static struct mapAln *chainToPsl(struct chain *ch)
/* convert a chain to a psl, ignoring match counts, etc */
{
struct psl *psl;
struct cBlock *cBlk;
int iBlk;
int qStart = ch->qStart, qEnd = ch->qEnd;
char strand[2];
strand[0] = ch->qStrand;
strand[1] = '\0';
if (ch->qStrand == '-')
reverseIntRange(&qStart, &qEnd, ch->qSize);
psl = pslNew(ch->qName, ch->qSize, qStart, qEnd,
ch->tName, ch->tSize, ch->tStart, ch->tEnd,
strand, slCount(ch->blockList), 0);
for (cBlk = ch->blockList, iBlk = 0; cBlk != NULL; cBlk = cBlk->next, iBlk++)
{
psl->blockSizes[iBlk] = (cBlk->tEnd - cBlk->tStart);
psl->qStarts[iBlk] = cBlk->qStart;
psl->tStarts[iBlk] = cBlk->tStart;
psl->match += psl->blockSizes[iBlk];
}
psl->blockCount = iBlk;
if (swapMap)
pslSwap(psl, FALSE);
return mapAlnNew(psl, ch->id);
}
static void pslMap(char* inPslFile, char *mapFile, char *outPslFile)
/* project inPsl query through mapFile query to mapFile target */
{
struct chromBins *mapAlns;
struct psl* inPsl;
struct lineFile* inPslLf = pslFileOpen(inPslFile);
FILE *outPslFh, *mapInfoFh = NULL, *mappingPslFh = NULL;
if (chainMapFile)
mapAlns = loadMapChains(mapFile);
else
mapAlns = loadMapPsls(mapFile);
outPslFh = mustOpen(outPslFile, "w");
if (mapInfoFile != NULL)
{
mapInfoFh = mustOpen(mapInfoFile, "w");
fputs(mapInfoHdr, mapInfoFh);
}
if (mappingPslFile != NULL)
mappingPslFh = mustOpen(mappingPslFile, "w");
while ((inPsl = pslNext(inPslLf)) != NULL)
{
if (swapIn)
pslSwap(inPsl, FALSE);
mapQueryPsl(inPsl, mapAlns, outPslFh, mapInfoFh, mappingPslFh);
pslFree(&inPsl);
}
carefulClose(&mappingPslFh);
carefulClose(&mapInfoFh);
carefulClose(&outPslFh);
lineFileClose(&inPslLf);
}
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 struct chromBins* loadMapPsls(char *pslFile)
/* read a psl file and chromBins by query, linking multiple PSLs for the
* same query.*/
{
struct dyString* idBuf = NULL;
struct chromBins* mapAlns = chromBinsNew((chromBinsFreeFunc*)pslFree);
int id = 0;
struct psl* psl;
struct lineFile *pslLf = pslFileOpen(pslFile);
while ((psl = pslNext(pslLf)) != NULL)
{
if (swapMap)
pslSwap(psl, FALSE);
chromBinsAdd(mapAlns, getMappingId(psl->qName, &idBuf), psl->qStart, psl->qEnd,
mapAlnNew(psl, id));
id++;
}
lineFileClose(&pslLf);
dyStringFree(&idBuf);
return mapAlns;
}
