JAL-2909 soft clip and handclap features (should use SO terms for ‘Clipped’)

diff --git a/src/jalview/datamodel/CigarParser.java b/src/jalview/datamodel/CigarParser.java
index cfbe842..a1124d4 100644 (file)
--- 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;
     }