From 5f7564bf0ae441e2a689f42772b710ac63d2b115 Mon Sep 17 00:00:00 2001 From: ebanks Date: Thu, 15 Apr 2010 18:08:07 +0000 Subject: [PATCH] Better naming of output columns git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3175 348d0f76-0448-11de-a6fe-93d51630548a --- .../walkers/varianteval2/DbSNPPercentage.java | 21 ++++++++----------- .../VariantEval2IntegrationTest.java | 10 ++++----- 2 files changed, 14 insertions(+), 17 deletions(-) diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/DbSNPPercentage.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/DbSNPPercentage.java index 11cb7829e..95daf705e 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/DbSNPPercentage.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/DbSNPPercentage.java @@ -8,9 +8,6 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele; import org.broadinstitute.sting.playground.utils.report.tags.Analysis; import org.broadinstitute.sting.playground.utils.report.tags.DataPoint; -import java.util.List; -import java.util.Arrays; - /** * The Broad Institute * SOFTWARE COPYRIGHT NOTICE AGREEMENT @@ -32,11 +29,11 @@ public class DbSNPPercentage extends VariantEvaluator { @DataPoint(name = "novel snps", description = "number of total snp sites") private long novelSites = 0; - @DataPoint(name = "snps at dbsnp", description = "number of SNP sites at DPSNP sites") - private long nSNPsAtdbSNPs = 0; + @DataPoint(name = "snps at comp", description = "number of SNP sites at comp sites") + private long nSNPsAtComp = 0; - @DataPoint(name = "% eval in comp", description = "percentage of SNP sites at DPSNP sites") - private double dbSNPRate = 0.0; + @DataPoint(name = "% snps at comp", description = "percentage of SNP sites at comp sites") + private double compRate = 0.0; @DataPoint(name = "concordant", description = "number of concordant sites") private long nConcordant = 0; @@ -56,12 +53,12 @@ public class DbSNPPercentage extends VariantEvaluator { return 2; // we need to see each eval track and each comp track } - public long nNovelSites() { return Math.abs(nEvalSNPs - nSNPsAtdbSNPs); } - public double dbSNPRate() { return rate(nSNPsAtdbSNPs, nEvalSNPs); } - public double concordanceRate() { return rate(nConcordant, nSNPsAtdbSNPs); } + public long nNovelSites() { return Math.abs(nEvalSNPs - nSNPsAtComp); } + public double dbSNPRate() { return rate(nSNPsAtComp, nEvalSNPs); } + public double concordanceRate() { return rate(nConcordant, nSNPsAtComp); } public void finalizeEvaluation() { - dbSNPRate = 100 * dbSNPRate(); + compRate = 100 * dbSNPRate(); concordantRate = 100 * concordanceRate(); novelSites = nNovelSites(); } @@ -94,7 +91,7 @@ public class DbSNPPercentage extends VariantEvaluator { if (evalIsGood) nEvalSNPs++; // count the number of dbSNP events if (dbSNPIsGood && evalIsGood) { - nSNPsAtdbSNPs++; + nSNPsAtComp++; if (!discordantP(eval, dbsnp)) // count whether we're concordant or not with the dbSNP value nConcordant++; diff --git a/java/test/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2IntegrationTest.java b/java/test/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2IntegrationTest.java index 82d217bdf..0438faaa7 100755 --- a/java/test/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2IntegrationTest.java +++ b/java/test/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2IntegrationTest.java @@ -18,8 +18,8 @@ public class VariantEval2IntegrationTest extends WalkerTest { @Test public void testVE2Simple() { HashMap expectations = new HashMap(); - expectations.put("-L 1:1-10,000,000", "8b93fda4a4b61c8b284063de62c84644"); - expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "d232220a2b0d13e3a2b077310cad4540"); + expectations.put("-L 1:1-10,000,000", "278c9c2798fed510a0cc3e65f3749b26"); + expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "98ceb8dab20af47e724a0b47f82ba698"); for ( Map.Entry entry : expectations.entrySet() ) { String extraArgs = entry.getKey(); @@ -39,10 +39,10 @@ public class VariantEval2IntegrationTest extends WalkerTest { " -B dbsnp_130,dbSNP," + GATKDataLocation + "dbsnp_130_b36.rod" + " -B comp_hapmap,VCF," + validationDataLocation + "CEU_hapmap_nogt_23.vcf"; - String eqMD5s = "9e5a207f445febc8b432254a6cf9a182"; // next two examples should be the same! + String eqMD5s = "fe4b6bd3e46d956a829fa08f3594427d"; // next two examples should be the same! expectations.put("", eqMD5s); expectations.put(" -known comp_hapmap -known dbsnp", eqMD5s); - expectations.put(" -known comp_hapmap", "f6aedc4911c5c9ebfd4de1383bb1aafa"); + expectations.put(" -known comp_hapmap", "cb8ce4b0f15e1b01c7aee5106dad4e95"); for ( Map.Entry entry : expectations.entrySet() ) { String extraArgs2 = entry.getKey(); @@ -60,7 +60,7 @@ public class VariantEval2IntegrationTest extends WalkerTest { 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("e11a104981a3d959458bc11d3c540355", "a3ce1d70d8ae3874807e9d61994d42af")); + Arrays.asList("782b569e213b494c19598d3f4dacba49", "a3ce1d70d8ae3874807e9d61994d42af")); executeTest("testVE2WriteVCF", spec); } }