091a7e46fe5e9397ec47ba8aa026a8d400040714
galt
  Mon Dec 8 10:08:44 2025 -0800
Fixes hgTables Sequence output with CDS casing. Bug caused introns to be upper case and has existed since 2002. fixes #34381

diff --git src/hg/cgilib/hgSeq.c src/hg/cgilib/hgSeq.c
index ef74d91d694..d7a57002888 100644
--- src/hg/cgilib/hgSeq.c
+++ src/hg/cgilib/hgSeq.c
@@ -768,31 +768,31 @@
 			       bedItem->chromStarts[i], bedItem->blockSizes[i],
 			       TRUE, TRUE, chromSize);
 		    }
 		isCDS = ! ((bedItem->chromStarts[i] + bedItem->blockSizes[i]) >
 			   bedItem->thickEnd);
 		doIntron = (isCDS ? cdsIntron :
 			    ((!isRc) ? utrIntron3 : utrIntron5));
 		if (doIntron && (i < bedItem->blockCount - 1))
 		    {
 		    addFeature(&count, starts, sizes, exonFlags, cdsFlags,
 			       (bedItem->chromStarts[i] +
 				bedItem->blockSizes[i]),
 			       (bedItem->chromStarts[i+1] -
 				bedItem->chromStarts[i] -
 				bedItem->blockSizes[i]),
-			       FALSE, isCDS, chromSize);
+			       FALSE, FALSE, chromSize);
 		    }
 		}
 	    else
 		{
 		if ((!isRc && utrExon3)   || (isRc && utrExon5))
 		    {
 		    addFeature(&count, starts, sizes, exonFlags, cdsFlags,
 			       bedItem->chromStarts[i], bedItem->blockSizes[i],
 			       TRUE, FALSE, chromSize);
 		    }
 		if (((!isRc && utrIntron3) || (isRc && utrIntron5)) &&
 		    (i < bedItem->blockCount - 1))
 		    {
 		    addFeature(&count, starts, sizes, exonFlags, cdsFlags,
 			       (bedItem->chromStarts[i] +