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Updating integration tests now that standard annotations support multiple alleles

This commit is contained in:
Eric Banks 2012-02-27 11:32:26 -05:00
parent 64754e7870
commit 1ea34058c2
2 changed files with 4 additions and 4 deletions
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6
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -32,7 +32,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("604328867fc9aaf3e71fa0f9ca2ba5c9"));
Arrays.asList("3b7796fa7c7dc94878bedadf7938db4c"));
executeTest("test file has annotations, asking for annotations, #1", spec);
}
@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("bbde8c92d27ad2a7ec1ff2d095d459eb"));
Arrays.asList("279cace364f747f9bae7fe391b5026f0"));
executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
}
@ -82,7 +82,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testExcludeAnnotations() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard -XA FisherStrand -XA ReadPosRankSumTest --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("8ec9f79cab84f26d8250f00d99d18aac"));
Arrays.asList("e488abd05d6162758698a3a7579866a6"));
executeTest("test exclude annotations", spec);
}

2
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_HEADER -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + validationDataLocation + "multiallelic.snps.bam -o %s -L " + validationDataLocation + "multiallelic.snps.intervals", 1,
Arrays.asList("b53cb55a5f868663068812b13578af57"));
Arrays.asList("10027d13befaa07b7900a7af0ae0791c"));
executeTest("test Multiple SNP alleles", spec);
}