From 6fe80d53d0cbf6026bf3b2bea90214ce8a13b7c2 Mon Sep 17 00:00:00 2001
From: sooheelee <shlee@broadinstitute.org>
Date: Thu, 23 Jun 2016 16:20:00 -0400
Subject: [PATCH] Improve documentation

Clarified that this also filters supplementary alignments.
---
 .../gatk/engine/filters/NotPrimaryAlignmentFilter.java      | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

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 3088e26f7..386b86cc3 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
@@ -28,9 +28,9 @@ package org.broadinstitute.gatk.engine.filters;
 import htsjdk.samtools.SAMRecord;
 
 /**
- * Filter out reads that are secondary alignments
+ * Filter out reads that are non-primary alignments
  *
- * <p>This filter recognizes the SAM flag that identifies secondary alignments (ie not the best alignment).
+ * <p>This filter recognizes the SAM flag that identifies secondary and supplementary alignments, i.e. non-primary alignments.
  * It is intended to ensure that only reads that are likely to be mapped in the right place, and therefore to be
  * informative, will be used in analysis.</p>
  *
@@ -53,4 +53,4 @@ public class NotPrimaryAlignmentFilter extends ReadFilter {
     public boolean filterOut( final SAMRecord read ) {
         return read.getNotPrimaryAlignmentFlag();
     }
-}
\ No newline at end of file
+}