From 770c963afc6c95267d6b3a736301cad0e343803a Mon Sep 17 00:00:00 2001
From: Hannes Hauswedell <h2+github.com@fsfe.org>
Date: Fri, 19 Aug 2016 12:51:59 +0200
Subject: [PATCH] [FIX] sam/bam with new extension modes

---
 src/lambda.hpp | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/lambda.hpp b/src/lambda.hpp
index ccc179cb4..a2b9cec2c 100644
--- a/src/lambda.hpp
+++ b/src/lambda.hpp
@@ -2038,6 +2038,9 @@ iterateMatchesFullSimd(TLocalHolder & lH)
         appendValue(depSetV, source(bm.alignRow1));
 
         _setFrames(bm, *it, lH);
+
+        bm._n_qId = it->qryId / qNumFrames(TGlobalHolder::blastProgram);
+        bm._n_sId = it->subjId / sNumFrames(TGlobalHolder::blastProgram);
     }
 
     // fill up last batch
@@ -2219,6 +2222,9 @@ iterateMatchesFullSerial(TLocalHolder & lH)
         }
 
         _setFrames(bm, m, lH);
+
+        bm._n_qId = it->qryId / qNumFrames(TGlobalHolder::blastProgram);
+        bm._n_sId = it->subjId / sNumFrames(TGlobalHolder::blastProgram);
     }
 
     _writeRecord(record, lH);