From 585cc880a2f11037213d0cccdfa582782bc6e589 Mon Sep 17 00:00:00 2001 From: aaron Date: Thu, 1 Apr 2010 16:23:14 +0000 Subject: [PATCH] changed jexl expressions to jexl names in the VariantEval2 output, fixed integration test, and fixed a problem where a line was getting dropped in CSV output git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3108 348d0f76-0448-11de-a6fe-93d51630548a --- .../walkers/varianteval2/VariantEval2Walker.java | 6 ++++-- .../utils/report/templates/csv_readable.ftl | 6 ++---- .../varianteval2/VariantEval2IntegrationTest.java | 12 ++++++------ 3 files changed, 12 insertions(+), 12 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 95495f170..042b808a6 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java @@ -3,7 +3,9 @@ package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.*; +import org.broadinstitute.sting.gatk.contexts.variantcontext.MutableVariantContext; +import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext; +import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors; @@ -598,7 +600,7 @@ public class VariantEval2Walker extends RodWalker { */ private List createPrependNodeList(EvaluationContext group) { // add the branching nodes: jexl expression, comparison track, eval track etc - Node jexlNode = new Node("jexl_expression",(group.selectExp != null) ? group.selectExp.exp.toString() : "none","The jexl filtering expression"); + Node jexlNode = new Node("jexl_expression",(group.selectExp != null) ? group.selectExp.name : "none","The jexl filtering expression"); Node compNode = new Node("comparison_name",group.compTrackName,"The comparison track name"); Node evalNode = new Node("evaluation_name",group.evalTrackName,"The evaluation name"); Node filterNode = new Node("filter_name",group.filtered,"The filter name"); diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/templates/csv_readable.ftl b/java/src/org/broadinstitute/sting/playground/utils/report/templates/csv_readable.ftl index 6833d17f1..82a0c54c6 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/templates/csv_readable.ftl +++ b/java/src/org/broadinstitute/sting/playground/utils/report/templates/csv_readable.ftl @@ -9,17 +9,15 @@ Description,${root.description} <#list root.children as analysis> <#if analysis.complex> <#if analysis.value!=currentAnalysis> - <#assign currentAnalysis=analysis.value> + <#assign currentAnalysis=analysis.value> Analysis,${analysis.value} <@emit_tags analysis=analysis/> <@emit_column_names analysis=analysis/> - - <#else> - <@emit_row_values analysis=analysis/> + <@emit_row_values analysis=analysis/> <#-- -------------------- --> 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 5c33328ae..f5957cfb6 100755 --- a/java/test/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2IntegrationTest.java +++ b/java/test/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2IntegrationTest.java @@ -3,9 +3,9 @@ package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2; import org.broadinstitute.sting.WalkerTest; import org.junit.Test; +import java.util.Arrays; import java.util.HashMap; import java.util.Map; -import java.util.Arrays; public class VariantEval2IntegrationTest extends WalkerTest { private static String cmdRoot = "-T VariantEval2" + @@ -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", "ae10d06b5d30ee227c0e1e18661a18f5"); - expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "a9a682734dbb9a574383a6e7ab385dcc"); + expectations.put("-L 1:1-10,000,000", "cb65879db9d00132484fbe7e7c0460b9"); + expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "7126f47b9d87dc4e1e0f8dec5bab49c9"); 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 = "0fc336da6b77cd7bf1b9c2568a57e94a"; // next two examples should be the same! + String eqMD5s = "a3eeb0ba5bde0c57a290c917a87ec900"; // next two examples should be the same! expectations.put("", eqMD5s); expectations.put(" -known comp_hapmap -known dbsnp", eqMD5s); - expectations.put(" -known comp_hapmap", "b6072559ce2d01309639ebb2f6133fa9"); + expectations.put(" -known comp_hapmap", "575faa090abf1bfdc8394dca46f9b7a2"); 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("b42a8974ebb4354bf172ae5f81922f9e", "a3ce1d70d8ae3874807e9d61994d42af")); + Arrays.asList("2801558409c4ce3a5484b8e1b3a49e0d", "a3ce1d70d8ae3874807e9d61994d42af")); executeTest("testVE2WriteVCF", spec); } }