54406b80d5d435970989acff7b22dd6146c6b411
braney
  Sat Jan 22 15:24:59 2022 -0800
adding chrom alias support to big files

diff --git src/hg/hgTables/hgTables.c src/hg/hgTables/hgTables.c
index 6768dc7..76ec309 100644
--- src/hg/hgTables/hgTables.c
+++ src/hg/hgTables/hgTables.c
@@ -28,30 +28,31 @@
 #include "hgTables.h"
 #include "joiner.h"
 #include "bedCart.h"
 #include "hgMaf.h"
 #include "gvUi.h"
 #include "wikiTrack.h"
 #include "trackHub.h"
 #include "hubConnect.h"
 #include "hgConfig.h"
 #include "udc.h"
 #include "chromInfo.h"
 #include "knetUdc.h"
 #include "trashDir.h"
 #include "genbank.h"
 #include "windowsToAscii.h"
+#include "chromAlias.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgTables - Get table data associated with tracks and intersect tracks\n"
   "usage:\n"
   "   hgTables XXX\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 /* Global variables. */
 struct cart *cart;	/* This holds cgi and other variables between clicks. */
@@ -1670,30 +1671,31 @@
 
 oldVars = hashNew(10);
 
 /* Sometimes we output HTML and sometimes plain text; let each outputter
  * take care of headers instead of using a fixed cart*Shell(). */
 cart = cartAndCookieNoContent(hUserCookie(), excludeVars, oldVars);
 
 // Try to deal with virt chrom position used by hgTracks.
 if (startsWith(    MULTI_REGION_CHROM, cartUsualString(cart, "position", ""))
  || startsWith(OLD_MULTI_REGION_CHROM, cartUsualString(cart, "position", "")))
     cartSetString(cart, "position", cartUsualString(cart, "nonVirtPosition", ""));
 
 /* Set up global variables. */
 allJoiner = joinerRead("all.joiner");
 getDbGenomeClade(cart, &database, &genome, &clade, oldVars);
+chromAliasSetup(database);
 freezeName = hFreezeFromDb(database);
 
 initGenbankTableNames(database);
 
 int timeout = cartUsualInt(cart, "udcTimeout", 300);
 if (udcCacheTimeout() < timeout)
     udcSetCacheTimeout(timeout);
 knetUdcInstall();
 
 char *backgroundStatus = cartUsualString(cart, "backgroundStatus", NULL);
 if (backgroundStatus)
     {
     getBackgroundStatus(backgroundStatus);
     exit(0);
     }