static Seqpos *leftcontextofspecialchardist(unsigned int numofchars,
const Encodedsequence *encseq,
Readmode readmode)
{
GtUchar cc;
unsigned int idx;
Seqpos *specialchardist, totallength = getencseqtotallength(encseq);
specialchardist = gt_malloc(sizeof(*specialchardist) * numofchars);
for (idx = 0; idx<numofchars; idx++)
{
specialchardist[idx] = 0;
}
if (hasspecialranges(encseq))
{
Specialrangeiterator *sri;
Sequencerange range;
sri = newspecialrangeiterator(encseq,true);
if (ISDIRREVERSE(readmode))
{
Readmode thismode = (readmode == Reversemode) ? Forwardmode
: Complementmode;
while (nextspecialrangeiterator(&range,sri))
{
if (range.rightpos < totallength)
{
cc = getencodedchar(encseq,range.rightpos,thismode);
if (ISNOTSPECIAL(cc))
{
specialchardist[cc]++;
}
}
}
} else
{
while (nextspecialrangeiterator(&range,sri))
{
gt_assert(range.leftpos < totallength);
if (range.leftpos > 0)
{
cc = getencodedchar(encseq,range.leftpos-1,readmode);
if (ISNOTSPECIAL(cc))
{
specialchardist[cc]++;
}
}
}
}
freespecialrangeiterator(&sri);
}
if (getencseqlengthofspecialsuffix(encseq) == 0)
{
cc = getencodedchar(encseq,totallength-1,readmode);
gt_assert(ISNOTSPECIAL(cc));
specialchardist[cc]++;
}
return specialchardist;
}
int checkspecialrangesfast(const Encodedsequence *encseq)
{
GtArray *rangesforward, *rangesbackward;
bool haserr = false;
Specialrangeiterator *sri;
Sequencerange range;
if (!hasspecialranges(encseq))
{
return 0;
}
rangesforward = gt_array_new(sizeof (Sequencerange));
rangesbackward = gt_array_new(sizeof (Sequencerange));
sri = newspecialrangeiterator(encseq,true);
while (nextspecialrangeiterator(&range,sri))
{
gt_array_add(rangesforward,range);
}
freespecialrangeiterator(&sri);
sri = newspecialrangeiterator(encseq,false);
while (nextspecialrangeiterator(&range,sri))
{
gt_array_add(rangesbackward,range);
}
freespecialrangeiterator(&sri);
gt_array_reverse(rangesbackward);
if (!haserr)
{
if (array_compare(rangesforward,rangesbackward,
compareSequencerange) != 0)
{
exit(GT_EXIT_PROGRAMMING_ERROR);
}
}
gt_array_delete(rangesforward);
gt_array_delete(rangesbackward);
return haserr ? - 1 : 0;
}