// File: /workspace/github_c_makefile_star2_O0/genometools[P]genometools/src/tools/gt_condenseq_compress.c
// Function: gt_condenseq_compress_option_parser_new
static GtOptionParser*
gt_condenseq_compress_option_parser_new(void *tool_arguments)
{
  GtCondenseqCompressArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option,
           *option_fraction;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[options] INPUTENCSEQ",
                            "Compresses a GtEncseq to a UniqueEncseq.");

  /* -indexname */
  option = gt_option_new_string("indexname",
                                "path and basename of files to store",
                                arguments->indexname, NULL);
  gt_option_parser_add_option(op, option);

  /* -kmersize */
  option = gt_option_new_uint_min("kmersize",
                                  "kmer-size used for the seeds, default "
                                  "depends on alphabet size",
                                  &arguments->kmersize, GT_UNDEF_UINT, 2U);
  gt_option_parser_add_option(op, option);

  /* -windowsize */
  option = gt_option_new_uint("windowsize",
                              "Size of window in which to search for hit pairs "
                              "of kmers, has to be larger than kmersize" ,
                              &arguments->windowsize, GT_UNDEF_UINT);
  gt_option_parser_add_option(op, option);

  /* -initsize */
  option = gt_option_new_uword("initsize",
                               "length of initial unique database in bases, "
                               "should be larger than -alignlength",
                               &arguments->initsize, GT_UNDEF_UWORD);
  gt_option_parser_add_option(op, option);

  /* -alignlength */
  option = gt_option_new_uword("alignlength",
                               "required minimal length of an xdrop-alignment, "
                               "should be larger than -windowsize",
                               &arguments->minalignlength, GT_UNDEF_UWORD);
  gt_option_parser_add_option(op, option);

  /* -cutoff */
  option = gt_option_new_uword("cutoff",
                               "if a kmer is found more often than this value "
                               "it will be ignored for alignment searches. "
                               "Setting this to 0 will disable cutoffs, "
                               "leaving it undefined will use a cutoff based "
                               "on the mean number of occurrences of a k-word.",
                               &arguments->cutoff_value, GT_UNDEF_UWORD);
  gt_option_is_extended_option(option);
  gt_option_parser_add_option(op, option);

  /* -fraction */
  option_fraction = gt_option_new_uword("fraction",
                               "when cutoffs aren'd disabled and no specific "
                               "value is set the mean number of occurrences "
                               "of each kmer divided by -fraction will be used "
                               "as cutoff",
                               &arguments->fraction, (GtUword) 2);
  gt_option_is_extended_option(option_fraction);
  gt_option_exclude(option, option_fraction);
  gt_option_parser_add_option(op, option_fraction);

  /* -disable_prune */
  option = gt_option_new_bool("disable_prune",
                              "when cutoffs and this option are set, "
                              "the database will still save every kmer, even "
                              "though only cutoff many kmers will be used.",
                              &arguments->prune, false);
  gt_option_is_extended_option(option);
  gt_option_parser_add_option(op, option);

  /* -mat */
  option = gt_option_new_int("mat",
                             "matchscore for extension-alignment, "
                             "requirements: mat > mis, mat > 2ins, mat > 2del",
                             &arguments->scores.mat, 2);
  gt_option_is_extended_option(option);
  gt_option_parser_add_option(op, option);

  /* -mis */
  option = gt_option_new_int("mis",
                             "mismatchscore for extension-alignment, ",
                             &arguments->scores.mis, -1);
  gt_option_is_extended_option(option);
  gt_option_parser_add_option(op, option);

  /* -ins */
  option = gt_option_new_int("ins",
                             "insertionscore for extension-alignment",
                             &arguments->scores.ins, -2);
  gt_option_is_extended_option(option);
  gt_option_parser_add_option(op, option);

  /* -del */
  option = gt_option_new_int("del",
                             "deletionscore for extension-alignment",
                             &arguments->scores.del, -2);
  gt_option_is_extended_option(option);
  gt_option_parser_add_option(op, option);

  /* -xdrop */
  option = gt_option_new_word("xdrop",
                              "xdrop score for extension-alignment",
                              &arguments->xdrop, (GtWord) 3);
  gt_option_is_extended_option(option);
  gt_option_parser_add_option(op, option);

  /* -brute_force */
  option = gt_option_new_bool("brute_force", "disable filtering of seeds. "
                              "Incompatible with -diagonals yes "
                              "or -full_diags yes. For benchmarking use.",
                              &arguments->brute, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -diagonals */
  option = gt_option_new_bool("diagonals", "use sparse diagonals. "
                              "Incompatible with -brute_force yes. "
                              "Disabling both diagonals will result in simple "
                              "filtering of seed positions.",
                              &arguments->diags, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -full_diags */
  option = gt_option_new_bool("full_diags", "use full (time efficient "
                              "space inefficient) diagonals. "
                              "Incompatible with -brute_force yes. "
                              "Disabling both diagonals will result in simple "
                              "filtering of seed positions.",
                              &arguments->full_diags, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -clean_percent */
  option = gt_option_new_uint("diags_clean",
                              "Percentage of sparse diagonals that is allowed "
                              "to be marked as deletable. Sensible default is "
                              "set." ,
                              &arguments->clean_percent, GT_UNDEF_UINT);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -verbose */
  option = gt_option_new_bool("verbose", "enable verbose output",
                              &arguments->verbose, false);
  gt_option_parser_add_option(op, option);

  /* -kdb*/
  option = gt_option_new_bool("kdb", "prints out the kmer database (frequency "
                              "of each kmer), if -verbose each startposition "
                              "will be shown instead",
                              &arguments->kdb, false);
  gt_option_parser_add_option(op, option);

  return op;
}

// Assembly:
subq $0x28, %rsp
movq %rdi, 0x20(%rsp)
movq 0x20(%rsp), %rax
movq %rax, 0x18(%rsp)
cmpq $0x0, 0x18(%rsp)
jne 0x25d03
movq 0x6162ce(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x4f0337(%rip), %rsi    # 0x516013
leaq 0x554e7c(%rip), %rdx    # 0x57ab5f
leaq 0x4f3910(%rip), %rcx    # 0x5195fa
leaq 0x4f38e7(%rip), %r8     # 0x5195d8
movl $0x53, %r9d
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x25d05
leaq 0x4f3916(%rip), %rdi    # 0x519622
leaq 0x4f3925(%rip), %rsi    # 0x519638
callq 0xf1420
movq %rax, 0x10(%rsp)
movq 0x18(%rsp), %rax
movq 0x8(%rax), %rdx
leaq 0x5110b2(%rip), %rdi    # 0x536ddf
leaq 0x4f392d(%rip), %rsi    # 0x519661
xorl %eax, %eax
movl %eax, %ecx
callq 0xf69f0
movq %rax, 0x8(%rsp)
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x48, %rdx
leaq 0x591960(%rip), %rdi    # 0x5b76c1
leaq 0x4f391d(%rip), %rsi    # 0x519685
movl $0xffffffff, %ecx       # imm = 0xFFFFFFFF
movl $0x2, %r8d
callq 0xf6510
movq %rax, 0x8(%rsp)
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x4c, %rdx
leaq 0x4f3a1f(%rip), %rdi    # 0x5197bb
leaq 0x4f3921(%rip), %rsi    # 0x5196c4
movl $0xffffffff, %ecx       # imm = 0xFFFFFFFF
callq 0xf64b0
movq %rax, 0x8(%rsp)
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x38, %rdx
leaq 0x4f394c(%rip), %rdi    # 0x51971d
leaq 0x4f394e(%rip), %rsi    # 0x519726
movq $-0x1, %rcx
callq 0xf5fe0
movq %rax, 0x8(%rsp)
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x20, %rdx
leaq 0x4f3961(%rip), %rdi    # 0x519769
leaq 0x4f3966(%rip), %rsi    # 0x519775
movq $-0x1, %rcx
callq 0xf5fe0
movq %rax, 0x8(%rsp)
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x28, %rdx
leaq 0x4f3aef(%rip), %rdi    # 0x51992e
leaq 0x4f3980(%rip), %rsi    # 0x5197c6
movq $-0x1, %rcx
callq 0xf5fe0
movq %rax, 0x8(%rsp)
movq 0x8(%rsp), %rdi
callq 0xf6ff0
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x30, %rdx
leaq 0x525d9a(%rip), %rdi    # 0x54bc1a
leaq 0x4f3a1c(%rip), %rsi    # 0x5198a3
movl $0x2, %ecx
callq 0xf5fe0
movq %rax, (%rsp)
movq (%rsp), %rdi
callq 0xf6ff0
movq 0x8(%rsp), %rdi
movq (%rsp), %rsi
callq 0xf7320
movq 0x10(%rsp), %rdi
movq (%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x59, %rdx
leaq 0x531bc3(%rip), %rdi    # 0x557a8d
leaq 0x4f3a64(%rip), %rsi    # 0x519935
xorl %ecx, %ecx
callq 0xf5f20
movq %rax, 0x8(%rsp)
movq 0x8(%rsp), %rdi
callq 0xf6ff0
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x10, %rdx
leaq 0x506dfe(%rip), %rdi    # 0x52cd04
leaq 0x4f3aa8(%rip), %rsi    # 0x5199b5
movl $0x2, %ecx
callq 0xf6310
movq %rax, 0x8(%rsp)
movq 0x8(%rsp), %rdi
callq 0xf6ff0
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x10, %rdx
addq $0x4, %rdx
leaq 0x56c04b(%rip), %rdi    # 0x591f94
leaq 0x4f3ab9(%rip), %rsi    # 0x519a09
movl $0xffffffff, %ecx       # imm = 0xFFFFFFFF
callq 0xf6310
movq %rax, 0x8(%rsp)
movq 0x8(%rsp), %rdi
callq 0xf6ff0
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x10, %rdx
addq $0x8, %rdx
leaq 0x54b6aa(%rip), %rdi    # 0x571636
leaq 0x5089ac(%rip), %rsi    # 0x52e93f
movl $0xfffffffe, %ecx       # imm = 0xFFFFFFFE
callq 0xf6310
movq %rax, 0x8(%rsp)
movq 0x8(%rsp), %rdi
callq 0xf6ff0
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x10, %rdx
addq $0xc, %rdx
leaq 0x56a2e6(%rip), %rdi    # 0x5902b5
leaq 0x508998(%rip), %rsi    # 0x52e96e
movl $0xfffffffe, %ecx       # imm = 0xFFFFFFFE
callq 0xf6310
movq %rax, 0x8(%rsp)
movq 0x8(%rsp), %rdi
callq 0xf6ff0
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x40, %rdx
leaq 0x526093(%rip), %rdi    # 0x54c0a1
leaq 0x4f3a1c(%rip), %rsi    # 0x519a31
movl $0x3, %ecx
callq 0xf6650
movq %rax, 0x8(%rsp)
movq 0x8(%rsp), %rdi
callq 0xf6ff0
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x56, %rdx
leaq 0x542174(%rip), %rdi    # 0x5681c1
leaq 0x4f3a01(%rip), %rsi    # 0x519a55
xorl %ecx, %ecx
callq 0xf5f20
movq %rax, 0x8(%rsp)
movq 0x8(%rsp), %rdi
callq 0xf7040
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x54, %rdx
leaq 0x525c27(%rip), %rdi    # 0x54bcb0
leaq 0x4f3a2c(%rip), %rsi    # 0x519abc
xorl %ecx, %ecx
callq 0xf5f20
movq %rax, 0x8(%rsp)
movq 0x8(%rsp), %rdi
callq 0xf7040
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x55, %rdx
leaq 0x4f3a7d(%rip), %rdi    # 0x519b42
leaq 0x4f3a81(%rip), %rsi    # 0x519b4d
xorl %ecx, %ecx
callq 0xf5f20
movq %rax, 0x8(%rsp)
movq 0x8(%rsp), %rdi
callq 0xf7040
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x50, %rdx
leaq 0x5260cf(%rip), %rdi    # 0x54c1d0
leaq 0x4f3aec(%rip), %rsi    # 0x519bf4
movl $0xffffffff, %ecx       # imm = 0xFFFFFFFF
callq 0xf64b0
movq %rax, 0x8(%rsp)
movq 0x8(%rsp), %rdi
callq 0xf7040
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x57, %rdx
leaq 0x4f1fe7(%rip), %rdi    # 0x518127
leaq 0x4f3b10(%rip), %rsi    # 0x519c57
xorl %ecx, %ecx
callq 0xf5f20
movq %rax, 0x8(%rsp)
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x58, %rdx
leaq 0x4f3afb(%rip), %rdi    # 0x519c6d
leaq 0x4f3af8(%rip), %rsi    # 0x519c71
xorl %ecx, %ecx
callq 0xf5f20
movq %rax, 0x8(%rsp)
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x10(%rsp), %rax
addq $0x28, %rsp
retq
nop