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Merge pull request #1405 from broadinstitute/sl_issue_1281 

Added regression test for genotyping of spanning deletions in GenotypeGVCFs.
This commit is contained in:
samuelklee 2016-06-15 13:59:14 -04:00 committed by GitHub
parent 050bcbb06b e119feee61
commit 6b04f6ae14
2 changed files with 112 additions and 103 deletions
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10
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java
View File

@ -135,7 +135,7 @@ public class ReferenceConfidenceVariantContextMerger {
// record whether it's also a spanning deletion/event (we know this because the VariantContext type is no
// longer "symbolic" but "mixed" because there are real alleles mixed in with the symbolic non-ref allele)
sawSpanningDeletion |= ( isSpanningEvent && vc.isMixed() ) || vc.getAlternateAlleles().contains(Allele.SPAN_DEL) ||
vc.getAlternateAlleles().contains(GATKVCFConstants.SPANNING_DELETION_SYMBOLIC_ALLELE_DEPRECATED );
vc.getAlternateAlleles().contains(GATKVCFConstants.SPANNING_DELETION_SYMBOLIC_ALLELE_DEPRECATED);
sawNonSpanningEvent |= ( !isSpanningEvent && vc.isMixed() );
vcAndNewAllelePairs.add(new Pair<>(vc, isSpanningEvent ? replaceWithNoCallsAndDels(vc) : remapAlleles(vc, refAllele, finalAlleleSet)));
@ -186,7 +186,7 @@ public class ReferenceConfidenceVariantContextMerger {
//annotatorEngine.combineAnnotations removed the successfully combined annotations, so now parse those that are left
//here we're assuming that things that are left are scalars per sample
Map<String, List<Comparable>> parsedAnnotationMap = parseRemainingAnnotations(annotationMap);
final Map<String, List<Comparable>> parsedAnnotationMap = parseRemainingAnnotations(annotationMap);
// when combining remaining annotations use the median value from all input VCs which had annotations provided
for ( final Map.Entry<String, List<Comparable>> p : parsedAnnotationMap.entrySet() ) {
@ -469,11 +469,11 @@ public class ReferenceConfidenceVariantContextMerger {
if (perSampleIndexesOfRelevantAlleles == null)
throw new IllegalArgumentException("The per sample index of relevant alleles must not be null");
final List<Integer> sacIndexesToUse = new ArrayList(2 * perSampleIndexesOfRelevantAlleles.length);
final List<Integer> sacIndexesToUse = new ArrayList<>(2 * perSampleIndexesOfRelevantAlleles.length);
for (int item : perSampleIndexesOfRelevantAlleles) {
sacIndexesToUse.add(new Integer(2 * item));
sacIndexesToUse.add(new Integer(2 * item + 1));
sacIndexesToUse.add(2 * item);
sacIndexesToUse.add(2 * item + 1);
}
return sacIndexesToUse;

205
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
View File

@ -66,7 +66,6 @@ import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
@ -79,61 +78,61 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
return baseTestString(" -V " + privateTestDir + "gvcf.basepairResolution.vcf " + args, b37KGReference);
}
@Test(enabled = true)
@Test
public void testUpdatePGT() {
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf", b37KGReference),
1,
Arrays.asList("8d9788afd0de26bd9d9e55dd0e9fc3ed"));
Collections.singletonList("8d9788afd0de26bd9d9e55dd0e9fc3ed"));
executeTest("testUpdatePGT", spec);
}
@Test(enabled = true)
@Test
public void testUpdatePGTStrandAlleleCountsBySample() throws IOException{
final String logFileName = new String("testUpdatePGTStrandAlleleCountsBySample.log");
WalkerTestSpec spec = new WalkerTestSpec(
final String logFileName = "testUpdatePGTStrandAlleleCountsBySample.log";
final WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf -A StrandAlleleCountsBySample -log " + logFileName, b37KGReference),
1,
Arrays.asList("5dd4698da963a423446bb1e183eb75aa"));
Collections.singletonList("5dd4698da963a423446bb1e183eb75aa"));
executeTest("testUpdatePGTStrandAlleleCountsBySample", spec);
File file = new File(logFileName);
final File file = new File(logFileName);
Assert.assertTrue(FileUtils.readFileToString(file).contains(AnnotationUtils.ANNOTATION_HC_WARN_MSG));
}
@Test(enabled = true)
@Test
public void combineSingleSamplePipelineGVCF() {
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V:sample1 " + privateTestDir + "combine.single.sample.pipeline.1.vcf" +
" -V:sample2 " + privateTestDir + "combine.single.sample.pipeline.2.vcf" +
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
" -L 20:10,000,000-11,000,000", b37KGReference),
1,
Arrays.asList("c9edd4ca8c2801c4681322087d82e781"));
Collections.singletonList("c9edd4ca8c2801c4681322087d82e781"));
executeTest("combineSingleSamplePipelineGVCF", spec);
}
@Test(enabled = true)
@Test
public void testTetraploidRun() {
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V:sample1 " + privateTestDir + "tetraploid-gvcf-1.vcf" +
" -V:sample2 " + privateTestDir + "tetraploid-gvcf-2.vcf" +
" -V:sample3 " + privateTestDir + "tetraploid-gvcf-3.vcf" +
" -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference),
1,
Arrays.asList("64fa89f20ee25df21ad20ce4ada7e7ad"));
Collections.singletonList("64fa89f20ee25df21ad20ce4ada7e7ad"));
executeTest("testTetraploidRun", spec);
}
@Test(enabled= true)
@Test
public void testMixedPloidyRun() {
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V:sample1 " + privateTestDir + "haploid-gvcf-1.vcf" +
" -V:sample2 " + privateTestDir + "tetraploid-gvcf-2.vcf" +
" -V:sample3 " + privateTestDir + "diploid-gvcf-3.vcf" +
" -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference),
1,
Arrays.asList("b1d93f4cd93093c208be2c9842f38d12"));
Collections.singletonList("b1d93f4cd93093c208be2c9842f38d12"));
executeTest("testMixedPloidyRun", spec);
}
@ -146,121 +145,121 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -L " + privateTestDir + "tetraploid-gvcfs.intervals" +
" -maxNumPLValues 3", b37KGReference),
1,
Arrays.asList("c0dcf62fb116c4c0baabe432eceea52c"));
Collections.singletonList("c0dcf62fb116c4c0baabe432eceea52c"));
executeTest("testMixedPloidyMaxNumPLValuesRun", spec);
}
@Test(enabled = true)
@Test
public void combineSingleSamplePipelineGVCF_includeNonVariants() {
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V:sample1 " + privateTestDir + "combine.single.sample.pipeline.1.vcf" +
" -V:sample2 " + privateTestDir + "combine.single.sample.pipeline.2.vcf" +
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
" --includeNonVariantSites -L 20:10,030,000-10,033,000 -L 20:10,386,000-10,386,500", b37KGReference),
1,
Arrays.asList("c2f30f25ba4a84e38c04aa49b95694e8"));
Collections.singletonList("c2f30f25ba4a84e38c04aa49b95694e8"));
executeTest("combineSingleSamplePipelineGVCF_includeNonVariants", spec);
}
@Test(enabled = true)
@Test
public void combineSingleSamplePipelineGVCFHierarchical() {
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V " + privateTestDir + "combine.single.sample.pipeline.combined.vcf" +
" -V:sample1 " + privateTestDir + "combine.single.sample.pipeline.1.vcf" +
" -V:sample2 " + privateTestDir + "combine.single.sample.pipeline.2.vcf" +
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
" -L 20:10,000,000-20,000,000", b37KGReference),
1,
Arrays.asList("f48114bc6348cdc9dc4f0960f5dcf5f8"));
Collections.singletonList("f48114bc6348cdc9dc4f0960f5dcf5f8"));
executeTest("combineSingleSamplePipelineGVCFHierarchical", spec);
}
@Test(enabled = true)
@Test
public void combineSingleSamplePipelineGVCF_addDbsnp() {
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V:sample1 " + privateTestDir + "combine.single.sample.pipeline.1.vcf" +
" -V:sample2 " + privateTestDir + "combine.single.sample.pipeline.2.vcf" +
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
" -L 20:10,000,000-11,000,000 --dbsnp " + b37dbSNP132, b37KGReference),
1,
Arrays.asList("f88841deb5c2ce4f3bbea1e914a13898"));
Collections.singletonList("f88841deb5c2ce4f3bbea1e914a13898"));
executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec);
}
@Test(enabled = true)
@Test
public void combineBPresGVCFs() {
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V " + privateTestDir + "NA12891.BPres.g.vcf" +
" -V " + privateTestDir + "NA12892.BPres.g.vcf" +
" -L 20:10433000-10436909", b37KGReference),
1,
Arrays.asList("f342872f485e6978501facc78c354078"));
Collections.singletonList("f342872f485e6978501facc78c354078"));
executeTest("combineBPresGVCFs", spec);
}
@Test(enabled = true)
@Test
public void testJustOneSample() {
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -L 1:69485-69791 -o %s -R " + b37KGReference +
" -V " + privateTestDir + "gvcfExample1.vcf",
1,
Arrays.asList("9ff344a5ab87a2c3b128e435e2e86db0"));
Collections.singletonList("9ff344a5ab87a2c3b128e435e2e86db0"));
executeTest("testJustOneSample", spec);
}
@Test(enabled = true)
@Test
public void testSamplesWithDifferentLs() {
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -L 1:69485-69791 -o %s -R " + b37KGReference +
" -V " + privateTestDir + "gvcfExample1.vcf" +
" -V " + privateTestDir + "gvcfExample2.vcf",
1,
Arrays.asList("0c07ed795562ea96eab427e63a970384"));
Collections.singletonList("0c07ed795562ea96eab427e63a970384"));
executeTest("testSamplesWithDifferentLs", spec);
}
@Test(enabled = true)
@Test
public void testNoPLsException() {
// Test with input files with (1) 0/0 and (2) ./.
final String md5 = "2f3d71272fdac19ac861cc7159edfb08";
WalkerTestSpec spec1 = new WalkerTestSpec(
final WalkerTestSpec spec1 = new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -L 1:1115550-1115551 -o %s -R " + hg19Reference +
" --variant " + privateTestDir + "combined_genotype_gvcf_exception.vcf",
1,
Arrays.asList(md5));
WalkerTestSpec spec2 = new WalkerTestSpec(
Collections.singletonList(md5));
final WalkerTestSpec spec2 = new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -L 1:1115550-1115551 -o %s -R " + hg19Reference +
" --variant " + privateTestDir + "combined_genotype_gvcf_exception.nocall.vcf",
1,
Arrays.asList(md5));
Collections.singletonList(md5));
executeTest("testNoPLsException.1", spec1);
executeTest("testNoPLsException.2", spec2);
}
@Test
public void testNDA() {
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
baseBPResolutionString("-nda"),
1,
Arrays.asList("ce064429e6cbcaa956d52ef22e102f2f"));
Collections.singletonList("ce064429e6cbcaa956d52ef22e102f2f"));
executeTest("testNDA", spec);
}
@Test
public void testMaxAltAlleles() {
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
baseBPResolutionString("-maxAltAlleles 1"),
1,
Arrays.asList("1f1c0605fc8a500c9646132e0d7420a0"));
Collections.singletonList("1f1c0605fc8a500c9646132e0d7420a0"));
executeTest("testMaxAltAlleles", spec);
}
@Test
public void testStandardConf() {
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
baseBPResolutionString("-stand_call_conf 300 -stand_emit_conf 100"),
1,
Arrays.asList("0283e784ed49bc2dce32a26137c43409"));
Collections.singletonList("0283e784ed49bc2dce32a26137c43409"));
executeTest("testStandardConf", spec);
}
@ -274,7 +273,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
"--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("")
1, Collections.singletonList("")
);
specHaplotypeCaller.disableShadowBCF(); //TODO: Remove when BaseTest.assertAttributesEquals() works with SAC
final File gVCF = executeTest("testStrandAlleleCountsBySampleHaplotypeCaller", specHaplotypeCaller).getFirst().get(0);
@ -283,7 +282,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
final WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V " + gVCF.getAbsolutePath(), b37KGReference),
1,
Arrays.asList("34d76dc8dabc6a97e6d8f5365d7531e5"));
Collections.singletonList("34d76dc8dabc6a97e6d8f5365d7531e5"));
spec.disableShadowBCF(); //TODO: Remove when BaseTest.assertAttributesEquals() works with SAC
executeTest("testStrandAlleleCountsBySample", spec);
}
@ -291,7 +290,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
@Test
public void testUniquifiedSamples() throws IOException {
//two copies of 5 samples; will also test InbreedingCoeff calculation for uniquified samples
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V:sample1 " + privateTestDir + "combine.single.sample.pipeline.1.vcf" +
" -V:sample1B " + privateTestDir + "combine.single.sample.pipeline.1.vcf" +
" -V:sample2 " + privateTestDir + "combine.single.sample.pipeline.2.vcf" +
@ -300,7 +299,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:combined2 " + privateTestDir + "combine.single.sample.pipeline.combined.vcf" +
" --uniquifySamples", b37KGReference),
1,
Arrays.asList("16d7374502fa3cf99863d15d31b5ef86"));
Collections.singletonList("16d7374502fa3cf99863d15d31b5ef86"));
executeTest("testUniquifiedSamples", spec);
}
@ -321,7 +320,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
final LineIterator lineIteratorVCF = codec.makeSourceFromStream(new PositionalBufferedStream(s));
codec.readHeader(lineIteratorVCF);
List<String> attributeValues = new ArrayList<String>();
final List<String> attributeValues = new ArrayList<String>();
while (lineIteratorVCF.hasNext()) {
final String line = lineIteratorVCF.next();
Assert.assertFalse(line == null);
@ -352,7 +351,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + gvcf1 + " -V " + gvcf2 + " -V " + gvcf3,
1,
Arrays.asList(""));
Collections.singletonList(""));
genotypeBase.disableShadowBCF();
final File genotypeBaseVCF = executeTest("genotypeBase", genotypeBase).getFirst().get(0);
final List<VariantContext> BASE_VARIANT_CONTEXTS = getVariantContexts(genotypeBaseVCF);
@ -362,14 +361,14 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
"-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + gvcf1 + " -V " + gvcf2,
1,
Arrays.asList(""));
Collections.singletonList(""));
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(""));
Collections.singletonList(""));
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);
@ -380,14 +379,14 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
"-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + combined_gVCF12 + " -V " + gvcf3,
1,
Arrays.asList(""));
Collections.singletonList(""));
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(""));
Collections.singletonList(""));
genotype12then3.disableShadowBCF();
final File genotype12then3VCF = executeTest("genotype12then3", genotype12then3).getFirst().get(0);
final List<VariantContext> VARIANT_CONTEXTS_12then3 = getVariantContexts(genotype12then3VCF);
@ -398,21 +397,21 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
"-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + gvcf1 + " -V " + gvcf3,
1,
Arrays.asList(""));
Collections.singletonList(""));
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(""));
Collections.singletonList(""));
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(""));
Collections.singletonList(""));
genotype13then2.disableShadowBCF();
final File genotype13then2VCF = executeTest("genotype13then2", genotype13then2).getFirst().get(0);
final List<VariantContext> VARIANT_CONTEXTS_13then2 = getVariantContexts(genotype13then2VCF);
@ -423,14 +422,14 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
"-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + gvcf1 + " -V " + gvcf2 + " -V " + gvcf3,
1,
Arrays.asList(""));
Collections.singletonList(""));
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(""));
Collections.singletonList(""));
genotype123.disableShadowBCF();
final File genotype123VCF = executeTest("genotype123", genotype123).getFirst().get(0);
final List<VariantContext> VARIANT_CONTEXTS_123 = getVariantContexts(genotype123VCF);
@ -474,113 +473,114 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
private static final String simpleSpanningDeletionsMD5 = "4629c2f02ff58c111828269091cded82";
@Test(enabled = true)
@Test
public void testSpanningDeletionsMD5() {
WalkerTestSpec spec = new WalkerTestSpec(
final 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",
1,
Arrays.asList(simpleSpanningDeletionsMD5));
Collections.singletonList(simpleSpanningDeletionsMD5));
spec.disableShadowBCF();
executeTest("testSpanningDeletionsMD5", spec);
}
@Test(enabled = true)
@Test
public void testSpanningDeletionsFromCombinedGVCF() {
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + privateTestDir + "spanningDel.combined.g.vcf",
1,
Arrays.asList(simpleSpanningDeletionsMD5));
Collections.singletonList(simpleSpanningDeletionsMD5));
spec.disableShadowBCF();
executeTest("testSpanningDeletionsFromCombinedGVCFMD5", spec);
}
@Test(enabled = true)
@Test
public void testMultipleSpanningDeletionsMD5() {
WalkerTestSpec spec = new WalkerTestSpec(
final 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("7fe5364565585d31a0bb6a9dfa4a01d4"));
Collections.singletonList("7fe5364565585d31a0bb6a9dfa4a01d4"));
spec.disableShadowBCF();
executeTest("testMultipleSpanningDeletionsMD5", spec);
}
@Test(enabled = true)
@Test
public void testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles() {
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + privateTestDir + "spanningDel.delOnly.g.vcf",
1,
Arrays.asList("057f9368f380bf3c12b539a749deac61"));
Collections.singletonList("057f9368f380bf3c12b539a749deac61"));
spec.disableShadowBCF();
executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec);
}
@Test(enabled = true)
@Test
public void testDeprecatedSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles() {
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + privateTestDir + "spanningDel.depr.delOnly.g.vcf",
1,
Arrays.asList("e8f5186718050fe0784416e41425563f"));
Collections.singletonList("e8f5186718050fe0784416e41425563f"));
spec.disableShadowBCF();
executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec);
}
@Test(enabled = true)
@Test
public void testGenotypingSpanningDeletionOverSpan() {
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + privateTestDir + "spanningDel.delOverSpan.1.g.vcf -V " +
privateTestDir + "spanningDel.delOverSpan.2.g.vcf",
0,
Arrays.asList("")); // we do not care about the md5; we just want to make sure it doesn't blow up with an error
Collections.singletonList("")); // we do not care about the md5; we just want to make sure it doesn't blow up with an error
spec.disableShadowBCF();
executeTest("testGenotypingSpanningDeletionOverSpan", spec);
}
@Test(enabled = true)
@Test
public void testBadADPropagationHaploidBugTest() {
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + privateTestDir + "ad-bug-input.vcf",
1,
Arrays.asList("5ed5cb6aac68aa8943dc45b8b90eb508"));
Collections.singletonList("5ed5cb6aac68aa8943dc45b8b90eb508"));
spec.disableShadowBCF();
executeTest("testBadADPropagationHaploidBugTest", spec);
}
@Test(enabled = true)
@Test
public void testSAC() {
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + privateTestDir + "261_S01_raw_variants_gvcf.vcf",
1,
Arrays.asList("37eec6aedd26aa3430a15d90d7f8a011"));
Collections.singletonList("37eec6aedd26aa3430a15d90d7f8a011"));
spec.disableShadowBCF();
executeTest("testSAC", spec);
}
@Test(enabled = true)
@Test
public void testSACMultisampleTetraploid() {
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + privateTestDir + "tetraploid-multisample-sac.g.vcf",
1,
Arrays.asList("76532a74d4ba49f23362c149ad31a229"));
Collections.singletonList("76532a74d4ba49f23362c149ad31a229"));
spec.disableShadowBCF();
executeTest("testSACMultisampleTetraploid", spec);
}
@Test(enabled = true)
@Test
public void testSetZeroRGQsToNoCall() {
WalkerTestSpec spec = new WalkerTestSpec(
final WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V " + privateTestDir + "set.zero.RGQs.no.call.sample1.g.vcf" +
" -V " + privateTestDir + "set.zero.RGQs.no.call.sample2.g.vcf" +
" -L chr16:1279274-1279874 -allSites", hg19ReferenceWithChrPrefixInChromosomeNames),
Arrays.asList("b7106be316e43ca04204b78038f65c9f"));
Collections.singletonList("b7106be316e43ca04204b78038f65c9f"));
spec.disableShadowBCF();
executeTest("testSetZeroRGQsToNoCall", spec);
}
@ -588,7 +588,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
public void testAlleleSpecificAnnotations() {
final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V "
+ privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.chr20snippet.g.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("89712a9fe5b6db16be2257be2b0b4759"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("89712a9fe5b6db16be2257be2b0b4759"));
spec.disableShadowBCF();
executeTest("testAlleleSpecificAnnotations", spec);
}
@ -597,7 +597,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
public void testASMateRankSumAnnotation() {
final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -A AS_MQMateRankSumTest --disableDithering -V "
+ privateTestDir + "NA12878.AS.MateRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.MateRankSum.chr20snippet.g.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("8e41a139600ab58a67910cdc60053726"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("8e41a139600ab58a67910cdc60053726"));
spec.disableShadowBCF();
executeTest("testASMateRankSumAnnotation", spec);
}
@ -606,7 +606,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
public void testASInsertSizeRankSumAnnotation() {
final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V "
+ privateTestDir + "NA12878.AS.InsertSizeRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.InsertSizeRankSum.chr20snippet.g.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("b1334fbfbf21934aac1c1eda0b5062d5"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("b1334fbfbf21934aac1c1eda0b5062d5"));
spec.disableShadowBCF();
executeTest("testASInsertSizeRankSumAnnotation", spec);
}
@ -619,7 +619,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
public void testAlleleSpecificAnnotations_oneSample() {
final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V "
+ privateTestDir + "NA12878.AS.chr20snippet.g.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("7d86260e91fe74588e01339a2064b59c"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("7d86260e91fe74588e01339a2064b59c"));
spec.disableShadowBCF();
executeTest("testAlleleSpecificAnnotations_oneSample", spec);
}
@ -629,7 +629,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
public void testAlleleSpecificAnnotations_elevenSamples() {
final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V "
+ privateTestDir + "multiSamples.g.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("a889fe6775575513e84905b4fa98f8b3"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("a889fe6775575513e84905b4fa98f8b3"));
spec.disableShadowBCF();
executeTest("testAlleleSpecificAnnotations_elevenSamples", spec);
}
@ -652,4 +652,13 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
executeTest("testAlleleSpecificAnnotations", spec);
}
//Regression test for https://github.com/broadinstitute/gsa-unstable/issues/1281
@Test
public void testGenotypingSpanningDeletionWithAllSites() {
final WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V " + privateTestDir + "spanningDel.genotyping.g.vcf -allSites", b37KGReference),
Collections.singletonList("7cc3b08a37ed0c2e556debc1023cff2b"));
spec.disableShadowBCF();
executeTest("testGenotypingSpanningDeletionWithAllSites", spec);
}
}