JAL-2909 add sequence feature for insertions

[jalview.git] / src / jalview / io / BamFile.java

diff --git a/src/jalview/io/BamFile.java b/src/jalview/io/BamFile.java
index 277a61d..10e2d0e 100644 (file)
--- 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();