b622d147b7dbac52dbf3ba26928cd18e02d42bd8
braney
  Sat Feb 26 12:34:37 2022 -0800
add support for using a bigBed as the chromAlias file

diff --git src/hg/hgTables/bigWig.c src/hg/hgTables/bigWig.c
index 1f747eb..ccdb664 100644
--- src/hg/hgTables/bigWig.c
+++ src/hg/hgTables/bigWig.c
@@ -232,31 +232,31 @@
 resultCount = wigPrintDataVectorOut(dv, wigOutType, maxOut, NULL);
 dataVectorFree(&dv);
 return resultCount;
 }
 
 int bigWigOutRegion(char *table, struct sqlConnection *conn,
 			     struct region *region, int maxOut,
 			     enum wigOutputType wigOutType)
 /* Write out bigWig for region, doing intersecting and filtering as need be. */
 {
 boolean isMerged = anySubtrackMerge(table, database);
 int resultCount = 0;
 char *wigFileName = bigWigFileName(table, conn);
 if (wigFileName)
     {
-    struct bbiFile *bwf = bigWigFileOpenAlias(wigFileName, chromAliasChromToAliasHash(database));
+    struct bbiFile *bwf = bigWigFileOpenAlias(wigFileName, chromAliasFindAliases);
     if (bwf)
 	{
 	/* Easy case, just dump out data. */
 	if (!anyFilter() && !anyIntersection() && !isMerged && wigOutType == wigOutData)
 	    resultCount = bigWigIntervalDump(bwf, region->chrom, region->start, region->end,
 		    maxOut, stdout);
 	/* Pretty easy case, still do it ourselves. */
 	else if (!isMerged && wigOutType == wigOutData)
 	    {
 	    double ll, ul;
 	    enum wigCompare cmp;
 	    getWigFilter(database, curTable, &cmp, &ll, &ul);
 	    struct lm *lm = lmInit(0);
 	    struct bbiInterval *ivList, *iv;
 	    ivList = intersectedFilteredBbiIntervalsOnRegion(conn, bwf, region, cmp, ll, ul, lm);
@@ -284,31 +284,31 @@
 /* Put up page showing summary stats for bigWig track. */
 {
 struct trackDb *track = curTrack;
 char *table = curTable;
 char *shortLabel = (track == NULL ? table : track->shortLabel);
 char *fileName = bigWigFileName(table, conn);
 long startTime = clock1000();
 
 htmlOpen("%s (%s) Big Wig Summary Statistics", shortLabel, table);
 
 if (anySubtrackMerge(database, curTable))
     hPrintf("<P><EM><B>Note:</B> subtrack merge is currently ignored on this "
 	    "page (not implemented yet).  Statistics shown here are only for "
 	    "the primary table %s (%s).</EM>", shortLabel, table);
 
-struct bbiFile *bwf = bigWigFileOpenAlias(fileName, chromAliasChromToAliasHash(database));
+struct bbiFile *bwf = bigWigFileOpenAlias(fileName, chromAliasFindAliases);
 struct region *region, *regionList = getRegions();
 double sumData = 0, sumSquares = 0, minVal = 0, maxVal = 0;
 bits64 validCount = 0;
 
 if (!anyFilter() && !anyIntersection())
     {
     for (region = regionList; region != NULL; region = region->next)
 	{
 	struct bbiSummaryElement sum;
 	if (bbiSummaryArrayExtended(bwf, region->chrom, region->start, region->end,
 		bigWigIntervalQuery, 1, &sum))
 	    {
 	    if (validCount == 0)
 		{
 		minVal = sum.minVal;
@@ -373,58 +373,58 @@
 long wigFetchTime = clock1000() - startTime;
 floatStatRow("load and calc time", 0.001*wigFetchTime);
 hTableEnd();
 
 bbiFileClose(&bwf);
 htmlClose();
 }
 
 struct bed *bigWigIntervalsToBed(struct sqlConnection *conn, char *table, struct region *region,
 				 struct lm *lm)
 /* Return a list of unfiltered, unintersected intervals in region as bed (for
  * secondary table in intersection). */
 {
 struct bed *bed, *bedList = NULL;
 char *fileName = bigWigFileName(table, conn);
-struct bbiFile *bwf = bigWigFileOpenAlias(fileName, chromAliasChromToAliasHash(database));
+struct bbiFile *bwf = bigWigFileOpenAlias(fileName, chromAliasFindAliases);
 struct bbiInterval *iv, *ivList = bigWigIntervalQuery(bwf, region->chrom, region->start,
 						      region->end, lm);
 for (iv = ivList;  iv != NULL;  iv = iv->next)
     {
     lmAllocVar(lm, bed);
     bed->chrom = region->chrom;
     bed->chromStart = iv->start;
     bed->chromEnd = iv->end;
     slAddHead(&bedList, bed);
     }
 slReverse(&bedList);
 return bedList;
 }
 
 void bigWigFillDataVector(char *table, struct region *region,
 	struct sqlConnection *conn, struct dataVector *vector)
 /* Fill in data vector with bigWig info on region.  Handles filters and intersections. */
 {
 /* Figure out filter values if any. */
 double ll, ul;
 enum wigCompare cmp;
 getWigFilter(database, curTable, &cmp, &ll, &ul);
 
 /* Get intervals that pass filter and intersection. */
 struct lm *lm = lmInit(0);
 char *fileName = bigWigFileName(table, conn);
-struct bbiFile *bwf = bigWigFileOpenAlias(fileName, chromAliasChromToAliasHash(database));
+struct bbiFile *bwf = bigWigFileOpenAlias(fileName, chromAliasFindAliases);
 struct bbiInterval *iv, *ivList;
 ivList = intersectedFilteredBbiIntervalsOnRegion(conn, bwf, region, cmp, ll, ul, lm);
 int vIndex = 0;
 for (iv = ivList; iv != NULL; iv = iv->next)
     {
     int start = max(iv->start, region->start);
     int end = min(iv->end, region->end);
     double val = iv->val;
     int i;
     for (i=start; i<end && vIndex < vector->maxCount; ++i)
         {
 	vector->value[vIndex] = val;
 	vector->position[vIndex] = i;
 	++vIndex;
 	}