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I think we got out of sync with the HC tests as we were clobbering each other's changes. Only differences here are to some RankSumTest values.

This commit is contained in:
Eric Banks 2013-01-17 09:19:21 -05:00
parent ded659232b
commit 953592421b
1 changed files with 7 additions and 7 deletions
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14
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -68,12 +68,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "b8f7b741445ce6b6ea491c794ce75c17");
HCTest(CEUTRIO_BAM, "", "0e59153c6359d7cb7be44e25ab552790");
}
@Test
public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "a2c63f6e6e51a01019bdbd23125bdb15");
HCTest(NA12878_BAM, "", "d4b377aed2c8be2ebd81ee5e43b73a93");
}
@Test(enabled = false)
@ -113,7 +113,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSampleComplex() {
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "6c0c441b71848c2eea38ab5e2afe1120");
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "14ed8e5be2d2a0bf478d742b4baa5a46");
}
private void HCTestSymbolicVariants(String bam, String args, String md5) {
@ -124,7 +124,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleSymbolic() {
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "0761ff5cbf279be467833fa6708bf360");
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "76fe5e57ed96541bdfee74782331b061");
}
private void HCTestIndelQualityScores(String bam, String args, String md5) {
@ -135,7 +135,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "29f1125df5ab27cc937a144ae08ac735");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "25981f7706f61d930556fb128cd1e5c5");
}
// That problem bam came from a user on the forum and it spotted a problem where the ReadClipper
@ -146,7 +146,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void HCTestProblematicReadsModifiedInActiveRegions() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("8b1b8d1bd7feac1503fc4ffa6236cff7"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("4701887e1927814259560d85098b6440"));
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
}
@ -175,7 +175,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestReducedBam() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
Arrays.asList("8a400b0c46f41447fcc35a907e34f384"));
Arrays.asList("18d047bf8116b56e0c6212e0875eceea"));
executeTest("HC calling on a ReducedRead BAM", spec);
}