// File: /workspace/github_c_makefile_star2_O3/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:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x9a678
movq %rdi, %rbx
callq 0x11ac6c
movq %rax, 0x18(%rbx)
callq 0x11be10
movq %rax, 0x20(%rbx)
callq 0x11be10
movq %rax, 0x28(%rbx)
leaq 0x2abda1(%rip), %rdi    # 0x34629d
leaq 0x2abdb1(%rip), %rsi    # 0x3462b4
callq 0x107bfe
movq %rax, %r14
leaq 0x2abdba(%rip), %rsi    # 0x3462cc
movq %rax, %rdi
callq 0x107e5c
movq 0x18(%rbx), %rdx
leaq 0x32749d(%rip), %rdi    # 0x3c19c2
leaq 0x2abdbb(%rip), %rsi    # 0x3462e7
callq 0x10a7af
movq %rax, %r15
movq %r14, %rdi
movq %rax, %rsi
callq 0x107cc0
movq %r15, %rdi
callq 0x10a87b
movq 0x20(%rbx), %rdx
leaq 0x2abdca(%rip), %rdi    # 0x34631c
leaq 0x2abdca(%rip), %rsi    # 0x346323
callq 0x10a7a1
movq %rax, %r15
movq %rax, %rdi
callq 0x10ac2f
movq %r15, %rdi
callq 0x107bec
movq %rax, 0x40(%rbx)
movq %r14, %rdi
movq %r15, %rsi
callq 0x107cc0
movq 0x28(%rbx), %rdx
leaq 0x2fa16d(%rip), %rdi    # 0x3946f8
leaq 0x2abe82(%rip), %rsi    # 0x346414
callq 0x10a7a1
movq %rax, %r12
movq %rax, %rdi
callq 0x10ac2f
movq %r14, %rdi
movq %r12, %rsi
callq 0x107cc0
movq %r12, %rdi
callq 0x107bec
movq %rax, 0x48(%rbx)
movq %r12, %rdi
movq %r15, %rsi
callq 0x10ab96
leaq 0x8(%rbx), %rdx
leaq 0x2ac06d(%rip), %rdi    # 0x34663c
leaq 0x2ac069(%rip), %rsi    # 0x34663f
movsd 0x2abc4a(%rip), %xmm0   # 0x346228
callq 0x10a346
movq %rax, %r15
movq %rax, %rdi
callq 0x107bec
movq %rax, 0x38(%rbx)
movq %r14, %rdi
movq %r15, %rsi
callq 0x107cc0
leaq 0x10(%rbx), %rdx
leaq 0x2ac0b0(%rip), %rdi    # 0x3466b8
leaq 0x2ac0b0(%rip), %rsi    # 0x3466bf
xorl %ecx, %ecx
callq 0x10a2ab
movq %rax, %r15
movq %rax, %rdi
callq 0x107bec
movq %rax, 0x30(%rbx)
movq %r14, %rdi
movq %r15, %rsi
callq 0x107cc0
leaq 0x2bc28b(%rip), %rdi    # 0x3568c2
leaq 0x2ac0a7(%rip), %rsi    # 0x3466e5
movq %rbx, %rdx
xorl %ecx, %ecx
callq 0x10a235
movq %r14, %rdi
movq %rax, %rsi
callq 0x107cc0
incq %rbx
movq %rbx, %rdi
callq 0x10a257
movq %r14, %rdi
movq %rax, %rsi
callq 0x107cc0
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
callq 0x1853b