From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 23 Jan 2020 17:19:03 +0000 (+0000)
Subject: JAL-3121 update help page for GFF column 9 nested attributes
X-Git-Tag: Release_2_11_1_1~32^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=87828fe37d4da94c394322e807c132f1214046b0;p=jalview.git

JAL-3121 update help page for GFF column 9 nested attributes
---

diff --git a/help/help/html/features/featuresFormat.html b/help/help/html/features/featuresFormat.html
index 0226175..0e35e49 100755
--- a/help/help/html/features/featuresFormat.html
+++ b/help/help/html/features/featuresFormat.html
@@ -202,7 +202,11 @@
     GFF data (<em>this mixed format capability was added in Jalview
       2.6</em>).
   </p>
-
+  <p>Feature attributes can be included as <code>name=value</code> pairs in GFF3 column 9, including <em>(since Jalview 2.11.1.0)</em> 'nested' sub-attributes, for example:
+  <br><code>alleles=G,A,C;AF=6;CSQ=SIFT=deleterious,tolerated,PolyPhen=possibly_damaging(0.907)</code>
+  <br>where <code>SIFT</code> and <code>PolyPhen</code> are sub-attributes of <code>CSQ</code>. This data is preserved if features are output in GFF format (but not, currently,
+  in Jalview format).
+  </p>
   <p>
     <em>Jalview's sequence feature format</em>
   </p>