// File: /workspace/github_c_makefile_star2_O0/genometools[P]genometools/src/tools/gt_chain2dim.c
// Function: gt_chain2dim_option_parser_new
static GtOptionParser *gt_chain2dim_option_parser_new (void *tool_arguments)
{
  GtChain2dimoptions *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *optionglobal, *optionlocal;

  gt_assert (arguments != NULL);
  arguments->matchfile = gt_str_new ();
  arguments->globalargs = gt_str_array_new();
  arguments->localargs = gt_str_array_new();

  op = gt_option_parser_new("[options] -m matchfile",
                            "Chain pairwise matches.");

  gt_option_parser_set_mail_address(op, "<kurtz@zbh.uni-hamburg.de>");
  option = gt_option_new_filename("m","Specify file containing the matches\n"
                                  "mandatory option",
                                  arguments->matchfile);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  optionglobal = gt_option_new_string_array("global",
                   "perform global chaining\n"
                   "- optional parameter gc switches\n"
                   "  on gap costs (according to L1-model)\n"
                   "- optional parameter ov means\n"
                   "  that overlaps between matches are allowed\n"
                   "- optional parameter all means\n"
                   "  that all optimal chains are processed",
                   arguments->globalargs);
  gt_option_argument_is_optional(optionglobal);
  arguments->refoptionglobal = gt_option_ref (optionglobal);
  gt_option_parser_add_option(op, optionglobal);

  optionlocal = gt_option_new_string_array("local",
                   "perform local chaining\n"
                   "compute local chains (according to L1-model).\n"
                   "- If no parameter is given, compute local chains with\n"
                   "  maximums score.\n"
                   "- If parameter is given, this must be a positive number\n"
                   "  optionally followed by the character b or p.\n"
                   "- If only the number, say k, is given, this is the "
                   "minimum\n"
                   "  score of the chains output.\n"
                   "- If a number is followed by character b, then output all\n"
                   "  chains with the largest k scores.\n"
                   "- If a number is followed by character p, then output all\n"
                   "  chains with scores at most k percent away\n"
                   "  from the best score.",
                   arguments->localargs);
  gt_option_argument_is_optional(optionlocal);
  gt_option_parser_add_option(op, optionlocal);
  arguments->refoptionlocal = gt_option_ref(optionlocal);
  gt_option_exclude(optionlocal,optionglobal);
  option = gt_option_new_double("wf","specify weight factor > 0.0 to obtain "
                                     "score of a fragment\nrequires one of "
                                     "the options\n-local const\n-global "
                                     "gc\n-global ov",
                                     &arguments->weightfactor,1.0);
  arguments->refoptionweightfactor = gt_option_ref (option);
  gt_option_parser_add_option(op, option);
  option = gt_option_new_uword("maxgap","specify maximal width of gap in chain",
                                         &arguments->maxgap,0);
  arguments->refoptionmaxgap = gt_option_ref(option);
  gt_option_parser_add_option(op, option);
  option = gt_option_new_bool("silent","do not output the chains but only "
                                       "report their lengths and scores",
                                       &arguments->silent,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 $0x38, %rsp
movq %rdi, 0x30(%rsp)
movq 0x30(%rsp), %rax
movq %rax, 0x28(%rsp)
cmpq $0x0, 0x28(%rsp)
jne 0x1e733
movq 0x61d89e(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x4f7907(%rip), %rsi    # 0x516013
leaq 0x4f8b71(%rip), %rdx    # 0x517284
leaq 0x4f8b7c(%rip), %rcx    # 0x517296
leaq 0x4f8b4a(%rip), %r8     # 0x51726b
movl $0x35, %r9d
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x1e735
callq 0x11d4a0
movq %rax, %rcx
movq 0x28(%rsp), %rax
movq %rcx, 0x18(%rax)
callq 0x11f5c0
movq %rax, %rcx
movq 0x28(%rsp), %rax
movq %rcx, 0x20(%rax)
callq 0x11f5c0
movq %rax, %rcx
movq 0x28(%rsp), %rax
movq %rcx, 0x28(%rax)
leaq 0x4f8b46(%rip), %rdi    # 0x5172b5
leaq 0x4f8b56(%rip), %rsi    # 0x5172cc
callq 0xf1420
movq %rax, 0x20(%rsp)
movq 0x20(%rsp), %rdi
leaq 0x4f8b58(%rip), %rsi    # 0x5172e4
callq 0xf1a10
movq 0x28(%rsp), %rax
movq 0x18(%rax), %rdx
leaq 0x5765d2(%rip), %rdi    # 0x594d73
leaq 0x4f8b57(%rip), %rsi    # 0x5172ff
callq 0xf6aa0
movq %rax, 0x18(%rsp)
movq 0x20(%rsp), %rdi
movq 0x18(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdi
callq 0xf6ca0
movq 0x28(%rsp), %rax
movq 0x20(%rax), %rdx
leaq 0x4f8b59(%rip), %rdi    # 0x517334
leaq 0x4f8b59(%rip), %rsi    # 0x51733b
callq 0xf6a50
movq %rax, 0x10(%rsp)
movq 0x10(%rsp), %rdi
callq 0xf7450
movq 0x10(%rsp), %rdi
callq 0xf13c0
movq %rax, %rcx
movq 0x28(%rsp), %rax
movq %rcx, 0x40(%rax)
movq 0x20(%rsp), %rdi
movq 0x10(%rsp), %rsi
callq 0xf1600
movq 0x28(%rsp), %rax
movq 0x28(%rax), %rdx
leaq 0x548848(%rip), %rdi    # 0x567073
leaq 0x4f8bfa(%rip), %rsi    # 0x51742c
callq 0xf6a50
movq %rax, 0x8(%rsp)
movq 0x8(%rsp), %rdi
callq 0xf7450
movq 0x20(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x8(%rsp), %rdi
callq 0xf13c0
movq %rax, %rcx
movq 0x28(%rsp), %rax
movq %rcx, 0x48(%rax)
movq 0x8(%rsp), %rdi
movq 0x10(%rsp), %rsi
callq 0xf7320
movq 0x28(%rsp), %rdx
addq $0x8, %rdx
leaq 0x4f8dca(%rip), %rdi    # 0x517654
leaq 0x4f8dc6(%rip), %rsi    # 0x517657
movsd 0x4f89a7(%rip), %xmm0   # 0x517240
callq 0xf6160
movq %rax, 0x18(%rsp)
movq 0x18(%rsp), %rdi
callq 0xf13c0
movq %rax, %rcx
movq 0x28(%rsp), %rax
movq %rcx, 0x38(%rax)
movq 0x20(%rsp), %rdi
movq 0x18(%rsp), %rsi
callq 0xf1600
movq 0x28(%rsp), %rdx
addq $0x10, %rdx
leaq 0x4f8df8(%rip), %rdi    # 0x5176d0
leaq 0x4f8df8(%rip), %rsi    # 0x5176d7
xorl %eax, %eax
movl %eax, %ecx
callq 0xf5fe0
movq %rax, 0x18(%rsp)
movq 0x18(%rsp), %rdi
callq 0xf13c0
movq %rax, %rcx
movq 0x28(%rsp), %rax
movq %rcx, 0x30(%rax)
movq 0x20(%rsp), %rdi
movq 0x18(%rsp), %rsi
callq 0xf1600
movq 0x28(%rsp), %rdx
leaq 0x50907c(%rip), %rdi    # 0x52799a
leaq 0x4f8dd8(%rip), %rsi    # 0x5176fd
xorl %ecx, %ecx
callq 0xf5f20
movq %rax, 0x18(%rsp)
movq 0x20(%rsp), %rdi
movq 0x18(%rsp), %rsi
callq 0xf1600
movq 0x28(%rsp), %rdi
addq $0x1, %rdi
callq 0xf5f90
movq %rax, 0x18(%rsp)
movq 0x20(%rsp), %rdi
movq 0x18(%rsp), %rsi
callq 0xf1600
movq 0x20(%rsp), %rax
addq $0x38, %rsp
retq
nopl (%rax)