void setBitsN(DNA *dna, int size, Bits *bits)
/* Set bits in bitmap where there are N's in DNA. */
{
int i;
for (i=0; i<size; ++i)
{
if (dna[i] == 'n' || dna[i] == 'N')
bitSetOne(bits, i);
}
}
void axtSetBits(struct axt *axt, int chromSize, Bits *aliBits, Bits *matchBits)
/* Set bits where there are alignments and matches. */
{
char q, t, *qSym = axt->qSym, *tSym = axt->tSym;
int i, symCount = axt->symCount;
int tPos = axt->tStart;
assert(axt->tStrand == '+');
for (i=0; i<symCount; ++i)
{
assert(tPos < chromSize);
q = qSym[i];
t = tSym[i];
if (q != '-' && t != '-')
{
bitSetOne(aliBits, tPos);
if (ntChars[(int)q] == ntChars[(int)t])
bitSetOne(matchBits, tPos);
}
if (t != '-')
++tPos;
}
}
Bits *maskFromUpperCaseSeq(bioSeq *seq)
/* Allocate a mask for sequence and fill it in based on
* sequence case. */
{
int size = seq->size, i;
char *poly = seq->dna;
Bits *b = bitAlloc(size);
for (i=0; i<size; ++i)
{
if (isupper(poly[i]))
bitSetOne(b, i);
}
return b;
}
static void rMarkUsed(struct cnFill *fillList, Bits *bits, int maxId)
/* Recursively mark bits that are used. */
{
struct cnFill *fill;
for (fill = fillList; fill != NULL; fill = fill->next)
{
if (fill->chainId != 0)
{
if (fill->chainId >= maxId)
errAbort("chainId %d, can only handle up to %d",
fill->chainId, maxId);
bitSetOne(bits, fill->chainId);
}
if (fill->children != NULL)
rMarkUsed(fill->children, bits, maxId);
}
}