void initstorematch(Storematchinfo *storematch,
const Encodedsequence *encseq)
{
unsigned long numofdbsequences = getencseqnumofdbsequences(encseq);
storematch->encseq = encseq;
INITBITTAB(storematch->hasmatch,numofdbsequences);
}
void mergertrie_check(Mergertrierep *trierep,unsigned int numberofleaves,
unsigned int maxleafnum,GtError *err)
{
gt_error_check(err);
if (trierep->root != NULL)
{
Bitsequence *leafused;
unsigned int numberofbitsset = 0;
INITBITTAB(leafused,maxleafnum+1);
checkmergertrie2(trierep,trierep->root,NULL,leafused,&numberofbitsset);
#ifndef NDEBUG
if (numberofbitsset != numberofleaves)
{
fprintf(stderr,"numberofbitsset = %u != %u = numberofleaves\n",
numberofbitsset,
numberofleaves);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
#endif
gt_free(leafused);
}
}
static int gt_tyr_occratio_arguments_check(int rest_argc,
void *tool_arguments,
GtError *err)
{
Tyr_occratio_options *arguments = tool_arguments;
bool haserr = false;
Optionargmodedesc outputmodedesctable[] =
{
{"unique","number of unique mers",TYROCC_OUTPUTUNIQUE},
{"nonunique","number of nonunique mers (single count)",
TYROCC_OUTPUTNONUNIQUE},
{"nonuniquemulti","number of nonunique mers (multi count)",
TYROCC_OUTPUTNONUNIQUEMULTI},
{"relative","fraction of unique/non-unique mers relative to all mers",
TYROCC_OUTPUTRELATIVE},
{"total","number of all mers",TYROCC_OUTPUTTOTAL}
};
if (rest_argc != 0)
{
gt_error_set(err,"superfluous arguments");
return -1;
}
if (gt_option_is_set(arguments->refoptionmersizes))
{
unsigned long *mersizes = NULL;
unsigned long idx,
numofmersizes = gt_str_array_size(arguments->mersizesstrings);
if (numofmersizes == 0)
{
gt_error_set(err,"missing argument to option -mersizes:");
haserr = true;
} else
{
mersizes = gt_malloc(sizeof(*mersizes) * numofmersizes);
for (idx=0; idx<numofmersizes; idx++)
{
long readnum;
if (sscanf(gt_str_array_get(arguments->mersizesstrings,idx),
"%ld",&readnum) != 1 || readnum <= 0)
{
gt_error_set(err,"invalid argument \"%s\" of option -mersizes: "
"must be a positive integer",
gt_str_array_get(arguments->mersizesstrings,idx));
haserr = true;
break;
}
mersizes[idx] = (unsigned long) readnum;
if (idx > 0 && mersizes[idx-1] >= mersizes[idx])
{
gt_error_set(err,"invalid argumnt %s to option -mersizes: "
"positive numbers must be strictly increasing",
gt_str_array_get(arguments->mersizesstrings,idx));
haserr = true;
break;
}
}
}
if (!haserr)
{
gt_assert(mersizes != NULL);
arguments->minmersize = mersizes[0];
arguments->maxmersize = mersizes[numofmersizes-1];
INITBITTAB(arguments->outputvector,arguments->maxmersize+1);
for (idx=0; idx<numofmersizes; idx++)
{
SETIBIT(arguments->outputvector,mersizes[idx]);
}
}
gt_free(mersizes);
} else
{
if (arguments->minmersize == 0)
{
gt_error_set(err,"if option -mersizes is not used, then option "
"-minmersize is mandatory");
haserr = true;
}
if (!haserr)
{
if (arguments->maxmersize == 0)
{
gt_error_set(err,"if option -mersizes is not used, then option "
"-maxmersize is mandatory");
haserr = true;
}
}
if (!haserr)
{
if (arguments->minmersize > arguments->maxmersize)
{
gt_error_set(err,"minimum mer size must not be larger than "
"maximum mer size");
haserr = true;
}
}
if (!haserr)
{
if (arguments->minmersize+arguments->stepmersize > arguments->maxmersize)
{
gt_error_set(err,"minimum mer size + step value must be smaller or "
"equal to maximum mersize");
haserr = true;
}
}
if (!haserr)
{
unsigned long outputval;
INITBITTAB(arguments->outputvector,arguments->maxmersize+1);
for (outputval = arguments->minmersize;
outputval <= arguments->maxmersize;
outputval += arguments->stepmersize)
{
SETIBIT(arguments->outputvector,outputval);
}
}
}
if (!haserr)
{
unsigned long idx;
for (idx=0; idx<gt_str_array_size(arguments->outputspec); idx++)
{
if (optionargaddbitmask(outputmodedesctable,
sizeof (outputmodedesctable)/
sizeof (outputmodedesctable[0]),
&arguments->outputmode,
"-output",
gt_str_array_get(arguments->outputspec,idx),
err) != 0)
{
haserr = true;
break;
}
}
}
if (!haserr)
{
if ((arguments->outputmode & TYROCC_OUTPUTRELATIVE) &&
!(arguments->outputmode &
(TYROCC_OUTPUTUNIQUE | TYROCC_OUTPUTNONUNIQUE |
TYROCC_OUTPUTNONUNIQUEMULTI)))
{
gt_error_set(err,"argument relative to option -output requires that one "
"of the arguments unique, nonunique, or nonuniquemulti "
"is used");
haserr = true;
}
}
return haserr ? - 1: 0;
}
