargetids */
  option = gt_option_new_bool("subtargetids", "substitute the target IDs with "
                              "MD5 sums", &arguments->substitute_target_ids,
                              true);
  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);

  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xac32e
movq %rdi, %r14
leaq 0x29e24f(%rip), %rdi    # 0x34a4f9
leaq 0x2a2de4(%rip), %rsi    # 0x34f095
callq 0x107bfe
movq %rax, %rbx
movq 0x8(%r14), %rsi
movq %rax, %rdi
callq 0x172f86
leaq 0x1(%r14), %rdx
leaq 0x2a2e21(%rip), %rdi    # 0x34f0f1
leaq 0x2a2e27(%rip), %rsi    # 0x34f0fe
movl $0x1, %ecx
callq 0x10a235
movq %rbx, %rdi
movq %rax, %rsi
callq 0x107cc0
movq %r14, %rdi
callq 0x10a257
movq %rbx, %rdi
movq %rax, %rsi
callq 0x107cc0
movq 0x10(%r14), %rdi
addq $0x18, %r14
movq %rbx, %rsi
movq %r14, %rdx
callq 0x10ad87
leaq 0xa05ab(%rip), %rsi     # 0x14c8c4
movq %rbx, %rdi
xorl %edx, %edx
callq 0x107d3d
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x1bbd0
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_id_to_md5.c
// Function: gt_id_to_md5_runner
static int gt_id_to_md5_runner(GT_UNUSED int argc, const char **argv,
                                   int parsed_args, void *tool_arguments,
                                   GtError *err)
{
  GtNodeStream *gff3_in_stream, *id_to_md5_stream = NULL,
               *add_ids_stream = NULL, *gff3_out_stream = NULL;
  SeqidsToMD5Arguments *arguments = tool_arguments;
  GtRegionMapping *region_mapping;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

  /* create a gff3 input stream */
  gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
                                                  argv + parsed_args);
  if (arguments->verbose && arguments->outfp)
    gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) gff3_in_stream);
  /* add automatically generated sequence IDs later to avoid collisions */
  gt_gff3_in_stream_disable_add_ids(gff3_in_stream);

  /* create region mapping */
  region_mapping = gt_seqid2file_region_mapping_new(arguments->s2fi, err);
  if (!region_mapping)
    had_err = -1;

  if (!had_err) {
    /* create seqid to md5 stream */
    id_to_md5_stream =
      gt_id_to_md5_stream_new(gff3_in_stream, region_mapping,
                              arguments->substitute_target_ids);

    /* create add IDs stream */
    add_ids_stream = gt_add_ids_stream_new(id_to_md5_stream);

    /* create gff3 output stream */
    gff3_out_stream = gt_gff3_out_stream_new(add_ids_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(add_ids_stream);
  gt_node_stream_delete(id_to_md5_stream);
  gt_node_stream_delete(gff3_in_stream);

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r8, %r14
movq %rcx, %r15
movl %edx, %ebp
movq %rsi, %r12
movl %edi, %ebx
testq %r8, %r8
je 0xac360
movq %r14, %rdi
callq 0xfcc32
testb %al, %al
jne 0xac42a
testq %r15, %r15
je 0xac425
subl %ebp, %ebx
movslq %ebp, %rax
leaq (%r12,%rax,8), %rsi
movl %ebx, %edi
callq 0x145cdf
movq %rax, %rbx
cmpb $0x1, (%r15)
jne 0xac391
cmpq $0x0, 0x18(%r15)
je 0xac391
movq %rbx, %rdi
callq 0x145b36
movq %rbx, %rdi
callq 0x145c53
movq 0x8(%r15), %rdi
movq %r14, %rsi
callq 0x172fdd
testq %rax, %rax
je 0xac3e6
movzbl 0x1(%r15), %edx
movq %rbx, %rdi
movq %rax, %rsi
callq 0x155d18
movq %rax, %r12
movq %rax, %rdi
callq 0x1200ef
movq %rax, %r13
movq 0x18(%r15), %rsi
movq %rax, %rdi
callq 0x146fc0
movq %rax, %r15
movq %rax, %rdi
movq %r14, %rsi
callq 0x162f5d
movl %eax, %ebp
jmp 0xac3f4
movl $0xffffffff, %ebp       # imm = 0xFFFFFFFF
xorl %r15d, %r15d
xorl %r13d, %r13d
xorl %r12d, %r12d
movq %r15, %rdi
callq 0x162dee
movq %r13, %rdi
callq 0x162dee
movq %r12, %rdi
callq 0x162dee
movq %rbx, %rdi
callq 0x162dee
movl %ebp, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x1bc3e
callq 0x1bc07
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_idxlocali.c
// Function: gt_idxlocali_arguments_delete
static void gt_idxlocali_arguments_delete(void *tool_arguments)
{
  IdxlocaliOptions *arguments = tool_arguments;

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

// Assembly:
testq %rdi, %rdi
je 0xac4af
pushq %rbx
movq %rdi, %rbx
movq 0x8(%rdi), %rdi
callq 0x11bdbf
movq (%rbx), %rdi
callq 0x11c144
movq 0x10(%rbx), %rdi
callq 0x10a16a
movq 0x18(%rbx), %rdi
callq 0x10a16a
leaq 0x2a2c99(%rip), %rsi    # 0x34f13a
movq %rbx, %rdi
movl $0x2c, %edx
popq %rbx
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_idxlocali.c
// Function: gt_idxlocali_arguments_check
static int gt_idxlocali_arguments_check(GT_UNUSED int rest_argc,
                                        void *tool_arguments,
                                        GT_UNUSED GtError * err)
{
  IdxlocaliOptions *arguments = tool_arguments;

  if (gt_option_is_set(arguments->refoptionesaindex))
  {
    arguments->withesa = true;
  } else
  {
    gt_assert(gt_option_is_set(arguments->refoptionpckindex));
    arguments->withesa = false;
  }
  return 0;
}

// Assembly:
pushq %rbx
movq %rsi, %rbx
movq 0x10(%rsi), %rdi
callq 0x10ac3f
movb $0x1, %cl
testb %al, %al
jne 0xac740
movq 0x18(%rbx), %rdi
callq 0x10ac3f
testb %al, %al
je 0xac747
xorl %ecx, %ecx
movb %cl, 0x20(%rbx)
xorl %eax, %eax
popq %rbx
retq
callq 0x1bcac
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_idxlocali.c
// Function: gt_idxlocali_runner
static int gt_idxlocali_runner(GT_UNUSED int argc,
                               GT_UNUSED const char **argv,
                               GT_UNUSED int parsed_args,
                               void *tool_arguments,
                               GtError * err)
{
  IdxlocaliOptions *arguments = tool_arguments;
  bool haserr = false;
  GtUword idx;

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

  gt_assert(parsed_args == argc);
  printf("# indexname(%s)=%s\n", arguments->withesa ? "esa" : "pck",
         gt_str_get(arguments->indexname));
  for (idx = 0; idx < gt_str_array_size (arguments->queryfiles); idx++)
  {
    printf("# queryfile=%s\n",gt_str_array_get (arguments->queryfiles, idx));
  }
  printf("# threshold="GT_WU"\n", arguments->threshold);
  if (!haserr && gt_runidxlocali (arguments, err) != 0)
  {
    haserr = true;
  }
  return haserr ? -1 : 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movq %r8, %rbx
movq %rcx, %r14
movl %edx, %ebp
movl %edi, %r15d
testq %r8, %r8
je 0xac774
movq %rbx, %rdi
callq 0xfcc32
testb %al, %al
jne 0xac831
testq %r14, %r14
je 0xac827
cmpl %r15d, %ebp
jne 0xac82c
leaq 0x2ad498(%rip), %rax    # 0x359c25
cmpb $0x0, 0x20(%r14)
leaq 0x2a1015(%rip), %r15    # 0x34d7ae
cmovneq %rax, %r15
movq 0x8(%r14), %rdi
callq 0x11b0a1
leaq 0x2a2b33(%rip), %rdi    # 0x34f2e0
xorl %ebp, %ebp
movq %r15, %rsi
movq %rax, %rdx
xorl %eax, %eax
callq 0x17070
movq (%r14), %rdi
callq 0x11c131
testq %rax, %rax
je 0xac7fb
leaq 0x29d66a(%rip), %r15    # 0x349e3a
xorl %r12d, %r12d
movq (%r14), %rdi
movq %r12, %rsi
callq 0x11bfb3
movq %r15, %rdi
movq %rax, %rsi
xorl %eax, %eax
callq 0x17070
incq %r12
movq (%r14), %rdi
callq 0x11c131
cmpq %rax, %r12
jb 0xac7d3
movq 0x28(%r14), %rsi
leaq 0x2a2aee(%rip), %rdi    # 0x34f2f4
xorl %eax, %eax
callq 0x17070
movq %r14, %rdi
movq %rbx, %rsi
callq 0x1b3dab
negl %eax
sbbl %ebp, %ebp
movl %ebp, %eax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
callq 0x1bd57
callq 0x1bd1e
callq 0x1bce5
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_inlineseq_add.c
// Function: gt_inlineseq_add_arguments_new
static void *gt_inlineseq_add_arguments_new(void)
{
  InlineseqAddArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->s2fi = gt_seqid2file_info_new();
  arguments->ofi = gt_output_file_info_new();
  arguments->outfp = NULL;
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2a2aa2(%rip), %rdx    # 0x34f305
movl $0x1, %edi
movl $0x18, %esi
movl $0x24, %ecx
callq 0x10436a
movq %rax, %rbx
callq 0x172c40
movq %rax, (%rbx)
callq 0x10ad60
movq %rax, 0x8(%rbx)
movq $0x0, 0x10(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_inlineseq_add.c
// Function: gt_inlineseq_add_arguments_delete
static void gt_inlineseq_add_arguments_delete(void *tool_arguments)
{
  InlineseqAddArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_seqid2file_info_delete(arguments->s2fi);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xac8d0
pushq %rbx
movq %rdi, %rbx
movq 0x10(%rdi), %rdi
callq 0xff22c
movq (%rbx), %rdi
callq 0x172c87
movq 0x8(%rbx), %rdi
callq 0x10b00c
leaq 0x2a2a43(%rip), %rsi    # 0x34f305
movq %rbx, %rdi
movl $0x32, %edx
popq %rbx
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_inlineseq_add.c
// Function: gt_inlineseq_add_option_parser_new
static GtOptionParser* gt_inlineseq_add_option_parser_new(void *tool_arguments)
{
  GtOptionParser *op;
  GT_UNUSED GtOption *option;
  InlineseqAddArguments *arguments = tool_arguments;

  /* init */
  op = gt_option_parser_new("[options] [GFF3_file ...]",
                            "Adds inline sequences from external source to "
                            "GFF3 input.");

  gt_seqid2file_register_options(op, arguments->s2fi);
  gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);

  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
leaq 0x2a2a43(%rip), %rdi    # 0x34f322
leaq 0x2a2a56(%rip), %rsi    # 0x34f33c
callq 0x107bfe
movq %rax, %r14
movq (%rbx), %rsi
movq %rax, %rdi
callq 0x172f86
movq 0x8(%rbx), %rdi
addq $0x10, %rbx
movq %r14, %rsi
movq %rbx, %rdx
callq 0x10ad87
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_inlineseq_add.c
// Function: gt_inlineseq_add_runner
static int gt_inlineseq_add_runner(int argc, const char **argv, int parsed_args,
                               void *tool_arguments, GtError *err)
{
  GtNodeStream *gff3_in_stream = NULL,
               *add_stream = NULL,
               *gff3_out_stream = NULL,
               *last_stream = NULL;
  GtRegionMapping *rm = NULL;
  InlineseqAddArguments *arguments = tool_arguments;
  int had_err = 0;
  gt_error_check(err);

  /* add region mapping if given */
  if (gt_seqid2file_option_used(arguments->s2fi)) {
    rm = gt_seqid2file_region_mapping_new(arguments->s2fi, err);
    if (!rm)
      had_err = -1;
  }

  if (!had_err) {
    last_stream = gff3_in_stream = gt_gff3_in_stream_new_unsorted(
                                                            argc - parsed_args,
                                                            argv + parsed_args);
    gt_assert(gff3_in_stream);
    gt_gff3_in_stream_enable_tidy_mode((GtGFF3InStream*) gff3_in_stream);

    last_stream = add_stream = gt_sequence_node_add_stream_new(last_stream, rm,
                                                               err);
    if (!add_stream) {
      had_err = -1;
    }
  }

  if (!had_err) {
    last_stream = gff3_out_stream = gt_gff3_out_stream_new(last_stream,
                                                           arguments->outfp);
  }

  if (!had_err)
    had_err = gt_node_stream_pull(last_stream, err);

  /* free */
  gt_node_stream_delete(gff3_in_stream);
  gt_node_stream_delete(add_stream);
  gt_node_stream_delete(gff3_out_stream);
  gt_region_mapping_delete(rm);

  return had_err;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r8, %r14
movq %rcx, %r15
movl %edx, %r13d
movq %rsi, %r12
movl %edi, %ebp
testq %r8, %r8
je 0xac945
movq %r14, %rdi
callq 0xfcc32
testb %al, %al
jne 0xaca0e
movq (%r15), %rdi
callq 0x172f92
testb %al, %al
je 0xac976
movq (%r15), %rdi
movq %r14, %rsi
callq 0x172fdd
movq %rax, %rbx
testq %rax, %rax
jne 0xac978
movl $0xffffffff, %ebp       # imm = 0xFFFFFFFF
xorl %r15d, %r15d
xorl %ebx, %ebx
xorl %r13d, %r13d
xorl %r12d, %r12d
jmp 0xac9d8
xorl %ebx, %ebx
subl %r13d, %ebp
movslq %r13d, %rax
leaq (%r12,%rax,8), %rsi
movl %ebp, %edi
callq 0x145cdf
testq %rax, %rax
je 0xaca09
movq %rax, %r12
movq %rax, %rdi
callq 0x145c94
movq %r12, %rdi
movq %rbx, %rsi
movq %r14, %rdx
callq 0x173fcf
testq %rax, %rax
je 0xac9cd
movq %rax, %r13
movq 0x10(%r15), %rsi
movq %rax, %rdi
callq 0x146fc0
movq %rax, %r15
movq %rax, %rdi
movq %r14, %rsi
callq 0x162f5d
movl %eax, %ebp
jmp 0xac9d8
movl $0xffffffff, %ebp       # imm = 0xFFFFFFFF
xorl %r15d, %r15d
xorl %r13d, %r13d
movq %r12, %rdi
callq 0x162dee
movq %r13, %rdi
callq 0x162dee
movq %r15, %rdi
callq 0x162dee
movq %rbx, %rdi
callq 0x16d652
movl %ebp, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x1bdc7
callq 0x1bd90
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_inlineseq_split.c
// Function: gt_inlineseq_split_arguments_new
static void* gt_inlineseq_split_arguments_new(void)
{
  GtInlineseqSplitArguments *arguments
    = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->seqoutfile = gt_str_new();
  arguments->gffoutfile = gt_str_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2a295e(%rip), %rdx    # 0x34f39d
movl $0x1, %edi
movl $0x10, %esi
movl $0x26, %ecx
callq 0x10436a
movq %rax, %rbx
callq 0x11ac6c
movq %rax, (%rbx)
callq 0x11ac6c
movq %rax, 0x8(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_inlineseq_split.c
// Function: gt_inlineseq_split_arguments_delete
static void gt_inlineseq_split_arguments_delete(void *tool_arguments)
{
  GtInlineseqSplitArguments *arguments = tool_arguments;
  if (arguments != NULL) {
    gt_str_delete(arguments->seqoutfile);
    gt_str_delete(arguments->gffoutfile);
    gt_free(arguments);
  }
}

// Assembly:
testq %rdi, %rdi
je 0xaca9b
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x11bdbf
movq 0x8(%rbx), %rdi
callq 0x11bdbf
leaq 0x2a2910(%rip), %rsi    # 0x34f39d
movq %rbx, %rdi
movl $0x32, %edx
popq %rbx
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_inlineseq_split.c
// Function: gt_inlineseq_split_option_parser_new
static GtOptionParser* gt_inlineseq_split_option_parser_new(
                                                   void *tool_arguments)
{
  GtInlineseqSplitArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption GT_UNUSED *option, *seqopt, *gff3opt;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("(-seqfile <seqfile> | -gff3file <gff3file>) "
                            "[GFF3_file]",
                            "Split GFF3 annotations with inline sequences into "
                            "separate files.");

  /* -seqfile */
  seqopt = gt_option_new_string("seqfile", "output file for sequences as FASTA",
                                arguments->seqoutfile, NULL);
  gt_option_parser_add_option(op, seqopt);

  /* -gff3file */
  gff3opt = gt_option_new_string("gff3file", "output file for annotations "
                                             "as GFF3",
                                 arguments->gffoutfile, NULL);
  gt_option_parser_add_option(op, gff3opt);

  gt_option_is_mandatory_either(seqopt, gff3opt);

  return op;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0xacb20
movq %rdi, %r14
leaq 0x2a2931(%rip), %rdi    # 0x34f3e1
leaq 0x2a2962(%rip), %rsi    # 0x34f419
callq 0x107bfe
movq %rax, %rbx
movq (%r14), %rdx
leaq 0x2f12d1(%rip), %rdi    # 0x39dd9a
leaq 0x2a298b(%rip), %rsi    # 0x34f45b
xorl %ecx, %ecx
callq 0x10a770
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x107cc0
movq 0x8(%r14), %rdx
leaq 0x2d08d1(%rip), %rdi    # 0x37d3c1
leaq 0x2a2987(%rip), %rsi    # 0x34f47e
xorl %ecx, %ecx
callq 0x10a770
movq %rax, %r14
movq %rbx, %rdi
movq %rax, %rsi
callq 0x107cc0
movq %r15, %rdi
movq %r14, %rsi
callq 0x10a88b
movq %rbx, %rax
popq %rbx
popq %r14
popq %r15
retq
callq 0x1bdfe
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_interfeat.c
// Function: gt_interfeat_arguments_new
static void* gt_interfeat_arguments_new(void)
{
  InterFeatArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->outside_type = gt_str_new();
  arguments->inter_type = gt_str_new();
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2a281a(%rip), %rdx    # 0x34f4c9
movl $0x1, %edi
movl $0x20, %esi
movl $0x22, %ecx
callq 0x10436a
movq %rax, %rbx
callq 0x11ac6c
movq %rax, (%rbx)
callq 0x11ac6c
movq %rax, 0x8(%rbx)
callq 0x10ad60
movq %rax, 0x10(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_interfeat.c
// Function: gt_interfeat_arguments_delete
static void gt_interfeat_arguments_delete(void *tool_arguments)
{
  InterFeatArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_str_delete(arguments->inter_type);
  gt_str_delete(arguments->outside_type);
  gt_free(arguments);
}

// Assembly:
testq %rdi, %rdi
je 0xacd26
pushq %rbx
movq %rdi, %rbx
movq 0x18(%rdi), %rdi
callq 0xff22c
movq 0x10(%rbx), %rdi
callq 0x10b00c
movq 0x8(%rbx), %rdi
callq 0x11bdbf
movq (%rbx), %rdi
callq 0x11bdbf
leaq 0x2a27b1(%rip), %rsi    # 0x34f4c9
movq %rbx, %rdi
movl $0x31, %edx
popq %rbx
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_interfeat.c
// Function: gt_interfeat_option_parser_new
static GtOptionParser* gt_interfeat_option_parser_new(void *tool_arguments)
{
  InterFeatArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;

  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [GFF3_file ...]", "Add intermediary "
                            "features between outside features in given "
                            "GFF3 file(s).");

  /* -outside */
  option = gt_option_new_string("outside", "set outside type",
                                arguments->outside_type, gt_ft_exon);
  gt_option_parser_add_option(op, option);

  /* -inter */
  option = gt_option_new_string("inter", "set intermediary type",
                                arguments->inter_type, gt_ft_intron);
  gt_option_parser_add_option(op, option);

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

  return op;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xacdbc
movq %rdi, %rbx
leaq 0x29d7bb(%rip), %rdi    # 0x34a4f9
leaq 0x2a279d(%rip), %rsi    # 0x34f4e2
callq 0x107bfe
movq %rax, %r14
movq (%rbx), %rdx
leaq 0x3144b7(%rip), %rdi    # 0x3c120e
leaq 0x2a27ce(%rip), %rsi    # 0x34f52c
leaq 0x2e7a32(%rip), %rcx    # 0x394797
callq 0x10a770
movq %r14, %rdi
movq %rax, %rsi
callq 0x107cc0
movq 0x8(%rbx), %rdx
leaq 0x32a562(%rip), %rdi    # 0x3d72e2
leaq 0x2a27b6(%rip), %rsi    # 0x34f53d
leaq 0x2e7517(%rip), %rcx    # 0x3942a5
callq 0x10a770
movq %r14, %rdi
movq %rax, %rsi
callq 0x107cc0
movq 0x10(%rbx), %rdi
addq $0x18, %rbx
movq %r14, %rsi
movq %rbx, %rdx
callq 0x10ad87
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
callq 0x1bf11
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_interfeat.c
// Function: gt_interfeat_runner
static int gt_interfeat_runner(int argc, const char **argv, int parsed_args,
                          void *tool_arguments, GtError *err)
{
  InterFeatArguments *arguments = tool_arguments;
  GtNodeStream *gff3_in_stream,
               *inter_feature_stream,
               *gff3_out_stream;
  int had_err;

  gt_error_check(err);
  gt_assert(arguments);

  /* create a gff3 input stream */
  gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
                                                  argv + parsed_args);

  /* create intermediary feature stream */
  inter_feature_stream =
    gt_inter_feature_stream_new(gff3_in_stream,
                                gt_str_get(arguments->outside_type),
                                gt_str_get(arguments->inter_type));

  /* create gff3 output stream */
  gff3_out_stream = gt_gff3_out_stream_new(inter_feature_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(inter_feature_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, %r12d
movq %rsi, %r15
movl %edi, %ebp
testq %r8, %r8
je 0xacdec
movq %rbx, %rdi
callq 0xfcc32
testb %al, %al
jne 0xace6e
testq %r14, %r14
je 0xace69
subl %r12d, %ebp
movslq %r12d, %rax
leaq (%r15,%rax,8), %rsi
movl %ebp, %edi
callq 0x145cdf
movq %rax, %r15
movq (%r14), %rdi
callq 0x11b0a1
movq %rax, %r12
movq 0x8(%r14), %rdi
callq 0x11b0a1
movq %r15, %rdi
movq %r12, %rsi
movq %rax, %rdx
callq 0x1562d4
movq %rax, %r12
movq 0x18(%r14), %rsi
movq %rax, %rdi
callq 0x146fc0
movq %rax, %r14
movq %rax, %rdi
movq %rbx, %rsi
callq 0x162f5d
movl %eax, %ebx
movq %r14, %rdi
callq 0x162dee
movq %r12, %rdi
callq 0x162dee
movq %r15, %rdi
callq 0x162dee
movl %ebx, %eax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
callq 0x1bf7f
callq 0x1bf48
nop
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_kmer_database.c
// Function: gt_kmer_database_arguments_check
static int gt_kmer_database_arguments_check(int rest_argc,
                                            void *tool_arguments,
                                            GtError *err)
{
  GtKmerDatabaseArguments *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");
    had_err = -1;
  }

  if (!had_err && gt_str_length(arguments->print_filename) > 0UL) {
    if (!arguments->verbose) {
      gt_error_set(err, "-outfile needs -verbose option");
      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 0xad16e
movq %rbx, %rdi
callq 0xfcc32
testb %al, %al
jne 0xad1bb
testq %r14, %r14
je 0xad1b6
cmpl $0x1, %ebp
jne 0xad19b
movq 0x20(%r14), %rdi
callq 0x11b0ca
movq %rax, %rcx
xorl %eax, %eax
testq %rcx, %rcx
je 0xad1b1
cmpb $0x0, 0x18(%r14)
jne 0xad1b1
leaq 0x2a27b0(%rip), %rsi    # 0x34f949
jmp 0xad1a2
leaq 0x2a2788(%rip), %rsi    # 0x34f92a
movq %rbx, %rdi
xorl %eax, %eax
callq 0xfcb67
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
popq %rbx
popq %r14
popq %rbp
retq
callq 0x1c026
callq 0x1bfed
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_linspace_align.c
// Function: gt_linspace_align_arguments_new
static void* gt_linspace_align_arguments_new(void)
{
  GtLinspaceArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->outputfile = gt_str_new();
  arguments->strings = gt_str_array_new();
  arguments->files = gt_str_array_new();
  arguments->linearcosts = gt_str_array_new();
  arguments->affinecosts = gt_str_array_new();
  arguments->diagonalbonds = gt_str_array_new();
  return arguments;
}

// Assembly:
pushq %rbx
leaq 0x2a20cc(%rip), %rdx    # 0x34fa60
movl $0x1, %edi
movl $0x50, %esi
movl $0x54, %ecx
callq 0x10436a
movq %rax, %rbx
callq 0x11ac6c
movq %rax, (%rbx)
callq 0x11be10
movq %rax, 0x8(%rbx)
callq 0x11be10
movq %rax, 0x10(%rbx)
callq 0x11be10
movq %rax, 0x18(%rbx)
callq 0x11be10
movq %rax, 0x20(%rbx)
callq 0x11be10
movq %rax, 0x28(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_linspace_align.c
// Function: gt_linspace_align_arguments_delete
static void gt_linspace_align_arguments_delete(void *tool_arguments)
{
  GtLinspaceArguments *arguments = tool_arguments;
  if (arguments != NULL) {
    gt_str_delete(arguments->outputfile);
    gt_str_array_delete(arguments->strings);
    gt_str_array_delete(arguments->files);
    gt_str_array_delete(arguments->linearcosts);
    gt_str_array_delete(arguments->affinecosts);
    gt_str_array_delete(arguments->diagonalbonds);
    gt_free(arguments);
  }
}

// Assembly:
testq %rdi, %rdi
je 0xada38
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x11bdbf
movq 0x8(%rbx), %rdi
callq 0x11c144
movq 0x10(%rbx), %rdi
callq 0x11c144
movq 0x18(%rbx), %rdi
callq 0x11c144
movq 0x20(%rbx), %rdi
callq 0x11c144
movq 0x28(%rbx), %rdi
callq 0x11c144
leaq 0x2a2036(%rip), %rsi    # 0x34fa60
movq %rbx, %rdi
movl $0x68, %edx
popq %rbx
jmp 0x1045eb
retq
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_linspace_align.c
// Function: get_fastasequences
static int get_fastasequences(GtSequenceTable *sequence_table,
                              const GtStr *filename,
                              GtError *err)
{
  int had_err = 0;
  GtFastaReader *reader;

  gt_assert(sequence_table != NULL);
  reader = gt_fasta_reader_rec_new (filename);
  had_err = gt_fasta_reader_run(reader, NULL, save_fastasequence,
                                NULL, sequence_table, err);
  gt_fasta_reader_delete(reader);
  return had_err;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0xaebb4
movq %rdx, %rbx
movq %rdi, %r14
movq %rsi, %rdi
callq 0xfe82b
movq %rax, %r15
leaq 0x1ae(%rip), %rdx       # 0xaed3e
movq %rax, %rdi
xorl %esi, %esi
xorl %ecx, %ecx
movq %r14, %r8
movq %rbx, %r9
callq 0xfe3f8
movl %eax, %ebx
movq %r15, %rdi
callq 0xfe3bd
movl %ebx, %eax
popq %rbx
popq %r14
popq %r15
retq
callq 0x1c3b6
// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_linspace_align.c
// Function: gt_encode_sequence_table
static void gt_encode_sequence_table(const GtAlphabet *alphabet,
                                     GtSequenceTable *sequence_table)
{
  GtUword idx;

  for (idx = 0; idx < sequence_table->size; idx++)
  {
    GtStr *gt_str = sequence_table->seqarray[idx];
    GtUchar *seq = (GtUchar*) gt_str_get(gt_str);

    gt_alphabet_encode_seq(alphabet, seq,(const char*) seq,
                           gt_str_length(gt_str));
  }
}

// Assembly:
cmpq $0x0, 0x8(%rsi)
je 0xaec0f
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
movq %rsi, %rbx
movq %rdi, %r14
xorl %r13d, %r13d
movq (%rbx), %rax
movq (%rax,%r13,8), %r15
movq %r15, %rdi
callq 0x11b0a1
movq %rax, %r12
movq %r15, %rdi
callq 0x11b0ca
movq %r14, %rdi
movq %r12, %rsi
movq %r12, %rdx
movq %rax, %rcx
callq 0xd18c7
incq %r13
cmpq 0x8(%rbx), %r13
jb 0xaebd2
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq