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other fixes for some broken unit tests 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1181 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-07-07 05:53:13 +00:00
parent 033bafe7a1
commit f6a273a537
3 changed files with 2 additions and 49 deletions
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5
java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByReadsTest.java
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@ -103,11 +103,6 @@ public class SAMByReadsTest extends BaseTest {
*/ */
@Test @Test
public void testShardingOfReadsEvenSplit() { public void testShardingOfReadsEvenSplit() {
try {
Thread.sleep(5000);
} catch (InterruptedException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
}
ArtificialResourcePool gen = new ArtificialResourcePool(createArtificialSamHeader(1, 1, 10, 50), ArtificialResourcePool gen = new ArtificialResourcePool(createArtificialSamHeader(1, 1, 10, 50),
ArtificialSAMUtils.mappedAndUnmappedReadIterator(1, 1, 10, 10)); ArtificialSAMUtils.mappedAndUnmappedReadIterator(1, 1, 10, 10));
GenomeLocParser.setupRefContigOrdering(gen.getHeader().getSequenceDictionary()); GenomeLocParser.setupRefContigOrdering(gen.getHeader().getSequenceDictionary());

3
java/test/org/broadinstitute/sting/utils/UtilsTest.java
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@ -25,6 +25,7 @@
package org.broadinstitute.sting.utils; package org.broadinstitute.sting.utils;
import org.junit.Test; import org.junit.Test;
import org.broadinstitute.sting.BaseTest;
import junit.framework.Assert; import junit.framework.Assert;
/** /**
@ -34,7 +35,7 @@ import junit.framework.Assert;
* @version 0.1 * @version 0.1
*/ */
public class UtilsTest { public class UtilsTest extends BaseTest {
@Test @Test
public void testDupStringNoChars() { public void testDupStringNoChars() {

43
java/test/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtilsTest.java
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@ -1,43 +0,0 @@
package org.broadinstitute.sting.utils.fasta;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.junit.Assert;
import org.junit.Test;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
/**
* @author aaron
* <p/>
* Class ArtificialFastaUtilsTest
* <p/>
* test out the ArtificialFastaUtils functionality
*/
public class ArtificialFastaUtilsTest extends BaseTest {
/** generate a fake fasta */
@Test
public void testFastaGeneration() {
List<String> names = new ArrayList<String>();
List<Integer> sizes = new ArrayList<Integer>();
for (int x = 0; x < 5; x++) {
sizes.add(1000);
names.add("chr" + (x+1));
}
File temp = new File("tempFileFasta.fasta");
ArtificialFastaUtils.createArtificialFasta(temp.getName(),names,sizes,ArtificialFastaUtils.BASE_PATTERN.ALL_A);
// using the fasta sequence file to test, in reality we should use the indexed version
FastaSequenceFile2 fasta = new FastaSequenceFile2(temp);
Assert.assertEquals(5,fasta.getSequenceDictionary().getSequences().size());
ArtificialSAMUtils.createArtificialBamFile("tempFileBAM.bam",5,1,1000,600);
//temp.delete();
}
}