struct axt *netFillToAxt(struct cnFill *fill, struct dnaSeq *tChrom , int tSize,
struct hash *qChromHash, char *nibDir,
struct chain *chain, boolean swap)
/* Convert subset of chain as defined by fill to axt. swap query and target if swap is true*/
{
struct dnaSeq *qSeq;
boolean isRev = (chain->qStrand == '-');
struct chain *subChain, *chainToFree;
int qOffset;
struct axt *axtList = NULL , *axt;
struct nibInfo *nib = hashFindVal(qChromHash, fill->qName);
/* Get query sequence fragment. */
{
if (nib == NULL)
{
char path[512];
AllocVar(nib);
safef(path, sizeof(path), "%s/%s.nib", nibDir, fill->qName);
nib->fileName = cloneString(path);
nibOpenVerify(path, &nib->f, &nib->size);
hashAdd(qChromHash, fill->qName, nib);
}
qSeq = nibLoadPartMasked(NIB_MASK_MIXED, nib->fileName,
fill->qStart, fill->qSize);
if (isRev)
{
reverseComplement(qSeq->dna, qSeq->size);
qOffset = nib->size - (fill->qStart + fill->qSize);
}
else
qOffset = fill->qStart;
}
chainSubsetOnT(chain, fill->tStart, fill->tStart + fill->tSize,
&subChain, &chainToFree);
if (subChain != NULL)
{
axtList = chainToAxt(subChain, qSeq, qOffset, tChrom, fill->tStart, 100, BIGNUM);
if (swap)
{
for (axt = axtList ; axt != NULL ; axt = axt->next)
axtSwap(axt, tSize, nib->size);
}
}
chainFree(&chainToFree);
freeDnaSeq(&qSeq);
return axtList;
}
void axtSwapFile(char *source, char *targetSizes, char *querySizes, char *dest)
/* axtSwapFile - Swap source and query in an axt file. */
{
struct hash *tHash = loadIntHash(targetSizes);
struct hash *qHash = loadIntHash(querySizes);
struct lineFile *lf = lineFileOpen(source, TRUE);
FILE *f = mustOpen(dest, "w");
struct axt *axt;
while ((axt = axtRead(lf)) != NULL)
{
axtSwap(axt, hashIntVal(tHash, axt->tName), hashIntVal(qHash, axt->qName));
axtWrite(axt, f);
axtFree(&axt);
}
}
