From 8df6a91caf7afaedcb69272d7dc47b357fb16fa0 Mon Sep 17 00:00:00 2001
From: Brian Osborne <briano@bioteam.net>
Date: Thu, 18 Jul 2013 09:13:26 -0400
Subject: [PATCH] Fix warning, 'inclusion threshold'

---
 Bio/SearchIO/hmmer3.pm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/Bio/SearchIO/hmmer3.pm b/Bio/SearchIO/hmmer3.pm
index 9f7fc91dd..6d826e784 100644
--- a/Bio/SearchIO/hmmer3.pm
+++ b/Bio/SearchIO/hmmer3.pm
@@ -385,7 +385,8 @@ sub next_result {
             }
 
             # Complete sequence table data below inclusion threshold
-            # not currently fully implemented
+            # not currently fully implemented -
+            # Should all these lines simply be skipped?
             elsif ( /inclusion threshold/ ) {
                 while ( defined( $_ = $self->_readline ) ) {
                     if (   /Domain( and alignment)? annotation for each/
@@ -413,7 +414,7 @@ sub next_result {
                     $hitid      = shift @hitline;
                     $desc       = join " ", @hitline;
 
-                    $hitinfo{$hitid} = "below_inclusion";
+                    $hitinfo{$hitid} = "below_inclusion" if defined $hitid;
                 }
             }
 
-- 
2.11.4.GIT