static void doAggregateOverlaps(struct chromAnnReader* inCar, FILE *outFh, FILE *dropFh)
/* Do aggreate overlap processing */
{
struct chromAnn *inCa;
while ((inCa = inCar->caRead(inCar)) != NULL)
{
doAggregateOverlap(inCa, outFh, dropFh);
chromAnnFree(&inCa);
}
}
void chromAnnMapAdd(struct chromAnnMap *cam,
struct chromAnn *ca)
/* add a record to the table. */
{
/* don't add if zero-length, they can't select */
if (ca->start < ca->end)
genomeRangeTreeAddValList(cam->ranges, ca->chrom, ca->start, ca->end, ca);
else
chromAnnFree(&ca);
}
static void doItemOverlaps(struct chromAnnReader* inCar, FILE *outFh, FILE *dropFh)
/* Do individual item overlap processings */
{
struct chromAnn *inCa;
while ((inCa = inCar->caRead(inCar)) != NULL)
{
doItemOverlap(inCa, outFh, dropFh);
chromAnnFree(&inCa);
}
}
void chromAnnMapFree(struct chromAnnMap **camPtr)
/* free chromAnnMap structures. */
{
struct chromAnnMap *cam = *camPtr;
if (cam != NULL)
{
struct hashCookie chromCookie = hashFirst(cam->ranges->hash);
struct hashEl *chromEl;
for (chromEl = hashNext(&chromCookie); chromEl != NULL; chromEl = chromEl->next)
{
struct range *r, *ranges = genomeRangeTreeList(cam->ranges, chromEl->name);
for (r = ranges; r != NULL; r = r->next)
{
struct chromAnn *ca, *cas = r->val;
while ((ca = slPopHead(&cas)) != NULL)
chromAnnFree(&ca);
}
}
freez(camPtr);
}
}
