static void mapQueryPsl(struct psl* inPsl, struct chromBins *mapAlns,
FILE* outPslFh, FILE *mapInfoFh, FILE *mappingPslFh)
/* map a query psl to all targets */
{
static struct dyString *idBuf = NULL;
struct binElement *overMapAlns
= chromBinsFind(mapAlns, getMappingId(inPsl->tName, &idBuf), inPsl->tStart, inPsl->tEnd);
struct binElement *overMapAln;
for (overMapAln = overMapAlns; overMapAln != NULL; overMapAln = overMapAln->next)
mapPslPair(inPsl, (struct mapAln *)overMapAln->val, outPslFh, mapInfoFh, mappingPslFh);
slFreeList(&overMapAlns);
}
struct binElement *orgGenesFind(struct orgGenes *genes, struct mafComp *comp,
int sortDir)
/* Return list of references to exons overlapping the specified component,
* sorted into assending order sortDir is 1, descending if it's -1.
* slFreeList the returned list. */
{
char *chrom = skipSrcDb(comp->src);
int start = comp->start;
int end = (comp->start + comp->size);
struct binElement *exons;
/* get positive strand coordinate to match exon */
if (comp->strand == '-')
reverseIntRange(&start, &end, comp->srcSize);
exons = chromBinsFind(genes->bins, chrom, start, end);
slSort(&exons, (sortDir > 0) ? cmpExonsAscend : cmpExonsDescend);
return exons;
}
