X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FCigarParser.java;h=a1124d460dfd31811fe107c6b35286ef5a5181e3;hb=fe4666614489b0f7c98ba27c25a4432a5c10677d;hp=cfbe842fffa63a48563932a60ebcdea33be3c383;hpb=b8e7e1f0589c9aaa7a49866aff065b346cad7ec1;p=jalview.git

diff --git a/src/jalview/datamodel/CigarParser.java b/src/jalview/datamodel/CigarParser.java
index cfbe842..a1124d4 100644
--- a/src/jalview/datamodel/CigarParser.java
+++ b/src/jalview/datamodel/CigarParser.java
@@ -170,8 +170,14 @@ public class CigarParser
       break;
     case S:
       // soft clipping - just skip this bit of the read
+      seq.addSequenceFeature(new SequenceFeature("SOFTCLIP", "",
+              nextPos + 1, nextPos + length, "bamfile"));
+      break;
     case H:
       // hard clipping - this stretch will not appear in the read
+      seq.addSequenceFeature(new SequenceFeature("HARDCLIP", "",
+              nextPos + 1, nextPos + length, "bamfile"));
+      break;
     default:
       break;
     }