From 66a8b36cf55c043e1e72ce51bb5b44ffe08cda86 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Sat, 27 Aug 2011 23:25:26 -0400
Subject: [PATCH] Fixed most indexing bugs

* added bases and quals to consensus
* fixed consensus read cigar generation.
---
 .../org/broadinstitute/sting/utils/clipreads/ReadClipper.java | 4 ++++
 1 file changed, 4 insertions(+)

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 44b77533f..a4155db72 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
@@ -4,6 +4,7 @@ import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.SAMRecord;
 import org.broad.tribble.util.PositionalStream;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.jets3t.service.multi.ThreadedStorageService;
 
@@ -54,6 +55,9 @@ public class ReadClipper {
         int start = (refStart < 0) ? 0 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart);
         int stop =  (refStop  < 0) ? read.getReadLength() - 1 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop);
 
+        if (start < 0 || stop > read.getReadLength() - 1)
+            throw new ReviewedStingException("Trying to clip before the start or after the end of a read");
+
         //System.out.println("Clipping start/stop: " + start + "/" + stop);
         this.addOp(new ClippingOp(start, stop));
         return clipRead(ClippingRepresentation.HARDCLIP_BASES);