static GtCodetype qgram2codefillspecial(unsigned int numofchars,
unsigned int kmersize,
const GtEncseq *encseq,
GtReadmode readmode,
GtUword startpos,
GtUword totallength)
{
GtCodetype integercode;
GtUword pos;
bool foundspecial;
GtUchar cc;
if (startpos >= totallength)
{
integercode = (GtCodetype) (numofchars - 1);
foundspecial = true;
} else
{
/* for testing */
cc = gt_encseq_get_encoded_char(encseq,startpos,readmode);
if (ISSPECIAL(cc))
{
integercode = (GtCodetype) (numofchars - 1);
foundspecial = true;
} else
{
integercode = (GtCodetype) cc;
foundspecial = false;
}
}
for (pos = startpos + 1; pos < startpos + kmersize; pos++)
{
if (foundspecial)
{
ADDNEXTCHAR(integercode,numofchars-1,numofchars);
} else
{
if (pos >= totallength)
{
ADDNEXTCHAR(integercode,numofchars-1,numofchars);
foundspecial = true;
} else
{
/* for testing */
cc = gt_encseq_get_encoded_char(encseq,pos,readmode);
if (ISSPECIAL(cc))
{
ADDNEXTCHAR(integercode,numofchars-1,numofchars);
foundspecial = true;
} else
{
ADDNEXTCHAR(integercode,cc,numofchars);
}
}
}
}
return integercode;
}
static GtCodetype windowkmer2code(unsigned int numofchars,
unsigned int kmersize,
const GtUchar *cyclicwindow,
unsigned int firstindex)
{
unsigned int i;
GtCodetype integercode;
GtUchar cc;
bool foundspecial;
cc = cyclicwindow[firstindex];
if (ISSPECIAL(cc))
{
integercode = (GtCodetype) (numofchars-1);
foundspecial = true;
} else
{
integercode = (GtCodetype) cc;
foundspecial = false;
}
for (i=1U; i < kmersize; i++)
{
if (foundspecial)
{
ADDNEXTCHAR(integercode,numofchars-1,numofchars);
} else
{
cc = cyclicwindow[(firstindex+i) % kmersize];
if (ISSPECIAL(cc))
{
ADDNEXTCHAR(integercode,numofchars-1,numofchars);
foundspecial = true;
} else
{
ADDNEXTCHAR(integercode,cc,numofchars);
}
}
}
return integercode;
}
