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Elegant solution to the determinism problem: force testNG to run tests in the order that I want it to. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5312 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-02-24 21:32:35 +00:00
parent d9ea7daa73
commit cba88a8861
1 changed files with 17 additions and 12 deletions
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29
java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
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@ -14,45 +14,50 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
private static final String knownIndels = validationDataLocation + "indelRealignerTest.pilot1.ceu.vcf";
private static final String baseCommandPrefix = "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + mainTestBam + " -targetIntervals " + mainTestIntervals + " -compress 0 -L 20:49,500-55,500 ";
private static final String baseCommand = baseCommandPrefix + "-o %s ";
private static final String base_md5 = "282070822dc5495eb20dad157d827133";
@Test
public void testDefaults() {
String md5 = "282070822dc5495eb20dad157d827133";
WalkerTestSpec spec1 = new WalkerTestSpec(
baseCommand,
1,
Arrays.asList(md5));
Arrays.asList(base_md5));
executeTest("test realigner defaults", spec1);
WalkerTestSpec spec2 = new WalkerTestSpec(
baseCommand + "-B:indels,vcf " + knownIndels,
1,
Arrays.asList(md5));
Arrays.asList(base_md5));
executeTest("test realigner defaults with VCF", spec2);
WalkerTestSpec spec3 = new WalkerTestSpec(
baseCommand + "-D " + GATKDataLocation + "dbsnp_129_b36.rod",
1,
Arrays.asList(md5));
Arrays.asList(base_md5));
executeTest("realigner defaults with dbsnp", spec3);
}
@Test
@Test(dependsOnMethods = { "testNoTags" })
public void testStats() {
WalkerTestSpec spec = new WalkerTestSpec(
WalkerTestSpec spec1 = new WalkerTestSpec(
baseCommandPrefix + "-stats %s -o /dev/null",
1,
Arrays.asList("ed5a207ddf5bdda4bb76899fb3eae35c"));
executeTest("realigner stats", spec);
executeTest("realigner stats", spec1);
WalkerTestSpec spec2 = new WalkerTestSpec(
baseCommandPrefix + "-LOD 60 -stats %s -o /dev/null",
1,
Arrays.asList("ffab7d9ca19daa8a21e0b8f0072d39e9"));
executeTest("realigner stats", spec2);
}
@Test
@Test(dependsOnMethods = { "testKnownsOnly" })
public void testLods() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-LOD 60", "282070822dc5495eb20dad157d827133" );
e.put( "-LOD 60", base_md5 );
e.put( "-LOD 1", "c98d699d94f01bd0089f12646c764dfc" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
@ -64,7 +69,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
}
}
@Test
@Test(dependsOnMethods = { "testDefaults" })
public void testKnownsOnly() {
WalkerTestSpec spec1 = new WalkerTestSpec(
baseCommand + "-knownsOnly -B:indels,vcf " + knownIndels,
@ -79,7 +84,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
executeTest("realigner known indels only from dbsnp", spec2);
}
@Test
@Test(dependsOnMethods = { "testLongRun" })
public void testNoTags() {
WalkerTestSpec spec = new WalkerTestSpec(
baseCommand + "--noOriginalAlignmentTags",
@ -88,7 +93,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
executeTest("realigner no output tags", spec);
}
@Test
@Test(dependsOnMethods = { "testLods" })
public void testLongRun() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10,000,000-11,000,000 -targetIntervals " + validationDataLocation + "indelRealignerTest.NA12878.chrom1.intervals -compress 0 -o %s",