From f48d4cfa79cdae7bc02abf913cbd1ff3b8716786 Mon Sep 17 00:00:00 2001
From: Roger Zurawicki <roger@broadinstitute.org>
Date: Fri, 18 Nov 2011 00:19:59 -0500
Subject: [PATCH] Bug fix: fully clipping GATKSAMRecords and flushing ops

Reads that are emptied after clipping become new GATKSAMRecords.
When applying ClippingOps, the ops are cleared after the clipping
---
 .../broadinstitute/sting/utils/clipreads/ReadClipper.java    | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
index 6e4ddddc4..e4806838d 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
@@ -121,7 +121,7 @@ public class ReadClipper {
 
     public GATKSAMRecord hardClipSoftClippedBases () {
         if (read.isEmpty())
-            return read;
+            return new GATKSAMRecord(read.getHeader());
 
         int readIndex = 0;
         int cutLeft = -1;            // first position to hard clip (inclusive)
@@ -171,6 +171,9 @@ public class ReadClipper {
                     clippedRead = op.apply(algorithm, clippedRead);
                 }
                 wasClipped = true;
+                ops.clear();
+                if ( clippedRead.isEmpty() )
+                    return new GATKSAMRecord( clippedRead.getHeader() );
                 return clippedRead;
             } catch (CloneNotSupportedException e) {
                 throw new RuntimeException(e); // this should never happen