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another test-with-multiple outputs fix 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2934 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-03-04 22:46:15 +00:00
parent 9eb122924f
commit 366771d5a6
2 changed files with 16 additions and 11 deletions
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2
java/test/org/broadinstitute/sting/WalkerTest.java
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@ -46,7 +46,7 @@ public class WalkerTest extends BaseTest {
return filemd5sum;
} catch (Exception e) {
throw new RuntimeException("Failed to read bytes from calls file: " + resultsFile);
throw new RuntimeException("Failed to read bytes from calls file: " + resultsFile, e);
}
}

25
java/test/org/broadinstitute/sting/oneoffprojects/walkers/coverage/CoverageStatisticsIntegrationTest.java
View File

@ -16,7 +16,7 @@ import java.util.List;
*/
public class CoverageStatisticsIntegrationTest extends WalkerTest {
private boolean RUN_TESTS = false;
private boolean RUN_TESTS = true;
private String root = "-T CoverageStatistics ";
private String hg18 = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
private String b36 = "/broad/1KG/reference/human_b36_both.fasta";
@ -54,16 +54,21 @@ public class CoverageStatisticsIntegrationTest extends WalkerTest {
String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam","/broad/1KG/DCC_merged/freeze5/NA19240.pilot2.454.bam"};
String cmd = buildRootCmd(b36,new ArrayList<String>(Arrays.asList(bams)),new ArrayList<String>(Arrays.asList(intervals))) + " -mmq 0 -mbq 0 -dels -baseCounts";
String expected = "cb87d6069ac60c73f047efc6d9386619";
WalkerTestSpec spec = new WalkerTestSpec(cmd,1, Arrays.asList(expected));
WalkerTestSpec spec = new WalkerTestSpec(cmd,0, new ArrayList<String>());
// now add the expected files that get generated
spec.addAuxFile("aff2349d6dc221c08f6c469379aeaedf", new File(baseOutputFile.getAbsolutePath() + ".interval_statistics"));
spec.addAuxFile("6476ed0c54a4307a618aa6d3268b050f", new File(baseOutputFile.getAbsolutePath()+".interval_summary"));
spec.addAuxFile("c744a298b7541f3f823e6937e9a0bc67", new File(baseOutputFile.getAbsolutePath()+".locus_statistics"));
spec.addAuxFile("65318c1e73d98a59cc6f817cde12d3d4", new File(baseOutputFile.getAbsolutePath()+".summary_statistics"));
spec.addAuxFile("9fc19f773a7ddfbb473d124e675a3d94", new File(baseOutputFile.getAbsolutePath()+".sample_statistics"));
if ( RUN_TESTS )
execute("testBaseOutputNoFiltering",spec);
spec.addAuxFile("cb87d6069ac60c73f047efc6d9386619", baseOutputFile);
spec.addAuxFile("aff2349d6dc221c08f6c469379aeaedf", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".interval_statistics"));
spec.addAuxFile("6476ed0c54a4307a618aa6d3268b050f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".interval_summary"));
spec.addAuxFile("c744a298b7541f3f823e6937e9a0bc67", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".locus_statistics"));
spec.addAuxFile("65318c1e73d98a59cc6f817cde12d3d4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".summary_statistics"));
spec.addAuxFile("9fc19f773a7ddfbb473d124e675a3d94", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
execute("testBaseOutputNoFiltering",spec);
}
public File createTempFileFromBase(String name) {
File fl = new File(name);
fl.deleteOnExit();
return fl;
}
}