From fe4666614489b0f7c98ba27c25a4432a5c10677d Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Sat, 3 Mar 2018 11:17:34 +0000 Subject: [PATCH] =?utf8?q?JAL-2909=20soft=20clip=20and=20handclap=20features?= =?utf8?q?=20(should=20use=20SO=20terms=20for=20=E2=80=98Clipped=E2=80=99)?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- src/jalview/datamodel/CigarParser.java | 6 ++++++ 1 file changed, 6 insertions(+) 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; } -- 1.7.10.2