From 04909fa6ad42b93288f68857baabc94809170cc3 Mon Sep 17 00:00:00 2001 From: ebanks Date: Wed, 14 Apr 2010 17:46:39 +0000 Subject: [PATCH] Removing arbitrary selects git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3169 348d0f76-0448-11de-a6fe-93d51630548a --- .../walkers/varianteval2/VariantEval2Walker.java | 4 ++-- .../varianteval2/VariantEval2IntegrationTest.java | 10 +++++----- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java index 02f7c4dd9..bcd4af2e4 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java @@ -89,10 +89,10 @@ public class VariantEval2Walker extends RodWalker { // -------------------------------------------------------------------------------------------------------------- @Argument(shortName="select", doc="One or more stratifications to use when evaluating the data", required=false) - protected String[] SELECT_EXPS = {"QUAL > 500.0", "HARD_TO_VALIDATE==1", "GATK_STANDARD==1"}; + protected String[] SELECT_EXPS = {}; @Argument(shortName="selectName", doc="Names to use for the list of stratifications (must be a 1-to-1 mapping)", required=false) - protected String[] SELECT_NAMES = {"q500plus", "low_mapq", "gatk_std_filters"}; + protected String[] SELECT_NAMES = {}; @Argument(shortName="known", doc="Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets", required=false) protected String[] KNOWN_NAMES = {"dbsnp"}; 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 951e35fcd..82d217bdf 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", "44fca2e43dade85ca16fa9e323e4cc9b"); - expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "6910a9a49625a8df2ad797d751be9ed6"); + expectations.put("-L 1:1-10,000,000", "8b93fda4a4b61c8b284063de62c84644"); + expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "d232220a2b0d13e3a2b077310cad4540"); 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 = "a525597a34cd3fa84c75263dbd026acb"; // next two examples should be the same! + String eqMD5s = "9e5a207f445febc8b432254a6cf9a182"; // next two examples should be the same! expectations.put("", eqMD5s); expectations.put(" -known comp_hapmap -known dbsnp", eqMD5s); - expectations.put(" -known comp_hapmap", "35feda6c361408755e7f1dae245462d7"); + expectations.put(" -known comp_hapmap", "f6aedc4911c5c9ebfd4de1383bb1aafa"); 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("0d2ac5ea23f8cd3237836080c722711b", "a3ce1d70d8ae3874807e9d61994d42af")); + Arrays.asList("e11a104981a3d959458bc11d3c540355", "a3ce1d70d8ae3874807e9d61994d42af")); executeTest("testVE2WriteVCF", spec); } }