From 2478e5c501d21845d755f8a9b8195a84aecde3d5 Mon Sep 17 00:00:00 2001
From: Mathieu Giraud <mathieu@vidjil.org>
Date: Tue, 12 May 2020 11:42:57 +0200
Subject: [PATCH] doc/warnings.md, algo/vijdil.cpp: W09 when interrupted during
 second pass

---
 algo/vidjil.cpp | 4 +++-
 doc/warnings.md | 1 +
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/algo/vidjil.cpp b/algo/vidjil.cpp
index 0fdbcd9b8..21c10494b 100644
--- a/algo/vidjil.cpp
+++ b/algo/vidjil.cpp
@@ -1318,7 +1318,9 @@ int main (int argc, char **argv)
 
       if (global_interrupted)
       {
-        cout << WARNING_STRING << "Interrupted after analyzing " << num_clone << " clones" << endl ;
+        string msg = "Interrupted after analyzing " + string_of_int(num_clone) + " clones" ;
+        output.add_warning("W09", msg, LEVEL_WARN);
+        cout << WARNING_STRING << msg << endl ;
         break;
       }
 
diff --git a/doc/warnings.md b/doc/warnings.md
index facec043e..70995ecd0 100644
--- a/doc/warnings.md
+++ b/doc/warnings.md
@@ -14,6 +14,7 @@ Warnings which were implemented ([x]) have a fixed code that should not be chang
 - [ ]     Outdated germlines  
 - [ ]     Strange parameters: xxxx xxxx
 - [ ] W0z Unknown error
+- [x] W09 Program interrupted, output data may be not complete
 
 ## Output of a pre-process ~"server-pre-process" 
 - [ ] W10 Few assembled reads  #2243  
-- 
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