zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Adding both unit and integration tests to cover the previous edge case of mismatched PLs

This commit is contained in:
Eric Banks 2012-09-20 11:55:28 -04:00
parent 4b7edc72d1
commit 2e6f533996
2 changed files with 26 additions and 3 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

15
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModelUnitTest.java
View File

@ -109,4 +109,19 @@ public class ExactAFCalculationModelUnitTest extends BaseTest {
int calculatedAlleleCount = result.getAlleleCountsOfMAP()[0];
Assert.assertEquals(calculatedAlleleCount, 6);
}
@Test
public void testMismatchedGLs() {
final double[] AB = new double[]{-2000.0, 0.0, -2000.0, -2000.0, -2000.0, -2000.0};
final double[] AC = new double[]{-100.0, -100.0, -100.0, 0.0, -100.0, -100.0};
GetGLsTest cfg = new GetGLsTest("B1C1", 2, createGenotype("1", AC), createGenotype("2", AB));
final AlleleFrequencyCalculationResult result = new AlleleFrequencyCalculationResult(2);
ExactAFCalculationModel.linearExactMultiAllelic(cfg.GLs, cfg.numAltAlleles, priors, result);
Assert.assertEquals(result.getAlleleCountsOfMAP()[0], 1);
Assert.assertEquals(result.getAlleleCountsOfMAP()[1], 1);
}
}

14
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -60,7 +60,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultipleSNPAlleles() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
Arrays.asList("8472b1ad2fe1060e732da9e29d10cf99"));
Arrays.asList("cceb34ffbd2dbc45b8821f86ea255284"));
executeTest("test Multiple SNP alleles", spec);
}
@ -76,10 +76,18 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testReverseTrim() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
Arrays.asList("8a4ad38ec8015eea3461295148143428"));
Arrays.asList("00f54a0097e710c0f7b001444c237e32"));
executeTest("test reverse trim", spec);
}
@Test
public void testMismatchedPLs() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
Arrays.asList("b3fae6bf4c620458f4259dbc93125e37"));
executeTest("test mismatched PLs", spec);
}
// --------------------------------------------------------------------------------------------------------------
//
// testing compressed output
@ -335,7 +343,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSampleIndels1() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
Arrays.asList("c3f786a5228346b43a80aa80d22b1490"));
Arrays.asList("af04b81f0548ca22b8d1f6bf223b336e"));
List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst();
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(