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JAL-2909 soft clip and handclap features (should use SO terms for ‘Clipped’)
[jalview.git]
/
src
/
jalview
/
datamodel
/
CigarParser.java
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
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
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;
}
default:
break;
}