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Fix runtime public -> protected dependencies in the test suite 

-replace unnecessary uses of the UnifiedGenotyper by public integration tests
 with PrintReads

-move NanoSchedulerIntegrationTest to protected, since it's completely dependent
 on the UnifiedGenotyper
This commit is contained in:
David Roazen 2013-02-26 21:11:13 -05:00
parent 3ce0a32da7
commit 65d31ba4ad
4 changed files with 5 additions and 5 deletions
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0
public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java → protected/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java
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6
public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java
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@ -64,16 +64,16 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
} }
@Test() private void testMissingBAMnt1() { @Test() private void testMissingBAMnt1() {
testMissingFile("missing BAM", "-T UnifiedGenotyper -I missing.bam -nt 1"); testMissingFile("missing BAM", "-T PrintReads -I missing.bam -nt 1");
} }
@Test() private void testMissingBAMnt4() { @Test() private void testMissingBAMnt4() {
testMissingFile("missing BAM", "-T UnifiedGenotyper -I missing.bam -nt 4"); testMissingFile("missing BAM", "-T PrintReads -I missing.bam -nt 4");
} }
@Test() private void testMissingVCF() { @Test() private void testMissingVCF() {
testMissingFile("missing VCF", "-T SelectVariants -V missing.vcf"); testMissingFile("missing VCF", "-T SelectVariants -V missing.vcf");
} }
@Test() private void testMissingInterval() { @Test() private void testMissingInterval() {
testMissingFile("missing interval", "-T UnifiedGenotyper -L missing.interval_list -I " + b37GoodBAM); testMissingFile("missing interval", "-T PrintReads -L missing.interval_list -I " + b37GoodBAM);
} }

2
public/java/test/org/broadinstitute/sting/gatk/MaxRuntimeIntegrationTest.java
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@ -71,7 +71,7 @@ public class MaxRuntimeIntegrationTest extends WalkerTest {
@Test(enabled = true, dataProvider = "MaxRuntimeProvider", timeOut = 60 * 1000) @Test(enabled = true, dataProvider = "MaxRuntimeProvider", timeOut = 60 * 1000)
public void testMaxRuntime(final MaxRuntimeTestProvider cfg) { public void testMaxRuntime(final MaxRuntimeTestProvider cfg) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + hg18Reference "-T PrintReads -R " + hg18Reference
+ " -I " + validationDataLocation + "NA12878.WEx.downsampled20x.bam -o /dev/null" + " -I " + validationDataLocation + "NA12878.WEx.downsampled20x.bam -o /dev/null"
+ " -maxRuntime " + cfg.maxRuntime + " -maxRuntimeUnits " + cfg.unit, 0, + " -maxRuntime " + cfg.maxRuntime + " -maxRuntimeUnits " + cfg.unit, 0,
Collections.<String>emptyList()); Collections.<String>emptyList());

2
public/java/test/org/broadinstitute/sting/gatk/walkers/qc/DictionaryConsistencyIntegrationTest.java
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@ -75,7 +75,7 @@ public class DictionaryConsistencyIntegrationTest extends WalkerTest {
@Test public void failBAM8() { executeTest("hg18bam-v-lexhg18", testBAM(lexHG18, hg18BAM, "chr1", UserException.LexicographicallySortedSequenceDictionary.class)); } @Test public void failBAM8() { executeTest("hg18bam-v-lexhg18", testBAM(lexHG18, hg18BAM, "chr1", UserException.LexicographicallySortedSequenceDictionary.class)); }
private WalkerTest.WalkerTestSpec testBAM(String ref, String bam, String contig, Class c) { private WalkerTest.WalkerTestSpec testBAM(String ref, String bam, String contig, Class c) {
return new WalkerTest.WalkerTestSpec("-T UnifiedGenotyper -I " + bam + " -R " + ref + " -L " + contig + ":10,000,000-11,000,000 -o %s", return new WalkerTest.WalkerTestSpec("-T PrintReads -I " + bam + " -R " + ref + " -L " + contig + ":10,000,000-11,000,000 -o %s",
1, c); 1, c);
} }