caee2c1a226397ab30cbfdcf7f1c20dad8dff339
galt
  Wed Feb 5 12:10:12 2014 -0800
oops swap comments, thanks for catching, Tim.
diff --git src/hg/lib/hdb.c src/hg/lib/hdb.c
index 46c8187..cff33bc 100644
--- src/hg/lib/hdb.c
+++ src/hg/lib/hdb.c
@@ -5024,39 +5024,33 @@
 	return 0;
     }
 else if (sameString(str1, "M") && !sameString(str2, "M"))
     return 1;
 else if (!sameString(str1, "M") && sameString(str2, "M"))
     return -1;
 else if (str1[0] == 'U' && str2[0] != 'U')
     return 1;
 else if (str1[0] != 'U' && str2[0] == 'U')
     return -1;
 else
     return strcmp(str1, str2);
 }
 
 int chrSlNameCmp(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
- */
+/* 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_]+)?". */
 {
 struct slName *sln1 = *(struct slName **)el1;
 struct slName *sln2 = *(struct slName **)el2;
 return chrNameCmp(sln1->name, sln2->name);
 }
 
 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
@@ -5125,33 +5119,39 @@
 	return 0;
     }
 else if (str1[0] == 'U' && str2[0] != 'U')
     return 1;
 else if (str1[0] != 'U' && str2[0] == 'U')
     return -1;
 else if (sameString(str1, "M") && !sameString(str2, "M"))
     return 1;
 else if (!sameString(str1, "M") && sameString(str2, "M"))
     return -1;
 else
     return strcmp(str1, str2);
 }
 
 int chrSlNameCmpWithAltRandom(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_]+)?". */
+/* 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
+ */
 {
 struct slName *sln1 = *(struct slName **)el1;
 struct slName *sln2 = *(struct slName **)el2;
 return chrNameCmpWithAltRandom(sln1->name, sln2->name);
 }
 
 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 */
 {
 const struct bed *a = *((struct bed **)va);
 const struct bed *b = *((struct bed **)vb);
 int dif;
 dif = chrNameCmp(a->chrom, b->chrom);
 if (dif == 0)