struct bed *bigBedGetFilteredBedsOnRegions(struct sqlConnection *conn,
char *db, char *table, struct region *regionList, struct lm *lm,
int *retFieldCount)
/* Get list of beds from bigBed, in all regions, that pass filtering. */
{
/* Connect to big bed and get metadata and filter. */
char *fileName = bigBedFileName(table, conn);
struct bbiFile *bbi = bigBedFileOpen(fileName);
struct asObject *as = bigBedAsOrDefault(bbi);
struct asFilter *filter = asFilterFromCart(cart, db, table, as);
/* Get beds a region at a time. */
struct bed *bedList = NULL;
struct region *region;
for (region = regionList; region != NULL; region = region->next)
addFilteredBedsOnRegion(bbi, region, table, filter, lm, &bedList);
slReverse(&bedList);
/* Clean up and return. */
if (retFieldCount != NULL)
*retFieldCount = bbi->definedFieldCount;
bbiFileClose(&bbi);
freeMem(fileName);
return bedList;
}
struct bed *bamGetFilteredBedsOnRegions(struct sqlConnection *conn,
char *db, char *table, struct region *regionList, struct lm *lm,
int *retFieldCount)
/* Get list of beds from BAM, in all regions, that pass filtering. */
{
int maxOut = bigFileMaxOutput();
/* Figure out bam file name get column info and filter. */
struct asObject *as = bamAsObj();
struct asFilter *filter = asFilterFromCart(cart, db, table, as);
struct hash *idHash = identifierHash(db, table);
/* Get beds a region at a time. */
struct bed *bedList = NULL;
struct region *region;
for (region = regionList; region != NULL; region = region->next)
{
char *fileName = bamFileName(table, conn, region->chrom);
addFilteredBedsOnRegion(fileName, region, table, filter, lm, &bedList, idHash, &maxOut);
freeMem(fileName);
if (maxOut <= 0)
{
warn("Reached output limit of %d data values, please make region smaller,\n"
"\tor set a higher output line limit with the filter settings.", bigFileMaxOutput());
break;
}
}
slReverse(&bedList);
return bedList;
}
