X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBamFile.java;h=10e2d0ec7db91f30360e5d5309d81b05e075c896;hb=846629a1a7ab7715d14a18296bc3024c5de4ac5c;hp=277a61dea32a01ffc8f629e09b75b71f35c930dc;hpb=7798bd6a0235eb86769bb9987db735a3959ad031;p=jalview.git

diff --git a/src/jalview/io/BamFile.java b/src/jalview/io/BamFile.java
index 277a61d..10e2d0e 100644
--- a/src/jalview/io/BamFile.java
+++ b/src/jalview/io/BamFile.java
@@ -139,7 +139,7 @@ public class BamFile extends AlignFile
         seq.setEnd(rec.getReadLength());
 
         String newRead = parser.parseCigarToSequence(rec, insertions,
-                alignmentStart);
+                alignmentStart, seq);
 
         // make alignment sequences
         SequenceI alsq = seq.deriveSequence();