static void cnvGenePred(struct hash *chromHash, struct genePred *gp, FILE *pslFh, FILE *cdsFh)
/* convert a genePred to a psl and CDS */
{
int chromSize = hashIntValDefault(chromHash, gp->chrom, 0);
if (chromSize == 0)
errAbort("Couldn't find chromosome/scaffold '%s' in chromInfo", gp->chrom);
int e = 0, qSize=0;
for (e = 0; e < gp->exonCount; ++e)
qSize+=(gp->exonEnds[e] - gp->exonStarts[e]);
struct psl *psl = pslNew(gp->name, qSize, 0, qSize,
gp->chrom, chromSize, gp->txStart, gp->txEnd,
gp->strand, gp->exonCount, 0);
psl->blockCount = gp->exonCount;
for (e = 0; e < gp->exonCount; ++e)
{
psl->blockSizes[e] = (gp->exonEnds[e] - gp->exonStarts[e]);
psl->qStarts[e] = e==0 ? 0 : psl->qStarts[e-1] + psl->blockSizes[e-1];
psl->tStarts[e] = gp->exonStarts[e];
}
psl->match = qSize;
psl->tNumInsert = psl->blockCount-1;
psl->tBaseInsert = (gp->txEnd - gp->txStart) - qSize;
pslTabOut(psl, pslFh);
pslFree(&psl);
if (gp->cdsStart < gp->cdsEnd)
cnvGenePredCds(gp, qSize, cdsFh);
}
static void cnvGenePred(struct hash *chromHash, struct genePred *gp, FILE *pslFh, FILE *cdsFh)
/* convert a genePred to a psl and CDS */
{
int chromSize = hashIntValDefault(chromHash, gp->chrom, 0);
if (chromSize == 0)
errAbort("Couldn't find chromosome/scaffold '%s' in chromInfo", gp->chrom);
int qSize = 0;
if (qSizes != NULL)
qSize = hashIntValDefault(qSizeHash, gp->name, 0);
struct psl *psl = genePredToPsl(gp, chromSize, qSize);
pslTabOut(psl, pslFh);
pslFree(&psl);
if (gp->cdsStart < gp->cdsEnd)
cnvGenePredCds(gp, qSize, cdsFh);
}
