From 71d68c3d9384924897d3c264907e8ca79faf55ef Mon Sep 17 00:00:00 2001
From: Ron Levine <rlevine@broadinstitute.org>
Date: Thu, 5 Mar 2015 20:30:46 -0500
Subject: [PATCH] Fix NotPrimaryAlignmentFilter documentation

---
 .../gatk/engine/filters/NotPrimaryAlignmentFilter.java          | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java
index b09e1f6d5..4c8f412e2 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java
@@ -28,7 +28,7 @@ package org.broadinstitute.gatk.engine.filters;
 import htsjdk.samtools.SAMRecord;
 
 /**
- * Filter out duplicate reads.
+ * Filter out reads that are secondary alignments (not one of the best alignments)
  *
  * @author rpoplin
  * @since Dec 9, 2009