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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
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1 parent 3ce0a32 commit 65d31ba4adfecb5cfa7efbb4e30e60c7a7975c71 @droazen droazen committed Feb 27, 2013
@@ -64,16 +64,16 @@ private void testMissingFile(String name, String missingBinding) {
}
@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() {
- testMissingFile("missing BAM", "-T UnifiedGenotyper -I missing.bam -nt 4");
+ testMissingFile("missing BAM", "-T PrintReads -I missing.bam -nt 4");
}
@Test() private void testMissingVCF() {
testMissingFile("missing VCF", "-T SelectVariants -V missing.vcf");
}
@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);
}
@@ -71,7 +71,7 @@ public long expectedMaxRuntimeNano() {
@Test(enabled = true, dataProvider = "MaxRuntimeProvider", timeOut = 60 * 1000)
public void testMaxRuntime(final MaxRuntimeTestProvider cfg) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
- "-T UnifiedGenotyper -R " + hg18Reference
+ "-T PrintReads -R " + hg18Reference
+ " -I " + validationDataLocation + "NA12878.WEx.downsampled20x.bam -o /dev/null"
+ " -maxRuntime " + cfg.maxRuntime + " -maxRuntimeUnits " + cfg.unit, 0,
Collections.<String>emptyList());
@@ -75,7 +75,7 @@
@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) {
- 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);
}

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