cac8c67d46544187d0fb28cf78060d9d2cb97a5d
angie
  Tue Feb 5 14:09:20 2019 -0800
Update chrSlNameCmpWithAltRandom to handle _fix and _hap sequence names.  refs #18855 note-70

diff --git src/hg/inc/hdb.h src/hg/inc/hdb.h
index e23d72e..0318b45 100644
--- src/hg/inc/hdb.h
+++ src/hg/inc/hdb.h
@@ -905,50 +905,39 @@
  * exception cuz we're nice
  */
 
 int chrStrippedCmp(char *chrA, char *chrB);
 /*	compare chrom names after stripping chr, Scaffold_ or ps_ prefix */
 
 int chrNameCmp(char *str1, char *str2);
 /* Compare chromosome names by number, then suffix.  str1 and str2 must
  * match the regex "chr([0-9]+|[A-Za-z0-9]+)(_[A-Za-z0-9_]+)?". */
 
 int chrSlNameCmp(const void *el1, const void *el2);
 /* Compare chromosome names by number, then suffix.  el1 and el2 must be
  * slName **s (as passed in by slSort) whose names match the regex
  * "chr([0-9]+|[A-Za-z0-9]+)(_[A-Za-z0-9_]+)?". */
 
-int chrNameCmpWithAltRandom(char *str1, char *str2);
-/* Compare chromosome or linkage group names str1 and str2 
- * to achieve this order:
- * chr1 .. chr22
- * chrX
- * chrY
- * chrM
- * chr1_{alt, random} .. chr22_{alt, random}
- * chrUns
- */
-
 int chrSlNameCmpWithAltRandom(const void *el1, const void *el2);
 /* Compare chromosome or linkage group names str1 and str2 
  * to achieve this order:
  * chr1 .. chr22
  * chrX
  * chrY
  * chrM
- * chr1_{alt, random} .. chr22_{alt, random}
- * chrUns
+ * chr1_{alt,fix,hap*,random} .. chr22_{alt,fix,hap*,random}
+ * chrUn*
  */
 
 int bedCmpExtendedChr(const void *va, const void *vb);
 /* Compare to sort based on chrom,chromStart.  Use extended
  * chrom name comparison, that strip prefixes and does numeric compare */
 
 int compareDbs(char *dbA, char *dbB);
 /* Compare two org# e.g. mm6 vs. mm16 or mm6 vs. hg17
  * Return > 0 if dbA > dbB, < 0 if less than, and 0 if equal */
 
 int getTableSize(char *db, char *table);
 /* Get count of rows in a table in the primary database */
 
 struct slName *getDomainList(struct sqlConnection *conn, char *ucscGeneId,
        char *domainDb);