54256f85f370573466cad8249e55e6505eded45a
chmalee
  Tue Mar 1 10:10:44 2022 -0800
Fix missing chromAliasSetup in hgVai, refs #28956

diff --git src/hg/hgVai/hgVai.c src/hg/hgVai/hgVai.c
index fd4fd87..337ac33 100644
--- src/hg/hgVai/hgVai.c
+++ src/hg/hgVai/hgVai.c
@@ -29,30 +29,31 @@
 #include "gpFx.h"
 #include "bigGenePred.h"
 #include "udc.h"
 #include "knetUdc.h"
 #include "md5.h"
 #include "regexHelper.h"
 #include "hAnno.h"
 #include "annoGratorQuery.h"
 #include "annoGratorGpVar.h"
 #include "annoFormatVep.h"
 #include "annoStreamBigBed.h"
 #include "annoStreamDb.h"
 #include "annoStreamVcf.h"
 #include "windowsToAscii.h"
 #include "obscure.h"
+#include "chromAlias.h"
 
 #include "libifyMe.h"
 
 #define GENCODE_TAG_DOC_URL "\"http://www.gencodegenes.org/gencode_tags.html\""
 #define GENCODE_BASIC_DOC_URL "\"http://www.gencodegenes.org/faq.html\""
 #define REFSEQ_STATUS_DOC_URL "\"https://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_status_codes\""
 #define APPRIS_DOC_URL "\"http://appris.bioinfo.cnio.es/#/help/database\""
 
 #define HGVS_MUST_USE_ACC "Note: HGVS terms must use versioned transcript or genomic accessions " \
     "(e.g. NM_000023.3, NC_000012.11, ENST00000000233.9), not gene symbols."
 
 /* Global Variables */
 struct cart *cart;		/* CGI and other variables */
 struct hash *oldVars = NULL;	/* The cart before new cgi stuff added. */
 char *genome = NULL;		/* Name of genome - mouse, human, etc. */
@@ -3028,30 +3029,31 @@
         // No HTTP header for command-line use.
         cart = cartForSession(hUserCookie(), excludeVars, oldVars);
     else
         cart = cartAndCookieNoContent(hUserCookie(), excludeVars, oldVars);
     }
 else
     cart = cartAndCookie(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. */
 getDbAndGenome(cart, &database, &genome, oldVars);
+chromAliasSetup(database);
 initGenbankTableNames(database);
 regionType = cartUsualString(cart, hgvaRegionType, hgvaRegionTypeGenome);
 if (isEmpty(cartOptionalString(cart, hgvaRange)))
     cartSetString(cart, hgvaRange, hDefaultPos(database));
 
 int timeout = cartUsualInt(cart, "udcTimeout", 300);
 if (udcCacheTimeout() < timeout)
     udcSetCacheTimeout(timeout);
 knetUdcInstall();
 
 char *range = trimSpaces(windowsToAscii(cartUsualString(cart, hgvaRange, "")));
 cartSetLastPosition(cart, range, oldVars);
 cartTrackDbInit(cart, &fullTrackList, &fullGroupList, TRUE);
 struct dyString *dyWarn = dyStringNew(0);
 boolean noShort = (cartOptionalString(cart, "noShort") != NULL); // is this the second page of results