From ad63633b1cf02e027c7c730d28245e5f306a270f Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 31 Mar 2009 20:28:20 +0000
Subject: [PATCH] forgot to change the chunks dir to shards before

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@241 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/gatk/dataSources/DataSource.java   | 2 +-
 .../gatk/dataSources/{chunks => shards}/BasicDataShard.java     | 2 +-
 .../sting/gatk/dataSources/{chunks => shards}/DataShard.java    | 2 +-
 .../sting/gatk/dataSources/{chunks => shards}/LociShard.java    | 2 +-
 .../sting/gatk/dataSources/{chunks => shards}/ReadShard.java    | 2 +-
 .../sting/gatk/dataSources/{chunks => shards}/SAMDataShard.java | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)
 rename java/src/org/broadinstitute/sting/gatk/dataSources/{chunks => shards}/BasicDataShard.java (91%)
 rename java/src/org/broadinstitute/sting/gatk/dataSources/{chunks => shards}/DataShard.java (90%)
 rename java/src/org/broadinstitute/sting/gatk/dataSources/{chunks => shards}/LociShard.java (98%)
 rename java/src/org/broadinstitute/sting/gatk/dataSources/{chunks => shards}/ReadShard.java (97%)
 rename java/src/org/broadinstitute/sting/gatk/dataSources/{chunks => shards}/SAMDataShard.java (94%)

diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/DataSource.java b/java/src/org/broadinstitute/sting/gatk/dataSources/DataSource.java
index 2ddcea799..47c67c7e8 100644
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/DataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/dataSources/DataSource.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.dataSources;
 
-import org.broadinstitute.sting.gatk.dataSources.chunks.DataShard;
+import org.broadinstitute.sting.gatk.dataSources.shards.DataShard;
 
 /**
  * User: aaron
diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/chunks/BasicDataShard.java b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/BasicDataShard.java
similarity index 91%
rename from java/src/org/broadinstitute/sting/gatk/dataSources/chunks/BasicDataShard.java
rename to java/src/org/broadinstitute/sting/gatk/dataSources/shards/BasicDataShard.java
index 76f111674..8a7096da1 100644
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/chunks/BasicDataShard.java
+++ b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/BasicDataShard.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.dataSources.chunks;
+package org.broadinstitute.sting.gatk.dataSources.shards;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/chunks/DataShard.java b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/DataShard.java
similarity index 90%
rename from java/src/org/broadinstitute/sting/gatk/dataSources/chunks/DataShard.java
rename to java/src/org/broadinstitute/sting/gatk/dataSources/shards/DataShard.java
index d40f9b6f3..994fbcb16 100644
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/chunks/DataShard.java
+++ b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/DataShard.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.dataSources.chunks;
+package org.broadinstitute.sting.gatk.dataSources.shards;
 
 import java.util.Iterator;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/chunks/LociShard.java b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/LociShard.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/gatk/dataSources/chunks/LociShard.java
rename to java/src/org/broadinstitute/sting/gatk/dataSources/shards/LociShard.java
index 7dc6913de..c1f4a5a7f 100644
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/chunks/LociShard.java
+++ b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/LociShard.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.dataSources.chunks;
+package org.broadinstitute.sting.gatk.dataSources.shards;
 
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.dataSources.datum.LocusDatum;
diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/chunks/ReadShard.java b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ReadShard.java
similarity index 97%
rename from java/src/org/broadinstitute/sting/gatk/dataSources/chunks/ReadShard.java
rename to java/src/org/broadinstitute/sting/gatk/dataSources/shards/ReadShard.java
index a083ce45d..5854777a9 100644
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/chunks/ReadShard.java
+++ b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ReadShard.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.dataSources.chunks;
+package org.broadinstitute.sting.gatk.dataSources.shards;
 
 import edu.mit.broad.picard.sam.MergingSamRecordIterator;
 import org.broadinstitute.sting.gatk.dataSources.datum.ReadDatum;
diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/chunks/SAMDataShard.java b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/SAMDataShard.java
similarity index 94%
rename from java/src/org/broadinstitute/sting/gatk/dataSources/chunks/SAMDataShard.java
rename to java/src/org/broadinstitute/sting/gatk/dataSources/shards/SAMDataShard.java
index 53b105dcf..b178bdfd9 100644
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/chunks/SAMDataShard.java
+++ b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/SAMDataShard.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.dataSources.chunks;
+package org.broadinstitute.sting.gatk.dataSources.shards;
 
 import edu.mit.broad.picard.sam.MergingSamRecordIterator;
 import net.sf.samtools.SAMRecord;