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Again, fixing the add call when we really mean replace 

-- Updating MD5s for UG to reflect that what was previously called ./.:.:10:0,0,0 is now just ./.  Eric will fix long-standing bug in QD observed from this change
-- VFW MD5s restored to their old correct values.  There was a bug in my implementation to caused the genotypes to not be parsed from the lazy output even through the header was incorrect.
This commit is contained in:
Mark DePristo 2011-11-21 19:15:56 -05:00
parent 9ea7b70a02
commit 5443d3634a
3 changed files with 12 additions and 33 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
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@ -398,15 +398,15 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
for ( final Genotype genotype : GLs.iterateInSampleNameOrder() ) {
if ( !genotype.hasLikelihoods() )
continue;
Genotype g = GLs.get(genotype.getSampleName());
double[] likelihoods = genotype.getLikelihoods().getAsVector();
final Genotype g = GLs.get(genotype.getSampleName());
final double[] likelihoods = genotype.getLikelihoods().getAsVector();
if (MathUtils.sum(likelihoods) <= SUM_GL_THRESH_NOCALL)
continue; // regular likelihoods
final double qual = Genotype.NO_LOG10_PERROR;
calls.add(new Genotype(g.getSampleName(), NO_CALL_ALLELES, qual, null, g.getAttributes(), false));
calls.replace(new Genotype(g.getSampleName(), NO_CALL_ALLELES, qual, null, g.getAttributes(), false));
}
return calls;

37
public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
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@ -14,12 +14,9 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
@Test
public void testNoAction() {
// note that this input if slightly malformed, but with the new properly
// only when really needed genotype loading of VCF files we don't actually
// fix the file in the output
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("b7b7c218e219cd923ce5b6eefc5b7171"));
Arrays.asList("8a105fa5eebdfffe7326bc5b3d8ffd1c"));
executeTest("test no action", spec);
}
@ -27,73 +24,55 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testClusteredSnps() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -window 10 --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("6d45a19e4066e7de6ff6a61f43ffad2b"));
Arrays.asList("27b13f179bb4920615dff3a32730d845"));
executeTest("test clustered SNPs", spec);
}
@Test
public void testMask1() {
// note that this input if slightly malformed, but with the new properly
// only when really needed genotype loading of VCF files we don't actually
// fix the file in the output
WalkerTestSpec spec1 = new WalkerTestSpec(
baseTestString() + " -maskName foo --mask:VCF3 " + validationDataLocation + "vcfexample2.vcf --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("65b5006bf3ee9d9d08a36d6b854773f2"));
Arrays.asList("578f9e774784c25871678e6464fd212b"));
executeTest("test mask all", spec1);
}
@Test
public void testMask2() {
// note that this input if slightly malformed, but with the new properly
// only when really needed genotype loading of VCF files we don't actually
// fix the file in the output
WalkerTestSpec spec2 = new WalkerTestSpec(
baseTestString() + " -maskName foo --mask:VCF " + validationDataLocation + "vcfMask.vcf --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("a275d36baca81a1ce03dbb528e95a069"));
Arrays.asList("bfa86a674aefca1b13d341cb14ab3c4f"));
executeTest("test mask some", spec2);
}
@Test
public void testMask3() {
// note that this input if slightly malformed, but with the new properly
// only when really needed genotype loading of VCF files we don't actually
// fix the file in the output
WalkerTestSpec spec3 = new WalkerTestSpec(
baseTestString() + " -maskName foo -maskExtend 10 --mask:VCF " + validationDataLocation + "vcfMask.vcf --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("c9489e1c1342817c36ab4f0770609bdb"));
Arrays.asList("5939f80d14b32d88587373532d7b90e5"));
executeTest("test mask extend", spec3);
}
@Test
public void testFilter1() {
WalkerTestSpec spec = new WalkerTestSpec(
// note that this input if slightly malformed, but with the new properly
// only when really needed genotype loading of VCF files we don't actually
// fix the file in the output
baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("327a611bf82c6c4ae77fbb6d06359f9d"));
Arrays.asList("45219dbcfb6f81bba2ea0c35f5bfd368"));
executeTest("test filter #1", spec);
}
@Test
public void testFilter2() {
// note that this input if slightly malformed, but with the new properly
// only when really needed genotype loading of VCF files we don't actually
// fix the file in the output
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("7612b3460575402ad78fa4173178bdcc"));
Arrays.asList("c95845e817da7352b9b72bc9794f18fb"));
executeTest("test filter #2", spec);
}
@Test
public void testFilterWithSeparateNames() {
// note that this input if slightly malformed, but with the new properly
// only when really needed genotype loading of VCF files we don't actually
// fix the file in the output
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("dce33441f58b284ac9ab94f8e64b84e3"));
Arrays.asList("b8cdd7f44ff1a395e0a9b06a87e1e530"));
executeTest("test filter with separate names #2", spec);
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -295,7 +295,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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("1e02f57fafaa41db71c531eb25e148e1"));
Arrays.asList("9be28cb208d8b0314d2bc2696e2fd8d4"));
executeTest("test MultiSample 1000G Phase1 indels with complicated records emitting all sites", spec4);
}