From dea72c576e559e23847d586ce5ce99b2c969356f Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 10 Jul 2009 18:34:44 +0000
Subject: [PATCH] use the filter to ignore 454 reads in the traversal to speed
 up cleaning (since there's less area to actually clean against)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1220 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/gatk/walkers/indels/IntervalCleanerWalker.java | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
index 5e34544e8..a6e45fac1 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
@@ -4,18 +4,20 @@ import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.walkers.LocusWindowWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
+import org.broadinstitute.sting.gatk.walkers.ReadFilters;
 import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.filters.Platform454Filter;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.playground.indels.*;
 
 import net.sf.samtools.*;
-import net.sf.samtools.SAMFileHeader.SortOrder;
 
 import java.util.*;
 import java.io.File;
 import java.io.FileWriter;
  
 @WalkerName("IntervalCleaner")
+@ReadFilters(Platform454Filter.class)
 public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer> {
     @Argument(fullName="allow454Reads", shortName="454", doc="process 454 reads", required=false)
     boolean allow454 = false;