a58d6091194d0113ef52cd694579ec703924a79a
braney
  Mon Aug 26 16:52:00 2024 -0700
enable non-hub assemblies to use chromAlias.bb from /gbdb

diff --git src/hg/lib/chromAlias.c src/hg/lib/chromAlias.c
index 4db3d59..a95a91b 100644
--- src/hg/lib/chromAlias.c
+++ src/hg/lib/chromAlias.c
@@ -235,37 +235,34 @@
 
         struct chromAlias *chromAlias;
         AllocVar(chromAlias);
         chromAlias->chrom = native;
         chromAlias->alias = alias;
         chromAlias->source = source;
         hashAdd(chromAliasGlobals.chromToAliasHash, native, chromAlias);
         hashAdd(chromAliasGlobals.aliasToChromHash, alias, chromAlias);
         }
     }
 }
 
 static char * gbdbBbExists(char *database)
 /* use a gbdb bigBed as our alias file. */
 {
-// not supported at the moment
-/*
 char buffer[4096];
-safef(buffer, sizeof buffer, "/gbdb/%s/chromAlias.bb", database);
+safef(buffer, sizeof buffer, "/gbdb/%s/%s.chromAlias.bb", database,database);
 if (fileExists(buffer))
     return cloneString(buffer);
-    */
 return NULL;
 }
 
 void chromAliasSetupBb(char *database, char *bbFile)
 /* Look for a chromAlias bigBed file and open it. */
 {
 chromAliasGlobals.bbi = bigBedFileOpen(bbFile);
 struct slName *fieldNames = bbFieldNames(chromAliasGlobals.bbi);
 chromAliasGlobals.fieldCount = slCount(fieldNames) - chromAliasGlobals.bbi->definedFieldCount;
 AllocArray(chromAliasGlobals.fields, chromAliasGlobals.fieldCount);
 int ii;
 for(ii=0; ii < chromAliasGlobals.bbi->definedFieldCount; ii++, fieldNames = fieldNames->next)
     ;
 for(ii=0; ii < chromAliasGlobals.fieldCount; ii++, fieldNames = fieldNames->next)
     chromAliasGlobals.fields[ii] = fieldNames->name;