d26fd993b377f1d3426fbedba35bd98d2ba5c3da
braney
  Tue May 24 16:25:26 2022 -0700
fix problem with hgFind not using chromAlias refs #29447

diff --git src/hg/lib/hgFind.c src/hg/lib/hgFind.c
index 8ba941b..c3b19a7 100644
--- src/hg/lib/hgFind.c
+++ src/hg/lib/hgFind.c
@@ -29,30 +29,31 @@
 #include "refLink.h"
 #include "kgAlias.h"
 #include "kgProtAlias.h"
 #include "findKGAlias.h"
 #include "findKGProtAlias.h"
 #include "tigrCmrGene.h"
 #include "minGeneInfo.h"
 #include "pipeline.h"
 #include "hgConfig.h"
 #include "trix.h"
 #include "trackHub.h"
 #include "udc.h"
 #include "hubConnect.h"
 #include "bigBedFind.h"
 #include "genbank.h"
+#include "chromAlias.h"
 
 // Exhaustive searches can lead to timeouts on CGIs (#11626).
 // However, hgGetAnn requires exhaustive searches (#11665).
 #define NONEXHAUSTIVE_SEARCH_LIMIT 500
 #define EXHAUSTIVE_SEARCH_REQUIRED  -1
 
 char *hgAppName = "";
 
 /* alignment tables to check when looking for mrna alignments */
 static char *estTables[] = { "intronEst", "all_est", "xenoEst", NULL };
 static char *estLabels[] = { "Spliced ESTs", "ESTs", "Other ESTs", NULL };
 static char *mrnaTables[] = { "all_mrna", "xenoMrna", NULL };
 static char *mrnaLabels[] = { "mRNAs", "Other mRNAs", NULL };
 static struct dyString *hgpMatchNames = NULL;
 
@@ -2146,31 +2147,31 @@
     errCatchFree(&errCatch);
     if (hgp->singlePos != NULL)
 	{
 	if (retMultiChrom && chrom != NULL && differentString(chrom, hgp->singlePos->chrom))
             *retMultiChrom = cloneString(chrom);
 	chrom = hgp->singlePos->chrom;
 	if (hgp->singlePos->chromStart < start)
 	    start = hgp->singlePos->chromStart;
 	if (hgp->singlePos->chromEnd > end)
 	    end = hgp->singlePos->chromEnd;
 	}
     else if (hgp->posCount == 0 || (multiTerm && hgp->posCount > 1))
         break;
     }
 if (retChromName)
-    *retChromName = chrom;
+    *retChromName = chromAliasFindNative(chrom);
 if (retWinStart)
     *retWinStart  = start;
 if (retWinEnd)
     *retWinEnd    = end;
 return hgp;
 }
 
 static struct hgPositions *revertPosition(struct cart *cart, char **pPosition,
                                           char **retChrom, int *retStart, int *retEnd,
                                           char *hgAppName, struct dyString *dyWarn)
 /* Revert *pPosition to lastPosition (or default position).  Return a new hgp for the
  * resolved position.  Append warnings to dyWarn, errAbort if defaultPos doesn't work.  */
 {
 struct hgPositions *hgp = NULL;
 boolean isMultiTerm = FALSE;