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Fix for long-term VariantEval bug plus new intergration test to catch it 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1951 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-10-31 00:00:33 +00:00
parent 99337df929
commit 7d0ac7c6f2
2 changed files with 19 additions and 17 deletions
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4
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
View File

@ -72,7 +72,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
// the types of analysis we support, and the string tags we associate with the enumerated value
enum ANALYSIS_TYPE {
ALL_SNPS("all"), SINGLETON_SNPS("singletons"), TWOHIT_SNPS("2plus_hit"), KNOWN_SNPS("2plus_hit"), NOVEL_SNPS("2plus_hit");
ALL_SNPS("all"), SINGLETON_SNPS("singletons"), TWOHIT_SNPS("2plus_hit"), KNOWN_SNPS("known"), NOVEL_SNPS("novel");
private final String value;
ANALYSIS_TYPE(String value) { this.value = value;}
@ -226,7 +226,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
Variation eval = (Variation) tracker.lookup("eval", null);
// ensure that the variation we're looking at is bi-allelic
if (eval != null && !eval.isBiallelic())
if ( eval != null && ! eval.isBiallelic() )
eval = null;
if (eval != null)

32
java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java
View File

@ -4,8 +4,7 @@ import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
import java.util.*;
/**
* @author aaron
@ -18,8 +17,9 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
@Test
public void testEvalVariantROD() {
List<String> md5 = new ArrayList<String>();
md5.add("86582b57ec27dd9c4a6e0252eb010376");
HashMap<String, String> md5 = new HashMap<String, String>();
md5.put("", "86582b57ec27dd9c4a6e0252eb010376");
md5.put("-A", "ead904e334956435e6b586b697cd1905");
/**
* the above MD5 was calculated from running the following command:
@ -34,17 +34,19 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
* --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls
*
*/
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R /broad/1KG/reference/human_b36_both.fasta" +
" --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" +
" -T VariantEval" +
" --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
" -L 1:10,000,000-11,000,000" +
" --outerr %s" +
" --supressDateInformation",
1, // just one output file
md5);
List<File> result = executeTest("testEvalVariantROD", spec).getFirst();
for ( Map.Entry<String, String> e : md5.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R /broad/1KG/reference/human_b36_both.fasta" +
" --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" +
" -T VariantEval" +
" --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
" -L 1:10,000,000-11,000,000" +
" --outerr %s" +
" --supressDateInformation " + e.getKey(),
1, // just one output file
Arrays.asList(e.getValue()));
List<File> result = executeTest("testEvalVariantROD", spec).getFirst();
}
}
@Test