cb8f8b8e1fa7a5e122b4e0e5c7fb84bf4027d008
hiram
  Fri Sep 18 13:03:08 2020 -0700
assembly hubs and now display alias names on sequence display page refs #24396

diff --git src/hg/inc/trackHub.h src/hg/inc/trackHub.h
index 6da0cff..871aa91 100644
--- src/hg/inc/trackHub.h
+++ src/hg/inc/trackHub.h
@@ -117,30 +117,36 @@
 boolean trackHubDatabase(char *database);
 /* Is this an assembly from an Assembly Data hub? */
 
 char *trackHubDefaultChrom(char *database);
 /* Return the default chromosome for this track hub assembly. */
 
 char *trackHubAssemblyField(char *database, char *field);
 /* Get data field from a assembly data hub. */
 
 int trackHubChromCount(char *database);
 /* Return number of chromosomes in a assembly data hub. */
 
 struct slName *trackHubAllChromNames(char *database);
 /* Return a list of all the chrom names in this assembly hub database. */
 
+char *trackHubAliasFile(char *database);
+/* see if this assembly hub has an alias file, return url if present */
+
+struct hash *trackHubAllChromAlias(char *database);
+/* Return a hash of chroms with alias names from alias file if present */
+
 struct chromInfo *trackHubAllChromInfo(char *database);
 /* Return a chromInfo structure for all the chroms in this database. */
 
 struct chromInfo *trackHubMaybeChromInfo(char *database, char *chrom);
 /* Return a chromInfo structure for just this chrom in this database. 
  * Return NULL if chrom doesn't exist. */
 
 struct chromInfo *trackHubChromInfo(char *database, char *chrom);
 /* Return a chromInfo structure for just this chrom in this database. 
  * errAbort if chrom doesn't exist. */
 
 char *trackHubGenomeNameToDb(char *genome);
 /* Return assembly name given a genome name if one exists, otherwise NULL. */
 
 struct dbDb *trackHubGetDbDbs(char *clade);