b1555e4fe1146884d59fbca26c95e4b4b9f342c6
max
  Mon Feb 8 08:16:05 2021 -0800
adding notes about _alt/_fix etc to hgPcr and fixing the ones on hgBlat.c refs #26918

diff --git src/hg/hgBlat/hgBlat.c src/hg/hgBlat/hgBlat.c
index 3a7544d..275f2dd 100644
--- src/hg/hgBlat/hgBlat.c
+++ src/hg/hgBlat/hgBlat.c
@@ -639,34 +639,40 @@
 	    hgcUrl, psl->tStart, pslName, cgiEncode(faName), psl->qName,  psl->tName,
 	    psl->tStart, psl->tEnd, database, uiState);
 	printf("details</A> ");
 
 	printf("%s",psl->qName);
 	spaceOut(stdout, maxQChromNameSize - strlen(psl->qName));
 	printf(" %5d %5d %5d %5d   %5.1f%%  ",
 	    pslScore(psl), psl->qStart+1, psl->qEnd, psl->qSize,
 	    100.0 - pslCalcMilliBad(psl, TRUE) * 0.1);
 	printf("%s",psl->tName);
 	spaceOut(stdout, maxTChromNameSize - strlen(psl->tName));
 	printf("  %-2s  %9d %9d %6d",
 	    psl->strand, psl->tStart+1, psl->tEnd,
 	    psl->tEnd - psl->tStart);
 
-        if (endsWith(psl->tName, "_fix"))
-            printf("   <A target=_blank HREF=\"../FAQ/FAQblat.html#blat1c\">What is chrom_fix?</A>");
-        if (endsWith(psl->tName, "_alt"))
-            printf("   <SMALL><A target=_blank HREF=\"../FAQ/FAQblat.html#blat1c\">What is chrom_alt?</A></SMALL>");
+        // if you modify this, also modify hgPcr.c:doQuery, which implements a similar feature
+        char *seq = psl->tName;
+        if (endsWith(seq, "_fix"))
+            printf("   <A target=_blank HREF=\"../FAQ/FAQdownloads#downloadFix\">What is chrom_fix?</A>");
+        else if (endsWith(seq, "_alt"))
+            printf("   <A target=_blank HREF=\"../FAQ/FAQdownloads#downloadAlt\">What is chrom_alt?</A>");
+        else if (endsWith(seq, "_random"))
+            printf("   <A target=_blank HREF=\"../FAQ/FAQdownloads#download10\">What is chrom_random?</A>");
+        else if (startsWith(seq, "chrUn"))
+            printf("   <A target=_blank HREF=\"../FAQ/FAQdownloads#download11\">What is a chrUn sequence?</A>");
         puts("\n");
 	}
     printf("</PRE>\n");
     webNewSection("Help");
     puts("<P style=\"text-align:left\"><A target=_blank HREF=\"../FAQ/FAQblat.html#blat1b\">Missing a match?</A><br>");
     puts("<A target=_blank HREF=\"../FAQ/FAQblat.html#blat1c\">What is chr_alt & chr_fix?</A></P>\n");
     puts("</DIV>\n");
     }
 pslFreeList(&pslList);
 
 }
 
 void trimUniq(bioSeq *seqList)
 /* Check that all seq's in list have a unique name.  Try and
  * abbreviate longer sequence names. */