static GtOptionParser *gt_tyr_search_option_parser_new(void *tool_arguments)
{
GtOptionParser *op;
GtOption *option, *optiontyr, *optionqueries;
Tyr_search_options *arguments = tool_arguments;
op = gt_option_parser_new("[options] -tyr tallymer-index -q queryfile0 "
"[queryfile1..] [options]",
"Search a set of k-mers in an index constructed "
"by \"gt tyr mkindex\".");
gt_option_parser_set_mailaddress(op,"<*****@*****.**>");
optiontyr = gt_option_new_string("tyr","specify tallymer-index",
arguments->str_inputindex,
NULL);
gt_option_is_mandatory(optiontyr);
gt_option_parser_add_option(op, optiontyr);
optionqueries = gt_option_new_filenamearray("q","specify query file names",
arguments->queryfilenames);
gt_option_is_mandatory(optionqueries);
gt_option_parser_add_option(op, optionqueries);
option = gt_option_new_string("strand",
"specify the strand to be searched: "
"use f (for forward strand) or "
"p (for reverse complemented strand) or "
"fp (for both); default is f",
arguments->strandspec,
"f");
gt_option_parser_add_option(op, option);
option = gt_option_new_stringarray("output",
"specify output flags "
"(qseqnum, qpos, counts, sequence)",
arguments->showmodespec);
gt_option_parser_add_option(op, option);
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);
option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, option);
return op;
}
static GtOptionParser
*gt_cge_spacedseed_option_parser_new(void *tool_arguments)
{
GtOptionParser *op;
GtOption *option,
*optionesaindex,
*optionpckindex;
Cge_spacedseed_options *arguments = tool_arguments;
op = gt_option_parser_new("[options]",
"Match spaced seeds.");
gt_option_parser_set_mailaddress(op,"<*****@*****.**>");
optionesaindex = gt_option_new_string("esa",
"Specify index (enhanced suffix array)",
arguments->str_inputindex, NULL);
gt_option_parser_add_option(op, optionesaindex);
arguments->refoptionesaindex = gt_option_ref(optionesaindex);
optionpckindex = gt_option_new_string("pck",
"Specify index (packed index)",
arguments->str_inputindex, NULL);
gt_option_parser_add_option(op, optionpckindex);
arguments->refoptionpckindex = gt_option_ref(optionpckindex);
gt_option_exclude(optionesaindex,optionpckindex);
gt_option_is_mandatory_either(optionesaindex,optionpckindex);
option = gt_option_new_filenamearray("q",
"Specify files containing the "
"query sequences",
arguments->queryfilenames);
gt_option_parser_add_option(op, option);
gt_option_is_mandatory(option);
option = gt_option_new_bool("cmp","compare results of offline and online "
"searches",&arguments->docompare,false);
gt_option_parser_add_option(op, option);
gt_option_is_development_option(option);
option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, option);
return op;
}
static GtOptionParser *gt_idxlocali_option_parser_new (void *tool_arguments)
{
IdxlocaliOptions *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option, *optionesaindex, *optionpckindex, *optiononline, *optioncmp;
gt_assert (arguments != NULL);
arguments->indexname = gt_str_new ();
arguments->queryfiles = gt_str_array_new ();
op = gt_option_parser_new
("[options] -q query-file-names [-esa|-pck] indexname",
"Find all local alignments using suffix tree.");
gt_option_parser_set_mailaddress (op, "<*****@*****.**>");
option = gt_option_new_filenamearray ("q","Specify files containing the "
"query sequences",
arguments->queryfiles);
gt_option_parser_add_option (op, option);
option = gt_option_new_long ("match",
"Specify match score",
&arguments->matchscore, 1L);
gt_option_parser_add_option (op, option);
option = gt_option_new_long ("mismatch",
"Specify mismatch score",
&arguments->mismatchscore, -3L);
gt_option_parser_add_option (op, option);
option = gt_option_new_long ("gapstart",
"Specify gap start score",
&arguments->gapstart, -5L);
gt_option_parser_add_option (op, option);
option = gt_option_new_long ("gapextend",
"Specify gap extension score",
&arguments->gapextend, -2L);
gt_option_parser_add_option (op, option);
option = gt_option_new_ulong_min ("th",
"Specify the threshold",
&arguments->threshold, 0, 1UL);
gt_option_parser_add_option (op, option);
gt_option_is_mandatory (option);
optionesaindex = gt_option_new_string ("esa",
"Specify index "
"(enhanced suffix array)",
arguments->indexname, NULL);
gt_option_parser_add_option (op, optionesaindex);
arguments->refoptionesaindex = gt_option_ref (optionesaindex);
optionpckindex = gt_option_new_string ("pck",
"Specify index (packed index)",
arguments->indexname, NULL);
gt_option_parser_add_option (op, optionpckindex);
arguments->refoptionpckindex = gt_option_ref (optionpckindex);
gt_option_exclude (optionesaindex, optionpckindex);
gt_option_is_mandatory_either (optionesaindex, optionpckindex);
optiononline = gt_option_new_bool("online","Perform online searches",
&arguments->doonline, false);
gt_option_parser_add_option(op, optiononline);
gt_option_is_development_option(optiononline);
optioncmp = gt_option_new_bool("cmp","Compare results of offline and online "
"searches",
&arguments->docompare, false);
gt_option_parser_add_option(op,optioncmp);
gt_option_exclude(optiononline,optioncmp);
option = gt_option_new_bool("s",
"Show alignments",
&arguments->showalignment, false);
gt_option_parser_add_option (op, option);
option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, option);
return op;
}
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_mailaddress(op,"<*****@*****.**>");
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_ulong("mersize",
"Specify the mer size.",
&arguments->mersize,
20UL);
gt_option_parser_add_option(op, option);
optionminocc
= gt_option_new_ulong("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_ulong("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;
}
static GtOptionParser *gt_tyr_occratio_option_parser_new(void *tool_arguments)
{
GtOptionParser *op;
GtOption *optionmersizes, *optionesa, *optionminmersize, *optionmaxmersize,
*optionstep, *optionoutput, *option;
Tyr_occratio_options *arguments = tool_arguments;
op = gt_option_parser_new("[options] -esa suffixerator-index [options]",
"Compute occurrence ratio for a set of sequences "
"represented by an enhanced suffix array.");
gt_option_parser_set_mailaddress(op,"<*****@*****.**>");
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);
optionminmersize
= gt_option_new_ulong_min("minmersize",
"specify minimum mer size for which "
"to compute the occurrence distribution",
&arguments->minmersize,0,1UL);
gt_option_parser_add_option(op, optionminmersize);
optionmaxmersize
= gt_option_new_ulong_min("maxmersize",
"specify maximum mer size for which "
"to compute the occurrence distribution",
&arguments->maxmersize,0,1UL);
gt_option_parser_add_option(op, optionmaxmersize);
optionstep
= gt_option_new_ulong_min("step",
"specify step size when specifying mer sizes",
&arguments->stepmersize,1UL,1UL);
gt_option_parser_add_option(op, optionstep);
optionmersizes = gt_option_new_stringarray(
"mersizes",
"specify mer sizes as non-empty sequence of "
"non decreasing positive integers",
arguments->mersizesstrings);
arguments->refoptionmersizes = gt_option_ref(optionmersizes);
gt_option_parser_add_option(op, optionmersizes);
optionoutput = gt_option_new_stringarray(
"output",
"use combination of the following keywords: "
"unique nonunique nonuniquemulti relative total "
"to specify kind of output",
arguments->outputspec);
gt_option_parser_add_option(op, optionoutput);
option = gt_option_new_bool("scan",
"read suffixerator-index sequentially "
"instead of mapping it to memory",
&arguments->scanfile,
false);
gt_option_parser_add_option(op, option);
option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, option);
gt_option_exclude(optionmersizes,optionminmersize);
gt_option_exclude(optionmersizes,optionmaxmersize);
gt_option_exclude(optionmersizes,optionstep);
return op;
}
