diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java index e0956f7bf..88ebd5e72 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java @@ -64,7 +64,7 @@ public class CountVariants extends VariantEvaluator { @DataPoint(description = "deletion to insertion ratio") double deletionInsertionRatio = 0; - public CountVariants(VariantEval2Walker parent) { + public CountVariants(VariantEvalWalker parent) { // don't do anything } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/DbSNPPercentage.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/DbSNPPercentage.java index 74a13ea24..8b28f2439 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/DbSNPPercentage.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/DbSNPPercentage.java @@ -41,7 +41,7 @@ public class DbSNPPercentage extends VariantEvaluator { @DataPoint(name = "% concordant", description = "the concordance rate") double concordantRate = 0.0; - public DbSNPPercentage(VariantEval2Walker parent) { + public DbSNPPercentage(VariantEvalWalker parent) { // don't do anything } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java index a8b16df27..19269aeb9 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java @@ -187,7 +187,7 @@ public class GenotypeConcordance extends VariantEvaluator { private HashSet missedValidationData = new HashSet(); - public GenotypeConcordance(VariantEval2Walker parent) { + public GenotypeConcordance(VariantEvalWalker parent) { // don't do anything } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java index 6ee35ba78..3dda1c4df 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java @@ -59,7 +59,7 @@ public class MendelianViolationEvaluator extends VariantEvaluator { @DataPoint(name="KHV->PHR",description = "number of child hom variant calls where the parent was hom ref") long KidHomVar_ParentHomRef; - VariantEval2Walker parent; + VariantEvalWalker parent; TrioStructure trio; @@ -83,7 +83,7 @@ public class MendelianViolationEvaluator extends VariantEvaluator { } } - public MendelianViolationEvaluator(VariantEval2Walker parent) { + public MendelianViolationEvaluator(VariantEvalWalker parent) { this.parent = parent; if (enabled()) { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TiTvVariantEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TiTvVariantEvaluator.java index b059b6bea..74dd95464 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TiTvVariantEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TiTvVariantEvaluator.java @@ -23,7 +23,7 @@ public class TiTvVariantEvaluator extends VariantEvaluator { @DataPoint(name = "ti/tv ratio standard", description = "the transition to transversion ratio") double TiTvRatioStandard = 0.0; - public TiTvVariantEvaluator(VariantEval2Walker parent) { + public TiTvVariantEvaluator(VariantEvalWalker parent) { // don't do anything } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ValidationRate.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ValidationRate.java index eba2741b0..466e71802 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ValidationRate.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ValidationRate.java @@ -62,7 +62,7 @@ public class ValidationRate extends VariantEvaluator { private SiteStats evalOverlapAtMono = new SiteStats(); private SiteStats evalOverlapAtPoly = new SiteStats(); - public ValidationRate(VariantEval2Walker parent) { + public ValidationRate(VariantEvalWalker parent) { // don't do anything } @@ -108,8 +108,6 @@ public class ValidationRate extends VariantEvaluator { if (rawValidationData!= null && rawValidationData.hasGenotypes() && rawValidationData.isNotFiltered()) { VariantContext validation = rawValidationData; - //if ( eval != null ) // todo -- remove me when I can get the header from the VariantEval engine - // validation = rawValidationData.subContextFromGenotypes(eval.getGenotypes().values()); SiteStats overlap; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval2Walker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java similarity index 99% rename from java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval2Walker.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index b2ec2ab0c..2e284df48 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval2Walker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -82,7 +82,7 @@ import java.util.*; /** * Test routine for new VariantContext object */ -public class VariantEval2Walker extends RodWalker { +public class VariantEvalWalker extends RodWalker { // -------------------------------------------------------------------------------------------------------------- // // walker arguments diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantQualityScore.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantQualityScore.java index 1054756bc..895a1c115 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantQualityScore.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantQualityScore.java @@ -207,7 +207,7 @@ public class VariantQualityScore extends VariantEvaluator { } } - public VariantQualityScore(VariantEval2Walker parent) { + public VariantQualityScore(VariantEvalWalker parent) { // don't do anything } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval2IntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java similarity index 87% rename from java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval2IntegrationTest.java rename to java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index ca9f9fb8c..04a92fcc6 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval2IntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -7,8 +7,8 @@ import java.util.Arrays; import java.util.HashMap; import java.util.Map; -public class VariantEval2IntegrationTest extends WalkerTest { - private static String cmdRoot = "-T VariantEval2" + +public class VariantEvalIntegrationTest extends WalkerTest { + private static String cmdRoot = "-T VariantEval" + " -R " + oneKGLocation + "reference/human_b36_both.fasta -reportType Grep -all"; private static String root = cmdRoot + @@ -16,7 +16,7 @@ public class VariantEval2IntegrationTest extends WalkerTest { " -B eval,VCF," + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf"; @Test - public void testVE2Simple() { + public void testVESimple() { HashMap expectations = new HashMap(); expectations.put("-L 1:1-10,000,000", "278c9c2798fed510a0cc3e65f3749b26"); expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "98ceb8dab20af47e724a0b47f82ba698"); @@ -28,12 +28,12 @@ public class VariantEval2IntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( root + " " + extraArgs + " -o %s", 1, // just one output file Arrays.asList(md5)); - executeTest("testVE2Simple", spec); + executeTest("testVESimple", spec); } } @Test - public void testVE2Complex() { + public void testVEComplex() { HashMap expectations = new HashMap(); String extraArgs1 = "-L " + validationDataLocation + "chr1_b36_pilot3.interval_list -family NA19238+NA19239=NA19240 -MVQ 30" + " -B dbsnp_130,dbSNP," + GATKDataLocation + "dbsnp_130_b36.rod" + @@ -51,16 +51,16 @@ public class VariantEval2IntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( root + " " + extraArgs1 + extraArgs2 + " -o %s", 1, // just one output file Arrays.asList(md5)); - executeTest("testVE2Complex", spec); + executeTest("testVEComplex", spec); } } @Test - public void testVE2WriteVCF() { + public void testVEWriteVCF() { String extraArgs = "-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 30"; WalkerTestSpec spec = new WalkerTestSpec( root + " " + extraArgs + " -o %s -outputVCF %s", 2, Arrays.asList("782b569e213b494c19598d3f4dacba49", "a3ce1d70d8ae3874807e9d61994d42af")); - executeTest("testVE2WriteVCF", spec); + executeTest("testVEWriteVCF", spec); } }