static void mapToRefWithMapping(struct hapRegions *hr, struct cDnaAlign *hapAln, struct psl *mapping, struct psl **mappedHaps)
/* map an alignment on a haplotype chromosome using one mapping */
{
struct psl *m;
struct psl *mapped = pslTransMap(pslTransMapNoOpts, hapAln->psl, mapping);
while ((m = slPopHead(&mapped)) != NULL)
{
slAddHead(&mappedHaps, m);
if (hr->hapRefMappedFh != NULL)
pslTabOut(m, hr->hapRefMappedFh);
}
}
static struct psl *mapCDnaCDnaAln(struct hapRegions *hr, struct cDnaAlign *refAln, struct psl *mappedHap)
/* create cdna to cdna alignments from mappedHap and refAln, return
* NULL if can't be mapped */
{
struct psl *cDnaCDnaAln = NULL;
if (sameString(refAln->psl->tName, mappedHap->tName)
&& rangeIntersection(refAln->psl->tStart, refAln->psl->tEnd,
mappedHap->tStart, mappedHap->tEnd))
{
pslSwap(mappedHap, FALSE);
cDnaCDnaAln = pslTransMap(pslTransMapNoOpts, refAln->psl, mappedHap);
pslSwap(mappedHap, FALSE);
if ((hr->hapRefCDnaFh != NULL) && (cDnaCDnaAln != NULL))
cDnaAlignPslOut(cDnaCDnaAln, refAln->alnId, hr->hapRefCDnaFh);
}
return cDnaCDnaAln;
}
static void mapPslPair(struct psl *inPsl, struct mapAln *mapAln,
FILE* outPslFh, FILE *mapInfoFh, FILE *mappingPslFh)
/* map one pair of query and target PSL */
{
struct psl* mappedPsl;
if (inPsl->tSize != mapAln->psl->qSize)
errAbort("Error: inPsl %s tSize (%d) != mapping alignment %s qSize (%d) (perhaps you need to specify -swapMap?)\n",
inPsl->tName, inPsl->tSize, mapAln->psl->qName, mapAln->psl->qSize);
mappedPsl = pslTransMap(mapOpts, inPsl, mapAln->psl);
/* only output if blocks were actually mapped */
if (mappedPsl != NULL)
{
if (suffix != NULL)
addQNameSuffix(mappedPsl);
pslTabOut(mappedPsl, outPslFh);
if (mapInfoFh != NULL)
writeMapInfo(mapInfoFh, inPsl, mapAln, mappedPsl);
if (mappingPslFh != NULL)
pslTabOut(mapAln->psl, mappingPslFh);
}
pslFree(&mappedPsl);
}
