e2d7638b2848fe00bbf9b66bca395ec68a9ee9e6
braney
  Thu Oct 15 16:22:06 2015 -0700
first cut at bigMaf support #15935

diff --git src/hg/hgTracks/bigBedTrack.c src/hg/hgTracks/bigBedTrack.c
index 625dfb8..7f0c810 100644
--- src/hg/hgTracks/bigBedTrack.c
+++ src/hg/hgTracks/bigBedTrack.c
@@ -42,40 +42,47 @@
 	if (!trackHubDatabase(database))
 	    conn = hAllocConnTrack(database, track->tdb);
 	fileName = bbiNameFromSettingOrTable(track->tdb, conn, track->table);
 	hFreeConn(&conn);
 	}
     
     #ifdef USE_GBIB_PWD
     #include "gbib.c"
     #endif
 
     bbi = track->bbiFile = bigBedFileOpen(fileName);
     }
 return bbi;
 }
 
-struct bigBedInterval *bigBedSelectRange(struct track *track,
-	char *chrom, int start, int end, struct lm *lm)
+struct bigBedInterval *bigBedSelectRangeExtra(struct track *track,
+	char *chrom, int start, int end, struct lm *lm, char *variableName)
 /* Return list of intervals in range. */
 {
 struct bigBedInterval *result = NULL;
 /* protect against temporary network error */
 struct errCatch *errCatch = errCatchNew();
 if (errCatchStart(errCatch))
     {
-    struct bbiFile *bbi = fetchBbiForTrack(track);
+    struct bbiFile *bbi;
+    if (variableName == NULL)
+        bbi = fetchBbiForTrack(track);
+    else
+        {
+	char *fileName = trackDbSetting(track->tdb, variableName);
+        bbi =  bigBedFileOpen(fileName);
+        }
     int maxItems = min(BIGBEDMAXIMUMITEMS, maximumTrackItems(track)); // do not allow it to exceed BIGBEDMAXIMUMITEMS for bigBed
     result = bigBedIntervalQuery(bbi, chrom, start, end, maxItems + 1, lm);
     if (slCount(result) > maxItems)
 	{
 	track->limitedVis = tvDense;
 	track->limitedVisSet = TRUE;
 	result = NULL;
 	AllocArray(track->summary, insideWidth);
 	if (bigBedSummaryArrayExtended(bbi, chrom, start, end, insideWidth, track->summary))
 	    {
 	    char *denseCoverage = trackDbSettingClosestToHome(track->tdb, "denseCoverage");
 	    if (denseCoverage != NULL)
 		{
 		double endVal = atof(denseCoverage);
 		if (endVal <= 0)
@@ -92,30 +99,37 @@
     track->bbiFile = NULL;
     }
 errCatchEnd(errCatch);
 if (errCatch->gotError)
     {
     track->networkErrMsg = cloneString(errCatch->message->string);
     track->drawItems = bigDrawWarning;
     track->totalHeight = bigWarnTotalHeight;
     result = NULL;
     }
 errCatchFree(&errCatch);
 
 return result;
 }
 
+struct bigBedInterval *bigBedSelectRange(struct track *track,
+	char *chrom, int start, int end, struct lm *lm)
+/* Return list of intervals in range. */
+{
+return bigBedSelectRangeExtra(track, chrom, start, end, lm, NULL);
+}
+
 int bbExtraFieldIndex(struct trackDb *tdb, char* fieldName)
 /* return the index of a given extra field from the bbInterval
  * 0 is the name-field of bigBed and is used as an error code 
  * as this is the default anyways */
 {
 if (fieldName==NULL)
     return 0;
 // copied from hgc.c
 // get .as file for track
 struct sqlConnection *conn = NULL ;
 if (!trackHubDatabase(database))
     conn = hAllocConnTrack(database, tdb);
 struct asObject *as = asForTdb(conn, tdb);
 hFreeConn(&conn);
 if (as == NULL)