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can explicitly set the now required ReferenceDataSource in unit tests 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4977 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-01-12 18:25:12 +00:00
parent 7916ab0ed5
commit 8fe5641b2e
3 changed files with 10 additions and 6 deletions
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11
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -658,7 +658,7 @@ public class GenomeAnalysisEngine {
BAQ.DEFAULT_GOP = argCollection.BAQGOP; BAQ.DEFAULT_GOP = argCollection.BAQGOP;
validateSuppliedReference(); validateSuppliedReference();
referenceDataSource = openReferenceSequenceFile(argCollection.referenceFile); setReferenceDataSource(argCollection.referenceFile);
validateSuppliedReads(); validateSuppliedReads();
readsDataSource = createReadsDataSource(genomeLocParser, referenceDataSource.getReference()); readsDataSource = createReadsDataSource(genomeLocParser, referenceDataSource.getReference());
@ -852,15 +852,14 @@ public class GenomeAnalysisEngine {
} }
/** /**
* Opens a reference sequence file paired with an index. * Opens a reference sequence file paired with an index. Only public for testing purposes
* *
* @param refFile Handle to a reference sequence file. Non-null. * @param refFile Handle to a reference sequence file. Non-null.
* @return A thread-safe file wrapper. * @return A thread-safe file wrapper.
*/ */
private ReferenceDataSource openReferenceSequenceFile(File refFile) { public void setReferenceDataSource(File refFile) {
ReferenceDataSource ref = new ReferenceDataSource(refFile); this.referenceDataSource = new ReferenceDataSource(refFile);
genomeLocParser = new GenomeLocParser(ref.getReference()); genomeLocParser = new GenomeLocParser(referenceDataSource.getReference());
return ref;
} }
/** /**

4
java/test/org/broadinstitute/sting/gatk/traversals/TraverseDuplicatesUnitTest.java
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@ -37,6 +37,7 @@ import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test; import org.testng.annotations.Test;
import java.io.File;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
import java.util.Set; import java.util.Set;
@ -55,6 +56,8 @@ public class TraverseDuplicatesUnitTest extends BaseTest {
private SAMFileHeader header; private SAMFileHeader header;
private GenomeLocParser genomeLocParser; private GenomeLocParser genomeLocParser;
private GenomeAnalysisEngine engine; private GenomeAnalysisEngine engine;
private File refFile = new File(validationDataLocation + "Homo_sapiens_assembly17.fasta");
@BeforeMethod @BeforeMethod
public void doBefore() { public void doBefore() {
@ -62,6 +65,7 @@ public class TraverseDuplicatesUnitTest extends BaseTest {
genomeLocParser =new GenomeLocParser(header.getSequenceDictionary()); genomeLocParser =new GenomeLocParser(header.getSequenceDictionary());
engine = new GenomeAnalysisEngine(); engine = new GenomeAnalysisEngine();
engine.setReferenceDataSource(refFile);
engine.setGenomeLocParser(genomeLocParser); engine.setGenomeLocParser(genomeLocParser);
obj.initialize(engine); obj.initialize(engine);

1
java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java
View File

@ -84,6 +84,7 @@ public class TraverseReadsUnitTest extends BaseTest {
genomeLocParser = new GenomeLocParser(ref); genomeLocParser = new GenomeLocParser(ref);
engine = new GenomeAnalysisEngine(); engine = new GenomeAnalysisEngine();
engine.setReferenceDataSource(refFile);
engine.setGenomeLocParser(genomeLocParser); engine.setGenomeLocParser(genomeLocParser);
} }