// File: /workspace/github_c_makefile_star2_O2/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:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x1fd60
movq %rdi, %rbx
leaq 0x2c8bcb(%rip), %rdi    # 0x2e85b2
leaq 0x2c8bda(%rip), %rsi    # 0x2e85c8
callq 0x97df5
movq %rax, %r14
movq 0x8(%rbx), %rdx
leaq 0x2e605c(%rip), %rdi    # 0x305a5d
leaq 0x2c8be9(%rip), %rsi    # 0x2e85f1
xorl %ecx, %ecx
callq 0x9ad12
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x48(%rbx), %rdx
leaq 0x362a2c(%rip), %rdi    # 0x382451
leaq 0x2c8be9(%rip), %rsi    # 0x2e8615
pushq $-0x1
popq %rbp
pushq $0x2
popq %r15
movl %ebp, %ecx
movl %r15d, %r8d
callq 0x9abef
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x4c(%rbx), %rdx
leaq 0x2c8cf8(%rip), %rdi    # 0x2e874b
leaq 0x2c8bfa(%rip), %rsi    # 0x2e8654
movl %ebp, %ecx
callq 0x9abcd
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x38(%rbx), %rdx
leaq 0x2c8c36(%rip), %rdi    # 0x2e86ad
leaq 0x2c8c38(%rip), %rsi    # 0x2e86b6
pushq $-0x1
popq %r12
movq %r12, %rcx
callq 0x9a9e6
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x20(%rbx), %rdx
leaq 0x2c8c59(%rip), %rdi    # 0x2e86f9
leaq 0x2c8c5e(%rip), %rsi    # 0x2e8705
movq %r12, %rcx
callq 0x9a9e6
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x28(%rbx), %rdx
leaq 0x2c8df9(%rip), %rdi    # 0x2e88be
leaq 0x2c8c8a(%rip), %rsi    # 0x2e8756
movq %r12, %rcx
callq 0x9a9e6
movq %rax, %r12
movq %rax, %rdi
callq 0x9b0c7
movq %r14, %rdi
movq %r12, %rsi
callq 0x97f31
leaq 0x30(%rbx), %rdx
leaq 0x2fa10b(%rip), %rdi    # 0x319c00
leaq 0x2c8d37(%rip), %rsi    # 0x2e8833
pushq $0x2
popq %rcx
callq 0x9a9e6
movq %rax, %r13
movq %rax, %rdi
callq 0x9b0c7
movq %r12, %rdi
movq %r13, %rsi
callq 0x9b38d
movq %r14, %rdi
movq %r13, %rsi
callq 0x97f31
leaq 0x59(%rbx), %rdx
leaq 0x305c15(%rip), %rdi    # 0x325745
leaq 0x2c8d8e(%rip), %rsi    # 0x2e88c5
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r12
movq %rax, %rdi
callq 0x9b0c7
movq %r14, %rdi
movq %r12, %rsi
callq 0x97f31
leaq 0x10(%rbx), %rdx
leaq 0x2dbfae(%rip), %rdi    # 0x2fbb0d
leaq 0x2c8ddf(%rip), %rsi    # 0x2e8945
movl %r15d, %ecx
callq 0x9ab66
movq %rax, %r15
movq %rax, %rdi
callq 0x9b0c7
movq %r14, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x14(%rbx), %rdx
leaq 0x33f6c5(%rip), %rdi    # 0x35f254
leaq 0x2c8e03(%rip), %rsi    # 0x2e8999
movl %ebp, %ecx
callq 0x9ab66
movq %rax, %r15
movq %rax, %rdi
callq 0x9b0c7
movq %r14, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x18(%rbx), %rdx
leaq 0x31f2e8(%rip), %rdi    # 0x33eea6
leaq 0x2ddb72(%rip), %rsi    # 0x2fd737
pushq $-0x2
popq %r15
movl %r15d, %ecx
callq 0x9ab66
movq %rax, %r12
movq %rax, %rdi
callq 0x9b0c7
movq %r14, %rdi
movq %r12, %rsi
callq 0x97f31
leaq 0x1c(%rbx), %rdx
leaq 0x33d975(%rip), %rdi    # 0x35d567
leaq 0x2ddb6d(%rip), %rsi    # 0x2fd766
movl %r15d, %ecx
callq 0x9ab66
movq %rax, %r15
movq %rax, %rdi
callq 0x9b0c7
movq %r14, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x40(%rbx), %rdx
leaq 0x2fa465(%rip), %rdi    # 0x31a087
leaq 0x2c8d98(%rip), %rsi    # 0x2e89c1
pushq $0x3
popq %rcx
callq 0x9ac34
movq %rax, %r15
movq %rax, %rdi
callq 0x9b0c7
movq %r14, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x56(%rbx), %rdx
leaq 0x315f5b(%rip), %rdi    # 0x335bad
leaq 0x2c8d8c(%rip), %rsi    # 0x2e89e5
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r15
movq %rax, %rdi
callq 0x9b10a
movq %r14, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x54(%rbx), %rdx
leaq 0x2fa015(%rip), %rdi    # 0x319c96
leaq 0x2c8dc4(%rip), %rsi    # 0x2e8a4c
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r15
movq %rax, %rdi
callq 0x9b10a
movq %r14, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x55(%rbx), %rdx
leaq 0x2c8e22(%rip), %rdi    # 0x2e8ad2
leaq 0x2c8e26(%rip), %rsi    # 0x2e8add
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r15
movq %rax, %rdi
callq 0x9b10a
movq %r14, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x50(%rbx), %rdx
leaq 0x2fa4d7(%rip), %rdi    # 0x31a1b6
leaq 0x2c8e9e(%rip), %rsi    # 0x2e8b84
movl %ebp, %ecx
callq 0x9abcd
movq %rax, %r15
movq %rax, %rdi
callq 0x9b10a
movq %r14, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x57(%rbx), %rdx
leaq 0x2c73df(%rip), %rdi    # 0x2e70ed
leaq 0x2c8ed2(%rip), %rsi    # 0x2e8be7
xorl %ecx, %ecx
callq 0x9a997
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
addq $0x58, %rbx
leaq 0x2c8ecb(%rip), %rdi    # 0x2e8bfd
leaq 0x2c8ec8(%rip), %rsi    # 0x2e8c01
movq %rbx, %rdx
xorl %ecx, %ecx
callq 0x9a997
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x418201(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2c52a2(%rip), %rsi    # 0x2e5013
leaq 0x3288db(%rip), %rdx    # 0x348653
leaq 0x2c880b(%rip), %rcx    # 0x2e858a
leaq 0x2c87e2(%rip), %r8     # 0x2e8568
pushq $0x53
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390