diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByReadsTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByReadsTest.java index 3a69612d4..c2a356f5e 100755 --- a/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByReadsTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByReadsTest.java @@ -103,11 +103,6 @@ public class SAMByReadsTest extends BaseTest { */ @Test 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), ArtificialSAMUtils.mappedAndUnmappedReadIterator(1, 1, 10, 10)); GenomeLocParser.setupRefContigOrdering(gen.getHeader().getSequenceDictionary()); diff --git a/java/test/org/broadinstitute/sting/utils/UtilsTest.java b/java/test/org/broadinstitute/sting/utils/UtilsTest.java index e0cd2bdca..bd7d208c3 100644 --- a/java/test/org/broadinstitute/sting/utils/UtilsTest.java +++ b/java/test/org/broadinstitute/sting/utils/UtilsTest.java @@ -25,6 +25,7 @@ package org.broadinstitute.sting.utils; import org.junit.Test; +import org.broadinstitute.sting.BaseTest; import junit.framework.Assert; /** @@ -34,7 +35,7 @@ import junit.framework.Assert; * @version 0.1 */ -public class UtilsTest { +public class UtilsTest extends BaseTest { @Test public void testDupStringNoChars() { diff --git a/java/test/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtilsTest.java b/java/test/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtilsTest.java deleted file mode 100644 index e59140628..000000000 --- a/java/test/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtilsTest.java +++ /dev/null @@ -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 - *

- * Class ArtificialFastaUtilsTest - *

- * test out the ArtificialFastaUtils functionality - */ -public class ArtificialFastaUtilsTest extends BaseTest { - - /** generate a fake fasta */ - @Test - public void testFastaGeneration() { - List names = new ArrayList(); - List sizes = new ArrayList(); - - 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(); - } -}