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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
This commit is contained in:
aaron 2010-04-01 16:23:14 +00:00
parent d00bde22db
commit 585cc880a2
3 changed files with 12 additions and 12 deletions
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6
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java
View File

@ -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<Integer, Integer> {
*/
private List<Node> 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");

6
java/src/org/broadinstitute/sting/playground/utils/report/templates/csv_readable.ftl
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@ -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/>
</#if>
<@emit_row_values analysis=analysis/>
</#if>
</#list>
<#-- -------------------- -->

12
java/test/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2IntegrationTest.java
View File

@ -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<String, String> expectations = new HashMap<String, String>();
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<String, String> 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<String, String> 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);
}
}