// File: /workspace/github_c_makefile_star2_O0/genometools[P]genometools/src/tools/gt_idxlocali.c
// Function: gt_idxlocali_option_parser_new
static GtOptionParser *gt_idxlocali_option_parser_new(void *tool_arguments)
{
  IdxlocaliOptions *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *optionesaindex, *optionpckindex, *optiononline, *optioncmp;

  gt_assert(arguments != NULL);
  arguments->indexname = gt_str_new ();
  arguments->queryfiles = gt_str_array_new ();

  op = gt_option_parser_new
    ("[options] -q query-file-names [-esa|-pck] indexname",
     "Find all local alignments using suffix tree.");

  gt_option_parser_set_mail_address(op, "<kurtz@zbh.uni-hamburg.de>");
  option = gt_option_new_filename_array("q","Specify files containing the "
                                            "query sequences",
                                        arguments->queryfiles);
  gt_option_parser_add_option (op, option);

  option = gt_option_new_word("match",
                              "Specify match score",
                              &arguments->matchscore, 1L);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_word("mismatch",
                              "Specify mismatch score",
                              &arguments->mismatchscore, -3L);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_word("gapstart",
                              "Specify gap start score",
                              &arguments->gapstart, -5L);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_word("gapextend",
                              "Specify gap extension score",
                              &arguments->gapextend, -2L);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_uword_min("th",
                                   "Specify the threshold",
                                    &arguments->threshold, 0, 1UL);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  optionesaindex = gt_option_new_string("esa",
                                        "Specify index "
                                        "(enhanced suffix array)",
                                        arguments->indexname, NULL);
  gt_option_parser_add_option(op, optionesaindex);
  arguments->refoptionesaindex = gt_option_ref(optionesaindex);

  optionpckindex = gt_option_new_string("pck",
                                        "Specify index (packed index)",
                                        arguments->indexname, NULL);
  gt_option_parser_add_option(op, optionpckindex);
  arguments->refoptionpckindex = gt_option_ref (optionpckindex);
  gt_option_exclude (optionesaindex, optionpckindex);
  gt_option_is_mandatory_either(optionesaindex, optionpckindex);

  optiononline = gt_option_new_bool("online","Perform online searches",
                                    &arguments->doonline, false);
  gt_option_parser_add_option(op, optiononline);
  gt_option_is_development_option(optiononline);

  optioncmp = gt_option_new_bool("cmp","Compare results of offline and online "
                                 "searches",
                                 &arguments->docompare, false);
  gt_option_parser_add_option(op,optioncmp);
  gt_option_exclude(optiononline,optioncmp);

  option = gt_option_new_bool("s",
                              "Show alignments",
                              &arguments->showalignment, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);
  return op;
}

// Assembly:
subq $0x48, %rsp
movq %rdi, 0x40(%rsp)
movq 0x40(%rsp), %rax
movq %rax, 0x38(%rsp)
cmpq $0x0, 0x38(%rsp)
jne 0x3e493
movq 0x5fdb3e(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x4d7ba7(%rip), %rsi    # 0x516013
leaq 0x4d8e11(%rip), %rdx    # 0x517284
leaq 0x4e1d69(%rip), %rcx    # 0x5201e3
leaq 0x4e1d49(%rip), %r8     # 0x5201ca
movl $0x35, %r9d
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x3e495
callq 0x11d4a0
movq %rax, %rcx
movq 0x38(%rsp), %rax
movq %rcx, 0x8(%rax)
callq 0x11f5c0
movq %rax, %rcx
movq 0x38(%rsp), %rax
movq %rcx, (%rax)
leaq 0x4e1d45(%rip), %rdi    # 0x520202
leaq 0x4e1d72(%rip), %rsi    # 0x520236
callq 0xf1420
movq %rax, 0x30(%rsp)
movq 0x30(%rsp), %rdi
leaq 0x4d8e0a(%rip), %rsi    # 0x5172e4
callq 0xf1a10
movq 0x38(%rsp), %rax
movq (%rax), %rdx
leaq 0x51a8d1(%rip), %rdi    # 0x558dbf
leaq 0x4dc89f(%rip), %rsi    # 0x51ad94
callq 0xf6b00
movq %rax, 0x28(%rsp)
movq 0x30(%rsp), %rdi
movq 0x28(%rsp), %rsi
callq 0xf1600
movq 0x38(%rsp), %rdx
addq $0x30, %rdx
leaq 0x51ae5a(%rip), %rdi    # 0x559378
leaq 0x4e1d3e(%rip), %rsi    # 0x520263
movl $0x1, %ecx
callq 0xf6650
movq %rax, 0x28(%rsp)
movq 0x30(%rsp), %rdi
movq 0x28(%rsp), %rsi
callq 0xf1600
movq 0x38(%rsp), %rdx
addq $0x38, %rdx
leaq 0x565e27(%rip), %rdi    # 0x5a437a
leaq 0x4e1d1d(%rip), %rsi    # 0x520277
movq $-0x3, %rcx
callq 0xf6650
movq %rax, 0x28(%rsp)
movq 0x30(%rsp), %rdi
movq 0x28(%rsp), %rsi
callq 0xf1600
movq 0x38(%rsp), %rdx
addq $0x40, %rdx
leaq 0x4e1d04(%rip), %rdi    # 0x52028e
leaq 0x4e1d06(%rip), %rsi    # 0x520297
movq $-0x5, %rcx
callq 0xf6650
movq %rax, 0x28(%rsp)
movq 0x30(%rsp), %rdi
movq 0x28(%rsp), %rsi
callq 0xf1600
movq 0x38(%rsp), %rdx
addq $0x48, %rdx
leaq 0x50ba55(%rip), %rdi    # 0x54a016
leaq 0x4e1ce7(%rip), %rsi    # 0x5202af
movq $-0x2, %rcx
callq 0xf6650
movq %rax, 0x28(%rsp)
movq 0x30(%rsp), %rdi
movq 0x28(%rsp), %rsi
callq 0xf1600
movq 0x38(%rsp), %rdx
addq $0x28, %rdx
leaq 0x526611(%rip), %rdi    # 0x564c09
leaq 0x4e1ccc(%rip), %rsi    # 0x5202cb
xorl %eax, %eax
movl %eax, %ecx
movl $0x1, %r8d
callq 0xf66b0
movq %rax, 0x28(%rsp)
movq 0x30(%rsp), %rdi
movq 0x28(%rsp), %rsi
callq 0xf1600
movq 0x28(%rsp), %rdi
callq 0xf6ca0
movq 0x38(%rsp), %rax
movq 0x8(%rax), %rdx
leaq 0x4ec70c(%rip), %rdi    # 0x52ad48
leaq 0x4dc70e(%rip), %rsi    # 0x51ad51
xorl %eax, %eax
movl %eax, %ecx
callq 0xf69f0
movq %rax, 0x20(%rsp)
movq 0x30(%rsp), %rdi
movq 0x20(%rsp), %rsi
callq 0xf1600
movq 0x20(%rsp), %rdi
callq 0xf13c0
movq %rax, %rcx
movq 0x38(%rsp), %rax
movq %rcx, 0x10(%rax)
movq 0x38(%rsp), %rax
movq 0x8(%rax), %rdx
leaq 0x4e01c8(%rip), %rdi    # 0x51e84e
leaq 0x4dc6ea(%rip), %rsi    # 0x51ad77
xorl %eax, %eax
movl %eax, %ecx
callq 0xf69f0
movq %rax, 0x18(%rsp)
movq 0x30(%rsp), %rdi
movq 0x18(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdi
callq 0xf13c0
movq %rax, %rcx
movq 0x38(%rsp), %rax
movq %rcx, 0x18(%rax)
movq 0x20(%rsp), %rdi
movq 0x18(%rsp), %rsi
callq 0xf7320
movq 0x20(%rsp), %rdi
movq 0x18(%rsp), %rsi
callq 0xf6cf0
movq 0x38(%rsp), %rdx
addq $0x23, %rdx
leaq 0x4e1bf3(%rip), %rdi    # 0x5202e1
leaq 0x4e1bf3(%rip), %rsi    # 0x5202e8
xorl %ecx, %ecx
callq 0xf5f20
movq %rax, 0x10(%rsp)
movq 0x30(%rsp), %rdi
movq 0x10(%rsp), %rsi
callq 0xf1600
movq 0x10(%rsp), %rdi
callq 0xf7040
movq 0x38(%rsp), %rdx
addq $0x24, %rdx
leaq 0x4fdd75(%rip), %rdi    # 0x53c49f
leaq 0x4e1bcf(%rip), %rsi    # 0x520300
xorl %ecx, %ecx
callq 0xf5f20
movq %rax, 0x8(%rsp)
movq 0x30(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf7320
movq 0x38(%rsp), %rdx
addq $0x22, %rdx
leaq 0x4ee141(%rip), %rdi    # 0x52c8ac
leaq 0x4e1bbd(%rip), %rsi    # 0x52032f
xorl %ecx, %ecx
callq 0xf5f20
movq %rax, 0x28(%rsp)
movq 0x30(%rsp), %rdi
movq 0x28(%rsp), %rsi
callq 0xf1600
movq 0x38(%rsp), %rdi
addq $0x21, %rdi
callq 0xf5f90
movq %rax, 0x28(%rsp)
movq 0x30(%rsp), %rdi
movq 0x28(%rsp), %rsi
callq 0xf1600
movq 0x30(%rsp), %rax
addq $0x48, %rsp
retq
nopl (%rax)