From 9143822822fd3ac478085ddaeb60492270657c97 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 17 Dec 2009 17:41:42 +0000
Subject: [PATCH] Fix half-hearted attempt to try to move classes from package
 to package.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2389 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/qc/CountLociWalker.java            | 4 +++-
 .../sting/gatk/walkers/qc/CountReadsWalker.java           | 5 ++++-
 .../sting/gatk/walkers/qc/CountRodByRefWalker.java        | 8 ++++----
 .../sting/gatk/walkers/qc/CountRodWalker.java             | 3 ++-
 packages/GenomeAnalysisTK.xml                             | 8 ++++----
 5 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java
index 1241d18c2..e5480c6b3 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java
@@ -1,8 +1,10 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.gatk.walkers.qc;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 
 /**
  * Walks over the input data set, calculating the total number of covered loci for diagnostic purposes.
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java
index 5915bcb1b..84a424e9c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java
@@ -1,6 +1,9 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.gatk.walkers.qc;
 
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 
 /**
  * Walks over the input data set, calculating the number of reads seen for diagnostic purposes.
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java
index e0a0916a6..d0018d0ed 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java
@@ -1,9 +1,9 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.gatk.walkers.qc;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.walkers.RefWalker;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
@@ -26,8 +26,8 @@ public class CountRodByRefWalker extends RefWalker<CountRodWalker.Datum, Pair<Ex
     public void initialize() {
         crw.verbose = verbose;
         crw.showSkipped = showSkipped;
-        crw.out = out;
-        crw.err = err;
+        JVMUtils.setFieldValue(JVMUtils.findField(CountRodWalker.class,"out"),crw,out);
+        JVMUtils.setFieldValue(JVMUtils.findField(CountRodWalker.class,"err"),crw,err);
     }
 
     public CountRodWalker.Datum map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java
index 5dcb14611..78913ce5d 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java
@@ -1,10 +1,11 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.gatk.walkers.qc;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.RODRecordList;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml
index 02104f44d..acffff24c 100644
--- a/packages/GenomeAnalysisTK.xml
+++ b/packages/GenomeAnalysisTK.xml
@@ -6,11 +6,11 @@
     <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
     <dependencies>
       <package>org.broadinstitute.sting.gatk.filters</package>
-      <class>org.broadinstitute.sting.gatk.walkers.CountLociWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.CountReadsWalker</class>
       <class>org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker</class>
       <class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
       <class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker</class>
       <class>org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker</class>
       <!-- Quality scores recalibration -->
       <class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
@@ -66,11 +66,11 @@
   </executable>
   <resources>
     <!-- GATK sample code and build scripts -->
-    <file>java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java</file>
-    <file>java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java</file>
     <file>java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java</file>
     <file>java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java</file>
     <file>java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java</file>
+    <file>java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java</file>
+    <file>java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java</file>
     <file>java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java</file>
     <file>java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java</file>
     <file>java/src/org/broadinstitute/sting/gatk/examples/build.xml</file>