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

RankSum tests have lightly different MD5 results based on allele order 

-- UG GENOTYPE_GIVEN_ALLELES now uses the order of alleles in the VCF, so this changes the MD5
This commit is contained in:
Mark DePristo 2011-10-10 11:04:07 -04:00
parent 46e7370128
commit a4bb842958
1 changed files with 14 additions and 8 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

22
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -257,34 +257,40 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
}
@Test
public void testWithIndelAllelesPassedIn() {
public void testWithIndelAllelesPassedIn1() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("408d3aba4d094c067fc00a43992c2292"));
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1);
}
@Test
public void testWithIndelAllelesPassedIn2() {
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
+ validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("94977d6e42e764280e9deaf4e3ac8c80"));
Arrays.asList("5e4e09354410b76fc0d822050d84132a"));
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2);
}
@Test
public void testWithIndelAllelesPassedIn3() {
WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2.20101123.indels.sites.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,080,000", 1,
Arrays.asList("e66b7321e2ac91742ad3ef91040daafd"));
Arrays.asList("c599eedbeb422713b8a28529e805e4ae"));
executeTest("test MultiSample Pilot2 indels with complicated records", spec3);
}
@Test
public void testWithIndelAllelesPassedIn4() {
WalkerTest.WalkerTestSpec spec4 = new WalkerTest.WalkerTestSpec(
baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2_chr20_100_110K.20101123.indels.sites.vcf -I " + validationDataLocation +
"phase1_GBR_realigned.chr20.100K-110K.bam -o %s -L 20:100,000-110,000", 1,
Arrays.asList("37e891bf1ac40caec9ea228f39c27e44"));
Arrays.asList("37d908a682ac269f8f19dec939ff5b01"));
executeTest("test MultiSample 1000G Phase1 indels with complicated records emitting all sites", spec4);
}
}