// File: /workspace/github_c_makefile_star2_O3/genometools[P]genometools/src/tools/gt_tallymer.c
// Function: gt_tyr_mkindex_option_parser_new
static GtOptionParser *gt_tyr_mkindex_option_parser_new(void *tool_arguments)
{
  GtOptionParser *op;
  GtOption *option,
           *optionminocc,
           *optionmaxocc,
           *optionpl,
           *optionstoreindex,
           *optionstorecounts,
           *optionscan,
           *optionesa;
  Tyr_mkindex_options *arguments = tool_arguments;

  op = gt_option_parser_new("[options] -esa suffixerator-index [options]",
                            "Count and index k-mers in the given enhanced "
                            "suffix array for a fixed value of k.");
  gt_option_parser_set_mail_address(op, "<kurtz@zbh.uni-hamburg.de>");

  optionesa = gt_option_new_string("esa","specify suffixerator-index\n"
                                   "(mandatory option)",
                                   arguments->str_inputindex,
                                   NULL);
  gt_option_is_mandatory(optionesa);
  gt_option_parser_add_option(op, optionesa);

  option = gt_option_new_uword("mersize",
                               "Specify the mer size.",
                               &arguments->mersize,
                               20UL);
  gt_option_parser_add_option(op, option);

  optionminocc
    = gt_option_new_uword("minocc",
                          "Specify the minimum occurrence number for "
                          "the mers to output/index",
                          &arguments->userdefinedminocc,
                          0);
  gt_option_parser_add_option(op, optionminocc);

  optionmaxocc
    = gt_option_new_uword("maxocc",
                          "Specify the maximum occurrence number for "
                          "the mers to output/index",
                          &arguments->userdefinedmaxocc,
                          0);
  gt_option_parser_add_option(op, optionmaxocc);

  optionpl = gt_option_new_uint_min("pl",
                 "specify prefix length for bucket boundary construction\n"
                 "recommendation: use without argument;\n"
                 "then a reasonable prefix length is automatically determined",
                 &arguments->userdefinedprefixlength,
                 0,
                 1U);
  gt_option_argument_is_optional(optionpl);
  gt_option_parser_add_option(op, optionpl);
  arguments->refoptionpl = gt_option_ref(optionpl);

  optionstoreindex = gt_option_new_string("indexname",
                                          "store the mers specified by options "
                                          "-maxocc and -minocc in an index",
                                          arguments->str_storeindex, NULL);
  gt_option_parser_add_option(op, optionstoreindex);

  optionstorecounts = gt_option_new_bool("counts", "store counts of the mers",
                                         &arguments->storecounts,false);
  gt_option_parser_add_option(op, optionstorecounts);

  option = gt_option_new_bool("test", "perform tests to verify program "
                                      "correctness", &arguments->performtest,
                                      false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  optionscan = gt_option_new_bool("scan",
                                  "read enhanced suffix array sequentially "
                                  "instead of mapping it to memory",
                                  &arguments->scanfile,
                                  false);
  gt_option_parser_add_option(op, optionscan);

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

  gt_option_imply(optionpl, optionstoreindex);
  gt_option_imply(optionstorecounts, optionstoreindex);
  gt_option_imply_either_2(optionstoreindex,optionminocc,optionmaxocc);
  return op;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %rdi, %r14
leaq 0x28e562(%rip), %rdi    # 0x35c7db
leaq 0x28e587(%rip), %rsi    # 0x35c807
callq 0x107bfe
movq %rax, %rbx
leaq 0x27803d(%rip), %rsi    # 0x3462cc
movq %rax, %rdi
callq 0x107e5c
movq 0x38(%r14), %rdx
leaq 0x28b983(%rip), %rdi    # 0x359c25
leaq 0x28e5b0(%rip), %rsi    # 0x35c859
xorl %ecx, %ecx
callq 0x10a770
movq %rax, %r15
movq %rax, %rdi
callq 0x10a87b
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
leaq 0x28ece2(%rip), %rdi    # 0x35cfaf
leaq 0x28e5b3(%rip), %rsi    # 0x35c887
movl $0x14, %ecx
movq %r14, %rdx
callq 0x10a2ab
movq %rbx, %rdi
movq %rax, %rsi
callq 0x107cc0
leaq 0x8(%r14), %rdx
leaq 0x28e5a6(%rip), %rdi    # 0x35c89d
leaq 0x28e5a6(%rip), %rsi    # 0x35c8a4
xorl %ecx, %ecx
callq 0x10a2ab
movq %rax, 0x10(%rsp)
movq %rbx, %rdi
movq %rax, %rsi
callq 0x107cc0
leaq 0x10(%r14), %rdx
leaq 0x28e22c(%rip), %rdi    # 0x35c54c
leaq 0x28e5c0(%rip), %rsi    # 0x35c8e7
xorl %ecx, %ecx
callq 0x10a2ab
movq %rax, 0x8(%rsp)
movq %rbx, %rdi
movq %rax, %rsi
callq 0x107cc0
leaq 0x18(%r14), %rdx
leaq 0x2a15e9(%rip), %rdi    # 0x36f932
leaq 0x28e5da(%rip), %rsi    # 0x35c92a
xorl %ecx, %ecx
movl $0x1, %r8d
callq 0x10a51f
movq %rax, %r13
movq %rax, %rdi
callq 0x10ac2f
movq %rbx, %rdi
movq %r13, %rsi
callq 0x107cc0
movq %r13, %rdi
callq 0x107bec
movq %rax, 0x28(%r14)
movq 0x30(%r14), %rdx
leaq 0x2977a3(%rip), %rdi    # 0x365b2d
leaq 0x28e632(%rip), %rsi    # 0x35c9c3
xorl %ecx, %ecx
callq 0x10a770
movq %rax, %rbp
movq %rbx, %rdi
movq %rax, %rsi
callq 0x107cc0
leaq 0x40(%r14), %rdx
leaq 0x2c8922(%rip), %rdi    # 0x396cd3
leaq 0x28e64f(%rip), %rsi    # 0x35ca07
xorl %ecx, %ecx
callq 0x10a235
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x107cc0
leaq 0x41(%r14), %rdx
leaq 0x27960b(%rip), %rdi    # 0x3479e3
leaq 0x28e641(%rip), %rsi    # 0x35ca20
xorl %ecx, %ecx
callq 0x10a235
movq %rax, %r12
movq %rax, %rdi
callq 0x10a9d4
movq %rbx, %rdi
movq %r12, %rsi
callq 0x107cc0
leaq 0x43(%r14), %rdx
leaq 0x27f0af(%rip), %rdi    # 0x34d4b6
leaq 0x28e63e(%rip), %rsi    # 0x35ca4c
xorl %ecx, %ecx
callq 0x10a235
movq %rbx, %rdi
movq %rax, %rsi
callq 0x107cc0
addq $0x42, %r14
movq %r14, %rdi
callq 0x10a257
movq %rbx, %rdi
movq %rax, %rsi
callq 0x107cc0
movq %r13, %rdi
movq %rbp, %rsi
callq 0x10a9e4
movq %r15, %rdi
movq %rbp, %rsi
callq 0x10a9e4
movq %rbp, %rdi
movq 0x10(%rsp), %rsi
movq 0x8(%rsp), %rdx
callq 0x10aa54
movq %rbx, %rax
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq