From d6b9b788a8d461b618b4026eefc77628f6966680 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sat, 23 Jan 2010 18:19:28 +0000
Subject: [PATCH] Renamed -- PlinkRodWithGenomeLoc --> PlinkRod

Since binary files do not need encoded locus information in the SNP names there's no need to suggest that it is so in the name of the rod



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2671 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../refdata/{PlinkRodWithGenomeLoc.java => PlinkRod.java} | 4 ++--
 .../broadinstitute/sting/gatk/refdata/PlinkRodTest.java   | 8 ++++----
 2 files changed, 6 insertions(+), 6 deletions(-)
 rename java/src/org/broadinstitute/sting/gatk/refdata/{PlinkRodWithGenomeLoc.java => PlinkRod.java} (99%)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRodWithGenomeLoc.java b/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java
similarity index 99%
rename from java/src/org/broadinstitute/sting/gatk/refdata/PlinkRodWithGenomeLoc.java
rename to java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java
index bd7f96e8c..589f02a1c 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRodWithGenomeLoc.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java
@@ -20,7 +20,7 @@ import net.sf.samtools.SAMFileHeader;
  * Time: 10:24:18 AM
  * To change this template use File | Settings | File Templates.
  */
-public class PlinkRodWithGenomeLoc extends BasicReferenceOrderedDatum implements ReferenceOrderedDatum {
+public class PlinkRod extends BasicReferenceOrderedDatum implements ReferenceOrderedDatum {
     private final Set<String> headerEntries = new HashSet<String>(Arrays.asList("#Family ID","Individual ID","Sex",
                 "Paternal ID","Maternal ID","Phenotype", "FID","IID","PAT","MAT","SEX","PHENOTYPE"));
     private final byte SNP_MAJOR_MODE = 1;
@@ -37,7 +37,7 @@ public class PlinkRodWithGenomeLoc extends BasicReferenceOrderedDatum implements
 
     // // // CONSTRUCTOR // // //
 
-    public PlinkRodWithGenomeLoc(String name) {
+    public PlinkRod(String name) {
         super(name);
     }
 
diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/PlinkRodTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/PlinkRodTest.java
index e194cd85d..6b85a228c 100755
--- a/java/test/org/broadinstitute/sting/gatk/refdata/PlinkRodTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/refdata/PlinkRodTest.java
@@ -47,7 +47,7 @@ public class PlinkRodTest extends BaseTest {
 
     @Test
     public void testStandardPedFile() {
-        PlinkRodWithGenomeLoc rod = new PlinkRodWithGenomeLoc("test");
+        PlinkRod rod = new PlinkRod("test");
         try {
             rod.initialize( new File("/humgen/gsa-hpprojects/GATK/data/Validation_Data/test/plink_rod_test/standard_plink_test.ped") );
         } catch ( FileNotFoundException e ) {
@@ -117,7 +117,7 @@ public class PlinkRodTest extends BaseTest {
 
     @Test
     public void testStandardPedFileWithIndels() {
-        PlinkRodWithGenomeLoc rod = new PlinkRodWithGenomeLoc("test");
+        PlinkRod rod = new PlinkRod("test");
         try {
             rod.initialize(new File("/humgen/gsa-hpprojects/GATK/data/Validation_Data/test/plink_rod_test/standard_plink_with_indels.ped") );
         } catch ( FileNotFoundException e) {
@@ -155,7 +155,7 @@ public class PlinkRodTest extends BaseTest {
 
     @Test
     public void testBinaryPedFileNoIndels() {
-        PlinkRodWithGenomeLoc rod = new PlinkRodWithGenomeLoc("binaryTest1");
+        PlinkRod rod = new PlinkRod("binaryTest1");
         try {
             rod.initialize(new File("/humgen/gsa-hpprojects/GATK/data/Validation_Data/test/plink_rod_test/binary_noindel_test.bed"));
         } catch (FileNotFoundException e) {
@@ -206,7 +206,7 @@ public class PlinkRodTest extends BaseTest {
 
     @Test
     public void testIndelBinary() {
-        PlinkRodWithGenomeLoc rod = new PlinkRodWithGenomeLoc("binaryTest2");
+        PlinkRod rod = new PlinkRod("binaryTest2");
         try {
             rod.initialize(new File("/humgen/gsa-hpprojects/GATK/data/Validation_Data/test/plink_rod_test/binary_indel_test.bed"));
         } catch (FileNotFoundException e) {