static int gt_index_options_check_set_create_opts(void *oip, GtError *err)
{
int had_err = 0;
GtIndexOptions *oi = (GtIndexOptions*) oip;
gt_assert(oi != NULL && oi->type != GT_INDEX_OPTIONS_UNDEFINED);
gt_error_check(err);
/* readmode needs to be initialized to fwd */
oi->readmode = (GtReadmode) 0;
if (!had_err)
{
if (gt_option_is_set(oi->optionalgbounds))
{
if (gt_parse_algbounds(&oi->sfxstrategy,oi->algbounds,err) != 0)
{
had_err = -1;
}
} else
{
oi->sfxstrategy.maxinsertionsort = MAXINSERTIONSORTDEFAULT;
oi->sfxstrategy.maxbltriesort = MAXBLTRIESORTDEFAULT;
oi->sfxstrategy.maxcountingsort = MAXCOUNTINGSORTDEFAULT;
}
}
if (!had_err && oi->sfxstrategy.kmerswithencseqreader &&
oi->sfxstrategy.spmopt_minlength > 0)
{
gt_error_set(err,"options -spmopt and -kmerswithencseqreader are "
"not compatible");
had_err = -1;
}
if (!had_err
&& oi->optionmemlimit != NULL
&& gt_option_is_set(oi->optionmemlimit))
{
had_err = gt_option_parse_spacespec(&oi->maximumspace,"memlimit",
oi->memlimit,err);
}
if (!had_err)
{
if (oi->sfxstrategy.maxinsertionsort > oi->sfxstrategy.maxbltriesort)
{
gt_error_set(err,"first argument of option -algbds must not be larger "
"than second argument");
had_err = -1;
} else
{
if (oi->sfxstrategy.maxbltriesort > oi->sfxstrategy.maxcountingsort)
{
gt_error_set(err,"second argument of option -algbds must not be larger "
"than third argument");
had_err = -1;
}
}
}
return had_err;
}
static int gt_readjoiner_assembly_arguments_check(GT_UNUSED int rest_argc,
void *tool_arguments, GtError *err)
{
GtReadjoinerAssemblyArguments *arguments = tool_arguments;
int had_err = 0;
gt_error_check(err);
if (had_err == 0 && gt_option_is_set(arguments->refoptionbuffersize))
if (gt_option_parse_spacespec(&arguments->buffersize,
"buffersize", arguments->buffersizearg, err) != 0)
had_err = -1;
return had_err;
}
static int gt_seed_extend_arguments_check(int rest_argc, void *tool_arguments,
GtError *err)
{
GtSeedExtendArguments *arguments = tool_arguments;
int had_err = 0;
gt_error_check(err);
gt_assert(arguments != NULL);
/* -t parameter as alias for maxfreq := t - 1 */
if (arguments->dbs_suppress < GT_UWORD_MAX) {
arguments->dbs_maxfreq = arguments->dbs_suppress - 1;
}
/* no alignment output */
if (!gt_option_is_set(arguments->se_option_withali)) {
arguments->se_alignmentwidth = 0;
}
/* parse memlimit argument */
arguments->dbs_memlimit = GT_UWORD_MAX;
if (strcmp(gt_str_get(arguments->dbs_memlimit_str), "") != 0) {
had_err = gt_option_parse_spacespec(&arguments->dbs_memlimit,
"memlimit",
arguments->dbs_memlimit_str,
err);
if (!had_err && arguments->dbs_memlimit == 0) {
gt_error_set(err,
"argument to option \"-memlimit\" must be at least 1MB");
had_err = -1;
}
}
/* minimum maxfreq value for 1 input file */
if (!had_err && arguments->dbs_maxfreq == 1 &&
strcmp(gt_str_get(arguments->dbs_queryname), "") == 0) {
if (arguments->dbs_suppress == GT_UWORD_MAX) {
gt_error_set(err, "argument to option \"-maxfreq\" must be >= 2 to "
"find matching k-mers");
} else {
gt_error_set(err, "argument to option \"-t\" must be >= 3 to find "
"matching k-mers");
}
had_err = -1;
}
/* no extra arguments */
if (!had_err && rest_argc > 0) {
gt_error_set(err, "too many arguments (-help shows correct usage)");
had_err = -1;
}
return had_err;
}
static int gt_encseq2spm_arguments_check(int rest_argc,
void *tool_arguments,
GtError *err)
{
GtEncseq2spmArguments *arguments = tool_arguments;
bool haserr = false;
gt_error_check(err);
if (rest_argc != 0)
{
gt_error_set(err,"unnecessary arguments");
haserr = true;
}
if (!haserr && gt_str_length(arguments->spmspec) > 0)
{
const char *spmspecstring = gt_str_get(arguments->spmspec);
if (strcmp(spmspecstring,"show") == 0)
{
arguments->outputspms = true;
} else
{
if (strcmp(spmspecstring,"count") == 0)
{
arguments->countspms = true;
} else
{
gt_error_set(err,"illegal argument \"%s\" to option -spm",
spmspecstring);
haserr = true;
}
}
}
if (!haserr && gt_option_is_set(arguments->refoptionmemlimit))
{
if (gt_option_parse_spacespec(&arguments->maximumspace,
"memlimit",
arguments->memlimitarg,
err) != 0)
{
haserr = true;
}
if (!haserr && !gt_ma_bookkeeping_enabled()) {
gt_error_set(err, "option '-memlimit' requires "
"GT_MEM_BOOKKEEPING=on");
haserr = true;
}
}
if (!haserr && gt_option_is_set(arguments->refoptionphase2extra))
{
if (gt_option_parse_spacespec(&arguments->phase2extra,
"phase2extra",
arguments->phase2extraarg,
err) != 0)
{
haserr = true;
}
}
#ifdef GT_THREADS_ENABLED
if (!haserr) {
if (gt_jobs > 1 && gt_ma_bookkeeping_enabled()) {
gt_error_set(err, "gt option '-j' and GT_MEM_BOOKKEEPING=on "
"are incompatible");
haserr = true;
}
}
#endif
return haserr ? -1 : 0;
}
