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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
This commit is contained in:
chartl 2010-01-23 18:19:28 +00:00
parent ac983e7a0b
commit d6b9b788a8
2 changed files with 6 additions and 6 deletions
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4
java/src/org/broadinstitute/sting/gatk/refdata/PlinkRodWithGenomeLoc.java → java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java
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@ -20,7 +20,7 @@ import net.sf.samtools.SAMFileHeader;
* Time: 10:24:18 AM * Time: 10:24:18 AM
* To change this template use File | Settings | File Templates. * 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", 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")); "Paternal ID","Maternal ID","Phenotype", "FID","IID","PAT","MAT","SEX","PHENOTYPE"));
private final byte SNP_MAJOR_MODE = 1; private final byte SNP_MAJOR_MODE = 1;
@ -37,7 +37,7 @@ public class PlinkRodWithGenomeLoc extends BasicReferenceOrderedDatum implements
// // // CONSTRUCTOR // // // // // // CONSTRUCTOR // // //
public PlinkRodWithGenomeLoc(String name) { public PlinkRod(String name) {
super(name); super(name);
} }

8
java/test/org/broadinstitute/sting/gatk/refdata/PlinkRodTest.java
View File

@ -47,7 +47,7 @@ public class PlinkRodTest extends BaseTest {
@Test @Test
public void testStandardPedFile() { public void testStandardPedFile() {
PlinkRodWithGenomeLoc rod = new PlinkRodWithGenomeLoc("test"); PlinkRod rod = new PlinkRod("test");
try { try {
rod.initialize( new File("/humgen/gsa-hpprojects/GATK/data/Validation_Data/test/plink_rod_test/standard_plink_test.ped") ); rod.initialize( new File("/humgen/gsa-hpprojects/GATK/data/Validation_Data/test/plink_rod_test/standard_plink_test.ped") );
} catch ( FileNotFoundException e ) { } catch ( FileNotFoundException e ) {
@ -117,7 +117,7 @@ public class PlinkRodTest extends BaseTest {
@Test @Test
public void testStandardPedFileWithIndels() { public void testStandardPedFileWithIndels() {
PlinkRodWithGenomeLoc rod = new PlinkRodWithGenomeLoc("test"); PlinkRod rod = new PlinkRod("test");
try { try {
rod.initialize(new File("/humgen/gsa-hpprojects/GATK/data/Validation_Data/test/plink_rod_test/standard_plink_with_indels.ped") ); rod.initialize(new File("/humgen/gsa-hpprojects/GATK/data/Validation_Data/test/plink_rod_test/standard_plink_with_indels.ped") );
} catch ( FileNotFoundException e) { } catch ( FileNotFoundException e) {
@ -155,7 +155,7 @@ public class PlinkRodTest extends BaseTest {
@Test @Test
public void testBinaryPedFileNoIndels() { public void testBinaryPedFileNoIndels() {
PlinkRodWithGenomeLoc rod = new PlinkRodWithGenomeLoc("binaryTest1"); PlinkRod rod = new PlinkRod("binaryTest1");
try { try {
rod.initialize(new File("/humgen/gsa-hpprojects/GATK/data/Validation_Data/test/plink_rod_test/binary_noindel_test.bed")); rod.initialize(new File("/humgen/gsa-hpprojects/GATK/data/Validation_Data/test/plink_rod_test/binary_noindel_test.bed"));
} catch (FileNotFoundException e) { } catch (FileNotFoundException e) {
@ -206,7 +206,7 @@ public class PlinkRodTest extends BaseTest {
@Test @Test
public void testIndelBinary() { public void testIndelBinary() {
PlinkRodWithGenomeLoc rod = new PlinkRodWithGenomeLoc("binaryTest2"); PlinkRod rod = new PlinkRod("binaryTest2");
try { try {
rod.initialize(new File("/humgen/gsa-hpprojects/GATK/data/Validation_Data/test/plink_rod_test/binary_indel_test.bed")); rod.initialize(new File("/humgen/gsa-hpprojects/GATK/data/Validation_Data/test/plink_rod_test/binary_indel_test.bed"));
} catch (FileNotFoundException e) { } catch (FileNotFoundException e) {