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CpG is no longer a standard stratification. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5273 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2011-02-18 07:17:35 +00:00
parent 9ddee96f93
commit cb95e68fc0
2 changed files with 8 additions and 8 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
View File

@ -9,7 +9,7 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatc
import java.util.ArrayList;
import java.util.Set;
public class CpG extends VariantStratifier implements StandardStratification {
public class CpG extends VariantStratifier {
private ArrayList<String> states;
@Override

14
java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -333,7 +333,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
public void testSelect1() {
String extraArgs = "-L 1:1-10,000,000";
for (String tests : testsEnumerations) {
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -o %s",
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
1, Arrays.asList("0eed0ea48cb55164ba8d9383b96811c9"));
executeTestParallel("testSelect1", spec);
//executeTest("testSelect1", spec);
@ -353,7 +353,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
public void testVEGenotypeConcordance() {
String vcfFiles[] = {"GenotypeConcordanceEval.vcf", "GenotypeConcordanceEval.vcf.gz"};
for (String vcfFile : vcfFiles) {
WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -B:eval,VCF " + validationDataLocation + vcfFile + " -B:comp,VCF " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s",
WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG -B:eval,VCF " + validationDataLocation + vcfFile + " -B:comp,VCF " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s",
1,
Arrays.asList("1387fcf8d5c53ff2c820fe79cc999bcf"));
executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec);
@ -365,8 +365,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testVESimple() {
HashMap<String, String> expectations = new HashMap<String, String>();
expectations.put("-L 1:1-10,000,000", "60bbf3539212ff4ecb172e0ef848b297");
expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "c4a178c58464e367a5a0b22a99f35b25");
expectations.put("-L 1:1-10,000,000 -ST CpG", "60bbf3539212ff4ecb172e0ef848b297");
expectations.put("-L 1:1-10,000,000 -ST CpG -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "c4a178c58464e367a5a0b22a99f35b25");
for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
String extraArgs = entry.getKey();
@ -384,7 +384,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testVEComplex() {
HashMap<String, String> expectations = new HashMap<String, String>();
String extraArgs1 = "-L " + validationDataLocation + "chr1_b36_pilot3.interval_list -family NA19238+NA19239=NA19240 -mvq 30 -EV MendelianViolationEvaluator" +
String extraArgs1 = "-L " + validationDataLocation + "chr1_b36_pilot3.interval_list -family NA19238+NA19239=NA19240 -mvq 30 -EV MendelianViolationEvaluator -ST CpG" +
" -B:dbsnp_130,dbSNP " + GATKDataLocation + "dbsnp_130_b36.rod" +
" -B:comp_hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
@ -408,7 +408,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testCompVsEvalAC() {
String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -EV GenotypeConcordance -B:evalYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.fake.genotypes.ac.test.vcf";
String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance -B:evalYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.fake.genotypes.ac.test.vcf";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("2b969088abbfe69337fc3af663278323"));
executeTestParallel("testCompVsEvalAC",spec);
//executeTest("testCompVsEvalAC",spec);
@ -420,7 +420,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testTranches() {
String extraArgs = "-T VariantEval -R "+ hg18Reference +" -B:eval,vcf " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -tf " + testDir + "tranches.6.txt";
String extraArgs = "-T VariantEval -R "+ hg18Reference +" -B:eval,vcf " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -ST CpG -tf " + testDir + "tranches.6.txt";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("b018ca01b374def71fcd1bf164326485"));
executeTestParallel("testTranches",spec);
//executeTest("testTranches",spec);