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Merge pull request #1625 from broadinstitute/ldg_fixPLsubsettingGQproblem 

Update the GQ after PLs get subset
This commit is contained in:
Geraldine Van der Auwera 2017-08-07 17:43:49 -04:00 committed by GitHub
parent 02c8302290 d28b086862
commit 9ba104a6e9
5 changed files with 15 additions and 11 deletions
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4
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java
View File

@ -154,7 +154,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "multiallele-gt.vcf --no_cmdline_in_header -split",
1,
Arrays.asList("80b4a994a569ecfbd628121b85e64339"));
Arrays.asList("a7dcd0cf9542bf58153023d26deec06e"));
executeTest("test left alignment of multiple alleles with genoptypes", spec);
}
@ -172,7 +172,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "multiallele-gt.vcf --no_cmdline_in_header -split -keepOriginalAC",
1,
Arrays.asList("6774b43d9446278e716d7198717a5f85"));
Arrays.asList("26e67892c75ded1756709476520d4264"));
executeTest("test left alignment of multiple alleles with genoptypes, keep original AC", spec);
}

6
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -494,7 +494,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
{ privateTestDir+"forHardLeftAlignVariantsTest.vcf", "", "a835454cbd132f2d56defb55ba13b2dd"},
{ privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT", "b19e508640a89f176f7ea347babfcc66"},
{ privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env", "15d982a280754804fa384ccc0f3a2ccf"},
{ privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -trimAlternates", "cbad00c0722a94c382f75b428f2a8e6c"},
{ privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -trimAlternates", "41ffddc776a2af55db297dbefc6d2097"},
{ privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env -trimAlternates", "a9f448502a27e777b3112cf98e1d325f"}
};
}
@ -782,7 +782,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header -sn NA12891 -trimAlternates",
1,
Arrays.asList("c8203bea524cdb66717abbbc50a234b5"));
Arrays.asList("f068e449cf3c142c8c5758c5eab38780"));
spec.disableShadowBCF();
executeTest("testSACDiploid", spec);
}
@ -794,7 +794,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header -sn NA12891 -trimAlternates",
1,
Arrays.asList("f48a3c789898e24fbec6db9c6e8d800a"));
Arrays.asList("ade30e246b807e45cf6c54db96fc8627"));
spec.disableShadowBCF();
executeTest("testSACNonDiploid", spec);
}

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java
View File

@ -100,7 +100,7 @@ public class SelectVariantsParallelIntegrationTest extends WalkerTest {
{ // AD and PL decoding race condition
final String testfile = privateTestDir + "race_condition.vcf";
final String args = "-env -trimAlternates -sn SAMPLE -L 1:1-10,000,000 -V " + testfile;
new ParallelSelectTestProvider(b37KGReference, args, "9983e6a41472e8956dd32f967bf87f05", nt);
new ParallelSelectTestProvider(b37KGReference, args, "6bd8bf3ebd72e91eba9b4e0a44d1744f", nt);
}
}

4
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java
View File

@ -851,9 +851,13 @@ public class GATKVariantContextUtils {
if ( newLikelihoods == null || (originalVC.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0) == 0 && likelihoodsAreUninformative(newLikelihoods) )) {
gb.noPL();
gb.noGQ();
} else {
gb.PL(newLikelihoods);
final int PLindex = MathUtils.maxElementIndex(newLikelihoods);
gb.log10PError(GenotypeLikelihoods.getGQLog10FromLikelihoods(PLindex, newLikelihoods));
}
}
// create the new strand allele counts array from the used alleles

10
public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java
View File

@ -1503,7 +1503,7 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, homC3AllelesSAC).make()).make(),
new VariantContextBuilder(vcBase).alleles(AG).make(),
Arrays.asList(new GenotypeBuilder(base).alleles(Arrays.asList(Aref)).PL(new double[]{-20, 0}).AD(new int[]{0, 1}).
attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{0, 0, 1, 1}).GQ(100).make())});
attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{0, 0, 1, 1}).GQ(200).make())});
tests.add(new Object[]{
new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(Arrays.asList(Aref, Aref, Aref)).AD(homRef3AllelesAD).PL(triploidRef3AllelesPL).
@ -1522,7 +1522,7 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, homC3AllelesSAC).make()).make(),
new VariantContextBuilder(vcBase).alleles(AG).make(),
Arrays.asList(new GenotypeBuilder(base).alleles(Arrays.asList(Aref, Aref, G)).PL(new double[]{0, -40, -70, -90}).AD(new int[]{20, 1}).
attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{0, 0, 1, 1}).GQ(100).make())});
attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{0, 0, 1, 1}).GQ(400).make())});
tests.add(new Object[]{
new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(homRef3AllelesAD).PL(homRef3AllelesPL).
@ -1547,19 +1547,19 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, hetRefG3AllelesSAC).make()).make(),
new VariantContextBuilder(vcBase).alleles(AG).make(),
Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{-20, 0, -50}).AD(new int[]{10, 11}).
attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{10, 10, 11, 11}).GQ(100).make())});
attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{10, 10, 11, 11}).GQ(200).make())});
tests.add(new Object[]{
new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(hetCG3AllelesAD).PL(hetCG3AllelesPL).
attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, hetCG3AllelesSAC).make()).make(),
new VariantContextBuilder(vcBase).alleles(AG).make(),
Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{0, -20, -30}).AD(new int[]{0, 11}).
attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{0, 0, 11, 11}).GQ(100).make())});
attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{0, 0, 11, 11}).GQ(200).make())});
tests.add(new Object[]{
new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(homG3AllelesAD).PL(homG3AllelesPL).
attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, homG3AllelesSAC).make()).make(),
new VariantContextBuilder(vcBase).alleles(AG).make(),
Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{-20, -40, 0}).AD(new int[]{0, 21}).
attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{0, 0, 21, 21}).GQ(100).make())});
attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{0, 0, 21, 21}).GQ(200).make())});
return tests.toArray(new Object[][]{});
}