From 58f7ae8628831c764f366edf7cc305ee0384e562 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 8 Jun 2009 18:44:29 +0000
Subject: [PATCH] better filtering, plus deal with case where user doesn't
 input maxlength

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@939 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/gatk/walkers/indels/IndelIntervalWalker.java    | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelIntervalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelIntervalWalker.java
index 95ae30e1b..4a4f6cc31 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelIntervalWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelIntervalWalker.java
@@ -25,7 +25,8 @@ public class IndelIntervalWalker extends ReadWalker<IndelIntervalWalker.Interval
 
     public boolean filter(char[] ref, SAMRecord read) {
         return ( !read.getReadUnmappedFlag() &&            // mapped
-                 read.getReadLength() <= maxReadLength &&  // not too big
+                 (maxReadLength < 0 || read.getReadLength() <= maxReadLength) &&  // not too big
+                 read.getMappingQuality() != 0 &&          // positive mapping quality
                  read.getAlignmentBlocks().size() > 1);    // indel
     }