From 908b93f3c512cd5cc11a2a99029fb777ec192fee Mon Sep 17 00:00:00 2001
From: pad1989 <peteradavey@gmail.com>
Date: Mon, 14 Dec 2020 18:01:27 +0000
Subject: [PATCH] Update combineAndAnnotateReferences.pl

Changes allow for strain and isolate rank nodes. Previously fixed for annotateRefSeqSequencesWithUniqueTaxonIDs.pl . This script now updated to reflect the same changes.
---
 combineAndAnnotateReferences.pl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/combineAndAnnotateReferences.pl b/combineAndAnnotateReferences.pl
index 485c189..e8585dc 100644
--- a/combineAndAnnotateReferences.pl
+++ b/combineAndAnnotateReferences.pl
@@ -123,7 +123,7 @@
 	{
 		my $thisNode_rank = $taxonomy_href->{$taxonID}{rank};
 		die unless(defined $thisNode_rank);
-		unless(($thisNode_rank eq 'species') or ($thisNode_rank eq 'no rank') or ($thisNode_rank eq 'subspecies') or ($thisNode_rank eq 'varietas'))
+		unless(($thisNode_rank eq 'species') or ($thisNode_rank eq 'no rank') or ($thisNode_rank eq 'subspecies') or ($thisNode_rank eq 'varietas') or ($thisNode_rank eq 'strain') or ($thisNode_rank eq 'isolate'))
 		{
 			die Dumper("Unexpected rank", $thisNode_rank, $taxonID, $taxonID_2_files{$taxonID});
 		}	
@@ -247,4 +247,4 @@ sub print_help
 );
  
 exit; 
-}
\ No newline at end of file
+}