From 4f17004590522d139394ed127bbc4647fffbc2c6 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 8 Apr 2011 03:34:50 +0000
Subject: [PATCH] Allow walkers to enforce the ordering in which ReadFilters
 are applied (so that they're now done in the order specified in the walker). 
 Useful if you have a computationally expensive filter (like adaptor clipping)
 that should only be applied to reads passing all other filters.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5600 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/gatk/WalkerManager.java   | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
index f73f65e9f..21ce28173 100755
--- a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
@@ -445,10 +445,14 @@ public class WalkerManager extends PluginManager<Walker> {
      * @return An array of types extending from SamRecordFilter.  Will never be null.
      */
     public static Collection<Class<? extends SamRecordFilter>> getReadFilterTypes(Class<?> walkerClass) {
-        Set<Class<? extends SamRecordFilter>> filterTypes = new HashSet<Class<? extends SamRecordFilter>>();
+        List<Class<? extends SamRecordFilter>> filterTypes = new ArrayList<Class<? extends SamRecordFilter>>();
         while(walkerClass != null) {
-            if(walkerClass.isAnnotationPresent(ReadFilters.class))
-                filterTypes.addAll(Arrays.asList(walkerClass.getAnnotation(ReadFilters.class).value()));
+            if(walkerClass.isAnnotationPresent(ReadFilters.class)) {
+                for ( Class c : walkerClass.getAnnotation(ReadFilters.class).value() ) {
+                    if( !filterTypes.contains(c) )
+                        filterTypes.add(c);
+                }
+            }
             walkerClass = walkerClass.getSuperclass();
         }
         return filterTypes;