struct orgGenes *orgGenesNew(char *srcDb, char *genePredFile)
/* construct a new orgGenes object from the specified file */
{
struct orgGenes *genes;
AllocVar(genes);
genes->srcDb = cloneString(srcDb);
genes->bins = chromBinsNew(NULL);
genes->memPool = lmInit(1024*1024);
loadGenes(genes, genePredFile);
return genes;
}
static struct chromBins* loadMapChains(char *chainFile)
/* read a chain file, convert to mapAln object and chromBins by query locations. */
{
struct chromBins* mapAlns = chromBinsNew((chromBinsFreeFunc*)pslFree);
struct chain *ch;
struct lineFile *chLf = lineFileOpen(chainFile, TRUE);
while ((ch = chainRead(chLf)) != NULL)
{
struct mapAln *mapAln = chainToPsl(ch);
chromBinsAdd(mapAlns, mapAln->psl->qName, mapAln->psl->qStart, mapAln->psl->qEnd, mapAln);
chainFree(&ch);
}
lineFileClose(&chLf);
return mapAlns;
}
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;
}
