@Test
public void testStrandAlleleCountsBySample() throws IOException {
// HaplotypeCaller creates gVCF
final String CEUTRIO_BAM = validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam";
final WalkerTestSpec specHaplotypeCaller =
new WalkerTestSpec(
"-T HaplotypeCaller --disableDithering "
+ String.format("-R %s -I %s ", b37KGReference, CEUTRIO_BAM)
+ "--no_cmdline_in_header -o %s -L 20:10130000-10134800 "
+ "-ERC GVCF --sample_name NA12878 -variant_index_type LINEAR "
+ "-variant_index_parameter 128000 -A StrandAlleleCountsBySample",
1,
Arrays.asList(""));
specHaplotypeCaller
.disableShadowBCF(); // TODO: Remove when BaseTest.assertAttributesEquals() works with SC
final File gVCF =
executeTest("testStrandAlleleCountsBySampleHaplotypeCaller", specHaplotypeCaller)
.getFirst()
.get(0);
List<String> gVCFList = getAttributeValues(gVCF, new String("SAC"));
// Use gVCF from HaplotypeCaller
final WalkerTestSpec spec =
new WalkerTestSpec(
baseTestString(" -V " + gVCF.getAbsolutePath(), b37KGReference), 1, Arrays.asList(""));
final File outputVCF = executeTest("testStrandAlleleCountsBySample", spec).getFirst().get(0);
List<String> outputVCFList = getAttributeValues(outputVCF, new String("SAC"));
// All of the SAC values in the VCF were derived from the gVCF
Assert.assertTrue(gVCFList.containsAll(outputVCFList));
}
@Test(enabled = true)
public void testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles() {
WalkerTestSpec spec =
new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R "
+ b37KGReference
+ " -V "
+ privateTestDir
+ "spanningDel.delOnly.g.vcf",
1,
Arrays.asList("46169d08f93e5ff57856c7b64717314b"));
spec.disableShadowBCF();
executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec);
}
@Test(enabled = true)
public void testSpanningDeletionsFromCombinedGVCF() {
WalkerTestSpec spec =
new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R "
+ b37KGReference
+ " -V "
+ privateTestDir
+ "spanningDel.combined.g.vcf",
1,
Arrays.asList(simpleSpanningDeletionsMD5));
spec.disableShadowBCF();
executeTest("testSpanningDeletionsFromCombinedGVCFMD5", spec);
}
@Test
public void testSetVcfFilteredGtoNocall() {
String testfile = privateTestDir + "filteredSamples.vcf";
WalkerTestSpec spec =
new WalkerTestSpec(
"-T SelectVariants --setFilteredGtToNocall -R "
+ b37KGReference
+ " --variant "
+ testfile
+ " -o %s --no_cmdline_in_header",
1,
Arrays.asList("7771f07a9997296852ab367fac2c7a6c"));
spec.disableShadowBCF();
executeTest("testSetVcfFilteredGtoNocall--" + testfile, spec);
}
@Test(enabled = true)
public void testMultipleSpanningDeletionsMD5() {
WalkerTestSpec spec =
new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R "
+ b37KGReference
+ " -V "
+ privateTestDir
+ "spanningDel.1.g.vcf -V "
+ privateTestDir
+ "spanningDel.2.g.vcf -V "
+ privateTestDir
+ "spanningDel.3.g.vcf",
1,
Arrays.asList("1c418229117bc8f148a69eda9c496309"));
spec.disableShadowBCF();
executeTest("testMultipleSpanningDeletionsMD5", spec);
}
/** Section to test spanning deletions */
@Test
public void testSpanningDeletions() throws IOException {
final String gvcf1 = privateTestDir + "spanningDel.1.g.vcf";
final String gvcf2 = privateTestDir + "spanningDel.2.g.vcf";
final String gvcf3 = privateTestDir + "spanningDel.3.g.vcf";
// create the genotyped VCF to use as a basis for comparison against all of the combined
// versions
// case 0: GenotypeGVCFs(1.g.vcf, 2.g.vcf, 3.g.vcf)
final WalkerTestSpec genotypeBase =
new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R "
+ b37KGReference
+ " -V "
+ gvcf1
+ " -V "
+ gvcf2
+ " -V "
+ gvcf3,
1,
Arrays.asList(""));
genotypeBase.disableShadowBCF();
final File genotypeBaseVCF = executeTest("genotypeBase", genotypeBase).getFirst().get(0);
final List<VariantContext> BASE_VARIANT_CONTEXTS = getVariantContexts(genotypeBaseVCF);
// case 1: GenotypeGVCFs(CombineGVCFs(1.g.vcf, 2.g.vcf), 3.g.vcf)
final WalkerTestSpec combine12 =
new WalkerTestSpec(
"-T CombineGVCFs --no_cmdline_in_header -o %s -R "
+ b37KGReference
+ " -V "
+ gvcf1
+ " -V "
+ gvcf2,
1,
Arrays.asList(""));
combine12.disableShadowBCF();
final File combined_gVCF12 = executeTest("combine12", combine12).getFirst().get(0);
final WalkerTestSpec genotype12_3 =
new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R "
+ b37KGReference
+ " -V "
+ combined_gVCF12.getAbsolutePath()
+ " -V "
+ gvcf3,
1,
Arrays.asList(""));
genotype12_3.disableShadowBCF();
final File genotype12_3VCF = executeTest("genotype12_3", genotype12_3).getFirst().get(0);
final List<VariantContext> VARIANT_CONTEXTS_12_3 = getVariantContexts(genotype12_3VCF);
testVCsAreEqual(BASE_VARIANT_CONTEXTS, VARIANT_CONTEXTS_12_3);
// case 2: GenotypeGVCFs(CombineGVCFs(CombineGVCFs(1.g.vcf, 2.g.vcf), 3.g.vcf))
final WalkerTestSpec combine12then3 =
new WalkerTestSpec(
"-T CombineGVCFs --no_cmdline_in_header -o %s -R "
+ b37KGReference
+ " -V "
+ combined_gVCF12
+ " -V "
+ gvcf3,
1,
Arrays.asList(""));
combine12then3.disableShadowBCF();
final File combined_gVCF12then3 =
executeTest("combined_gVCF12then3", combine12then3).getFirst().get(0);
final WalkerTestSpec genotype12then3 =
new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R "
+ b37KGReference
+ " -V "
+ combined_gVCF12then3.getAbsolutePath(),
1,
Arrays.asList(""));
genotype12then3.disableShadowBCF();
final File genotype12then3VCF =
executeTest("genotype12then3", genotype12then3).getFirst().get(0);
final List<VariantContext> VARIANT_CONTEXTS_12then3 = getVariantContexts(genotype12then3VCF);
testVCsAreEqual(BASE_VARIANT_CONTEXTS, VARIANT_CONTEXTS_12then3);
// case 3: GenotypeGVCFs(CombineGVCFs(CombineGVCFs(1.g.vcf, 3.g.vcf), 2.g.vcf))
final WalkerTestSpec combine13 =
new WalkerTestSpec(
"-T CombineGVCFs --no_cmdline_in_header -o %s -R "
+ b37KGReference
+ " -V "
+ gvcf1
+ " -V "
+ gvcf3,
1,
Arrays.asList(""));
combine13.disableShadowBCF();
final File combined_gVCF13 = executeTest("combine13", combine13).getFirst().get(0);
final WalkerTestSpec combine13then2 =
new WalkerTestSpec(
"-T CombineGVCFs --no_cmdline_in_header -o %s -R "
+ b37KGReference
+ " -V "
+ combined_gVCF13
+ " -V "
+ gvcf2,
1,
Arrays.asList(""));
combine13then2.disableShadowBCF();
final File combined_gVCF13then2 =
executeTest("combined_gVCF13then2", combine13then2).getFirst().get(0);
final WalkerTestSpec genotype13then2 =
new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R "
+ b37KGReference
+ " -V "
+ combined_gVCF13then2.getAbsolutePath(),
1,
Arrays.asList(""));
genotype13then2.disableShadowBCF();
final File genotype13then2VCF =
executeTest("genotype13then2", genotype13then2).getFirst().get(0);
final List<VariantContext> VARIANT_CONTEXTS_13then2 = getVariantContexts(genotype13then2VCF);
testVCsAreEqual(BASE_VARIANT_CONTEXTS, VARIANT_CONTEXTS_13then2);
// case 4: GenotypeGVCFs(CombineGVCFs(1.g.vcf, 2.g.vcf, 3.g.vcf))
final WalkerTestSpec combine123 =
new WalkerTestSpec(
"-T CombineGVCFs --no_cmdline_in_header -o %s -R "
+ b37KGReference
+ " -V "
+ gvcf1
+ " -V "
+ gvcf2
+ " -V "
+ gvcf3,
1,
Arrays.asList(""));
combine123.disableShadowBCF();
final File combined_gVCF123 = executeTest("combine123", combine123).getFirst().get(0);
final WalkerTestSpec genotype123 =
new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R "
+ b37KGReference
+ " -V "
+ combined_gVCF123.getAbsolutePath(),
1,
Arrays.asList(""));
genotype123.disableShadowBCF();
final File genotype123VCF = executeTest("genotype123", genotype123).getFirst().get(0);
final List<VariantContext> VARIANT_CONTEXTS_123 = getVariantContexts(genotype123VCF);
testVCsAreEqual(BASE_VARIANT_CONTEXTS, VARIANT_CONTEXTS_123);
}