a137caa4731599f89daf08875f24bcb19b11e597
galt
  Thu Sep 11 14:32:31 2025 -0700
Deals with multi-region and bigBeds so limitWiggle optimization works properly with all windows or regions. Fixes error test cases in rm35580 as well as full chromosome and recount3 and lrg and unusual tracks etc. Also works with quickLift and bigLollly now. Tested all tracks on hg38 and some public trackhubs. fixes #35580

diff --git src/hg/hgTracks/bigBedTrack.c src/hg/hgTracks/bigBedTrack.c
index 8784208b144..4927afdc448 100644
--- src/hg/hgTracks/bigBedTrack.c
+++ src/hg/hgTracks/bigBedTrack.c
@@ -475,79 +475,159 @@
 {
 static boolean set = FALSE;
 static unsigned maxItems = 0;
 
 if (!set)
     {
     char *maxItemsStr = cfgOptionDefault("bigBedMaxItems", "10000");
 
     maxItems = sqlUnsigned(maxItemsStr);
     set = TRUE;
     }
 
 return maxItems;
 }
 
-struct bigBedInterval *bigBedSelectRangeExt(struct track *track,
-	char *chrom, int start, int end, struct lm *lm, int maxItems)
-/* Return list of intervals in range. */
+static boolean hasOverflowedInWindow(struct track *track)
+/* has it overlowed in the given track? */
 {
-struct bigBedInterval *result = NULL;
+uint resultCount = 0;  // do not use -1, it messes up the compare of signed resultsCount with unsigned bigMaxItems.
+char *resultCountString = trackDbSetting(track->tdb, "bigBedItemsCount");
+if (resultCountString)
+    resultCount = sqlUnsigned(resultCountString);
+return (resultCount > bigBedMaxItems());
+}
+
+
+static void loadBigBedSummary(struct track *track)
+/* Check if summary loading needed for bigBed */
+{
+if (track->subtracks)  // do tracks or subtracks but not parents.
+    {
+    return;
+    }
+
+struct lm *lm = lmInit(0);
+
+char *chrom = chromName;
+int start = winStart;
+int end = winEnd;
+
 /* protect against temporary network error */
 struct errCatch *errCatch = errCatchNew();
 boolean filtering = FALSE; // for the moment assume we're not filtering
 if (errCatchStart(errCatch))
     {
-    struct bbiFile *bbi = fetchBbiForTrack(track);
-    result = bigBedIntervalQuery(bbi, chrom, start, end, bigBedMaxItems() + 1, lm);
-    if (slCount(result) > bigBedMaxItems())
+    // scan all windows for errors and overflows
+    boolean errorsInWindows = FALSE;
+    boolean overFlowedInWindows = FALSE;
+
+    struct track *thisTrack;
+    for(thisTrack=track->prevWindow; thisTrack; thisTrack=thisTrack->prevWindow)
+        {
+        if (hasOverflowedInWindow(thisTrack))
+	    overFlowedInWindows = TRUE;
+        if (thisTrack->drawItems == bigDrawWarning)
+	    errorsInWindows = TRUE;
+        }
+    for(thisTrack=track->nextWindow; thisTrack; thisTrack=thisTrack->nextWindow)
+        {
+        if (hasOverflowedInWindow(thisTrack))
+	    overFlowedInWindows = TRUE;
+        if (thisTrack->drawItems == bigDrawWarning)
+	    errorsInWindows = TRUE;
+        }
+    
+    if (hasOverflowedInWindow(track))
+	overFlowedInWindows = TRUE;
+
+    if (!errorsInWindows && overFlowedInWindows)
 	{
         if (filtering)
             errAbort("Too many items in window to filter.Zoom in or remove filters to view track.");
         else
+            {
+	    struct bbiFile *bbi = fetchBbiForTrack(track);
+            if (bbi)
 		{
 		// use summary levels
 		if (track->visibility != tvDense)
 		    {
 		    track->limitedVis = tvFull;
 		    track->limitWiggle = TRUE;
 		    track->limitedVisSet = TRUE;
 		    }
 		else
 		    {
 		    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)
 			    {
 			    AllocVar(track->sumAll);
 			    *track->sumAll = bbiTotalSummary(bbi);
 			    }
 			}
 		    }
 		else
 		    freez(&track->summary);
 		}
 	    }
+        }
+    }
+errCatchEnd(errCatch);
+if (errCatch->gotError)
+    {
+    track->networkErrMsg = cloneString(errCatch->message->string);
+    track->drawItems = bigDrawWarning;
+    track->totalHeight = bigWarnTotalHeight;
+    }
+errCatchFree(&errCatch);
+lmCleanup(&lm);
+track->bbiFile = NULL;
+
+}
+
+struct bigBedInterval *bigBedSelectRangeExt(struct track *track,
+	char *chrom, int start, int end, struct lm *lm, int maxItems)
+/* 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);
+    result = bigBedIntervalQuery(bbi, chrom, start, end, bigBedMaxItems() + 1, lm);  // pass in desired limit or 0 for all.
+
+    char resultCount[32];
+    safef(resultCount, sizeof resultCount, "%u", slCount(result));
+    trackDbAddSetting(track->tdb, "bigBedItemsCount", resultCount);
+
+    if (slCount(result) > bigBedMaxItems())
+	    {
+            result = NULL;  // IS Having it return NULL a critical part of this?
+	    }
+
     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;
 }
 
@@ -965,29 +1045,31 @@
 #ifdef NOTNOW
 // let's help the user out and get the definedFieldCount if they didn't specify it on the type line
 if (!tdbIsSuper(track->tdb) && (track->tdb->subtracks == NULL) && (wordCount == 1) && sameString(words[0], "bigBed"))
     {
     int fieldCount = getFieldCount(track);
     if (fieldCount > 3) 
         {
         char buffer[1024];
         safef(buffer, sizeof buffer, "%d", fieldCount);
         newWords[1] = cloneString(buffer);
         wordCount = 2;
         }
     }
 #endif
 complexBedMethods(track, tdb, TRUE, wordCount, newWords);
+track->loadSummary = loadBigBedSummary;
 }
 
 void bigBedMethods(struct track *track, struct trackDb *tdb, 
                                 int wordCount, char *words[])
 /* Set up bigBed methods for tracks that are type bigBed. */
 {
 commonBigBedMethods(track, tdb, wordCount, words);
 if (sameWordOk(trackDbSetting(tdb, "style"), "heatmap"))
     {
     // Might want to check here if required heatmap settings/fields are in place,
     // maybe some combo of row count and labels.
     heatmapMethods(track);
     }
 }
+