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 headerEntries = new HashSet(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) {