85be21057a058a0bdb12caac2bae553376442f5a
angie
  Mon Apr 15 10:56:28 2013 -0700
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters.  Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152

diff --git src/lib/annoStreamBigBed.c src/lib/annoStreamBigBed.c
index ea3fb3d..651ce85 100644
--- src/lib/annoStreamBigBed.c
+++ src/lib/annoStreamBigBed.c
@@ -83,37 +83,37 @@
 static void asbbClose(struct annoStreamer **pVSelf)
 /* Close bbi handle and free self. */
 {
 if (pVSelf == NULL)
     return;
 struct annoStreamBigBed *self = *(struct annoStreamBigBed **)pVSelf;
 bigBedFileClose(&(self->bbi));
 self->intervalList = NULL;
 lmCleanup(&(self->intervalQueryLm));
 freeMem(self->row);
 freeMem(self->startBuf);
 freeMem(self->endBuf);
 annoStreamerFree(pVSelf);
 }
 
-struct annoStreamer *annoStreamBigBedNew(char *fileOrUrl, int maxItems)
+struct annoStreamer *annoStreamBigBedNew(char *fileOrUrl, struct annoAssembly *aa, int maxItems)
 /* Create an annoStreamer (subclass) object from a file or URL; if
  * maxItems is 0, all items from a query will be returned, otherwise
  * each query is limited to maxItems. */
 {
 struct bbiFile *bbi = bigBedFileOpen(fileOrUrl);
 struct asObject *asObj = bigBedAsOrDefault(bbi);
 struct annoStreamBigBed *self = NULL;
 AllocVar(self);
 struct annoStreamer *streamer = &(self->streamer);
-annoStreamerInit(streamer, asObj);
+annoStreamerInit(streamer, aa, asObj);
 streamer->rowType = arWords;
 streamer->setRegion = asbbSetRegion;
 streamer->nextRow = asbbNextRow;
 streamer->close = asbbClose;
 self->bbi = bbi;
 self->maxItems = maxItems;
 AllocArray(self->row, streamer->numCols + 1);
 self->startBuf = needMem(32);
 self->endBuf = needMem(32);
 return (struct annoStreamer *)self;
 }