b5a4ddd8543a87f46988a60069148b0f2e1a8031
max
  Mon Aug 10 08:37:29 2026 -0700
hgBlat/hgPcr: show the chrUn info note (fix swapped startsWith args), refs #37893

The chrUn branch of the sequence-type note used startsWith(name, "chrUn"),
but startsWith(start, string) tests whether string begins with start, so it
asked whether "chrUn" begins with the sequence name and never matched. As a
result chrUn (unplaced) sequences got no info icon on the new BLAT results
page, and no note on the classic results page or in hgPcr, while _alt/_fix/
_random (which use endsWith) worked. Fix the argument order in all three.

Also, on the new results page, check the sequence's aliases and not just its
single display name, so a hit whose displayed label is an accession but which
has a chrUn/alt/fix alias (e.g. a GenArk hub) still gets the note.

diff --git src/hg/hgPcr/hgPcr.c src/hg/hgPcr/hgPcr.c
index cabcf8a8241..9a3caa06a8b 100644
--- src/hg/hgPcr/hgPcr.c
+++ src/hg/hgPcr/hgPcr.c
@@ -611,31 +611,31 @@
     boolean isRandom = FALSE;
     boolean isChrUn = FALSE;
 
     if (gpoList != NULL)
         {
         struct gfPcrOutput *gpo;
         for (gpo = gpoList;  gpo != NULL;  gpo = gpo->next)
             {
             char *seq = gpo->seqName;
             if (endsWith(seq, "_fix"))
                 isFix = TRUE;
             else if (endsWith(seq, "_alt"))
                 isAlt = TRUE;
             else if (endsWith(seq, "_random"))
                 isRandom = TRUE;
-            else if (startsWith(seq, "chrUn"))
+            else if (startsWith("chrUn", seq))
                 isChrUn = TRUE;
             }
         }
 
     if (isFix || isRandom || isAlt || isChrUn)
         webNewSection("Notes on the results above");
 
     if (isFix)
         printf("<A target=_blank HREF=\"../FAQ/FAQdownloads#downloadFix\">What is chrom_fix?</A><BR>");
     if (isAlt)
         printf("<A target=_blank HREF=\"../FAQ/FAQdownloads#downloadAlt\">What is chrom_alt?</A><BR>");
     if (isRandom)
         printf("<A target=_blank HREF=\"../FAQ/FAQdownloads#download10\">What is chrom_random?</A><BR>");
     if (isChrUn)
         printf("<A target=_blank HREF=\"../FAQ/FAQdownloads#download11\">What is a chrUn sequence?</A><BR>");