diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java b/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java index 0eecfb234..955aa9363 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java +++ b/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java @@ -75,7 +75,7 @@ public class SAMBAMDataSourceTest extends BaseTest { /** Test out that we can shard the file and iterate over every read */ - //@Test + @Test public void testLinearBreakIterateAll() { logger.warn("Executing testLinearBreakIterateAll"); // the sharding strat. @@ -103,6 +103,11 @@ public class SAMBAMDataSourceTest extends BaseTest { readCount++; } datum.close(); + + // if we're over 100 shards, break out + if (count > 100) { + break; + } } } catch (SimpleDataSourceLoadException e) { diff --git a/java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorTest.java b/java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorTest.java new file mode 100755 index 000000000..d613898d1 --- /dev/null +++ b/java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorTest.java @@ -0,0 +1,131 @@ +package org.broadinstitute.sting.gatk.iterators; + +import static junit.framework.Assert.fail; +import net.sf.samtools.SAMRecord; +import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.sting.gatk.dataSources.shards.Shard; +import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy; +import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategyFactory; +import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SAMBAMDataSource; +import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SimpleDataSourceLoadException; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; +import org.junit.Before; +import org.junit.Test; + +import java.io.File; +import java.util.ArrayList; +import java.util.List; + +/** + * + * User: aaron + * Date: Apr 14, 2009 + * Time: 5:48:48 PM + * + * The Broad Institute + * SOFTWARE COPYRIGHT NOTICE AGREEMENT + * This software and its documentation are copyright 2009 by the + * Broad Institute/Massachusetts Institute of Technology. All rights are reserved. + * + * This software is supplied without any warranty or guaranteed support whatsoever. Neither + * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality. + * + */ + + +/** + * @author aaron + * @version 1.0 + * @date Apr 14, 2009 + *
+ * Class BoundedReadIteratorTest + * + * A descriptions should go here. Blame aaron if it's missing. + */ +public class BoundedReadIteratorTest extends BaseTest { + + /** the file list and the fasta sequence */ + private List