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Merged bug fix from Stable into Unstable

This commit is contained in:
Eric Banks 2012-05-03 10:37:58 -04:00
parent 0f4cc1884d 567d01cee8
commit 1fc7b5d58b
4 changed files with 64 additions and 14 deletions
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12
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
View File

@ -4,6 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
@ -16,10 +17,7 @@ import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.*;
/**
@ -33,8 +31,12 @@ import java.util.Map;
public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
private static final int MIN_SAMPLES = 10;
private Set<String> founderIds;
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
//If available, get the founder IDs and cache them. the IC will only be computed on founders then.
if(founderIds == null)
founderIds = ((Walker)walker).getSampleDB().getFounderIds();
return calculateIC(vc);
}
@ -43,7 +45,7 @@ public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnno
}
private Map<String, Object> calculateIC(final VariantContext vc) {
final GenotypesContext genotypes = vc.getGenotypes();
final GenotypesContext genotypes = (founderIds == null || founderIds.isEmpty()) ? vc.getGenotypes() : vc.getGenotypes(founderIds);
if ( genotypes == null || genotypes.size() < MIN_SAMPLES )
return null;

23
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
View File

@ -82,6 +82,9 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
@Argument(shortName = "prior",required = false,fullName = "DeNovoPrior", doc="Prior for de novo mutations. Default: 1e-8")
private double deNovoPrior=1e-8;
@Argument(shortName = "fatherAlleleFirst",required = false,fullName = "FatherAlleleFirst", doc="Ouputs the father allele as the first allele in phased child genotype. i.e. father|mother rather than mother|father.")
private boolean fatherFAlleleFirst=false;
@Output
protected VCFWriter vcfWriter = null;
@ -183,12 +186,15 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
ArrayList<Allele> parentPhasedAlleles = new ArrayList<Allele>(2);
ArrayList<Allele> childPhasedAlleles = new ArrayList<Allele>(2);
//If there is a possible phasing between the mother and child => phase
//If there is a possible phasing between the parent and child => phase
int childTransmittedAlleleIndex = childAlleles.indexOf(parentAlleles.get(0));
if(childTransmittedAlleleIndex > -1){
trioPhasedGenotypes.put(parent, new Genotype(DUMMY_NAME, parentAlleles, Genotype.NO_LOG10_PERROR, null, null, true));
childPhasedAlleles.add(childAlleles.remove(childTransmittedAlleleIndex));
childPhasedAlleles.add(childAlleles.get(0));
if(parent.equals(FamilyMember.MOTHER))
childPhasedAlleles.add(childAlleles.get(0));
else
childPhasedAlleles.add(0,childAlleles.get(0));
trioPhasedGenotypes.put(FamilyMember.CHILD, new Genotype(DUMMY_NAME, childPhasedAlleles, Genotype.NO_LOG10_PERROR, null, null, true));
}
else if((childTransmittedAlleleIndex = childAlleles.indexOf(parentAlleles.get(1))) > -1){
@ -196,7 +202,10 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
parentPhasedAlleles.add(parentAlleles.get(0));
trioPhasedGenotypes.put(parent, new Genotype(DUMMY_NAME, parentPhasedAlleles, Genotype.NO_LOG10_PERROR, null, null, true));
childPhasedAlleles.add(childAlleles.remove(childTransmittedAlleleIndex));
childPhasedAlleles.add(childAlleles.get(0));
if(parent.equals(FamilyMember.MOTHER))
childPhasedAlleles.add(childAlleles.get(0));
else
childPhasedAlleles.add(0,childAlleles.get(0));
trioPhasedGenotypes.put(FamilyMember.CHILD, new Genotype(DUMMY_NAME, childPhasedAlleles, Genotype.NO_LOG10_PERROR, null, null, true));
}
//This is a Mendelian Violation => Do not phase
@ -296,6 +305,14 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
else{
phaseFamilyAlleles(mother, father, child);
}
//If child should phased genotype should be father first, then swap the alleles
if(fatherFAlleleFirst && trioPhasedGenotypes.get(FamilyMember.CHILD).isPhased()){
ArrayList<Allele> childAlleles = new ArrayList<Allele>(trioPhasedGenotypes.get(FamilyMember.CHILD).getAlleles());
childAlleles.add(childAlleles.remove(0));
trioPhasedGenotypes.put(FamilyMember.CHILD,new Genotype(DUMMY_NAME,childAlleles,Genotype.NO_LOG10_PERROR,null,null,true));
}
}
/**

10
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -198,4 +198,14 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
executeTest("Testing ChromosomeCounts annotation with PED file", spec);
}
@Test
public void testInbreedingCoeffPed() {
final String MD5 = "7f1314fada5cb1f35ba1996f8a7a686b";
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantAnnotator -R " + b37KGReference + " -A InbreedingCoeff --variant:vcf " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf" +
" -L " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf -NO_HEADER -ped " + validationDataLocation + "ug.random50000.family.ped -o %s", 1,
Arrays.asList(MD5));
executeTest("Testing InbreedingCoeff annotation with PED file", spec);
}
}

33
public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java
View File

@ -29,7 +29,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
"-o %s"
),
2,
Arrays.asList("16fefda693156eadf1481fd9de23facb","9418a7a6405b78179ca13a67b8bfcc14")
Arrays.asList("d54a142d68dca54e478c13f9a0e4c95c","1a37fcc93a73429f9065b942ab771233")
);
executeTest("testTrueNegativeMV", spec);
}
@ -48,7 +48,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
"-o %s"
),
2,
Arrays.asList("14cf1d21a54d8b9fb506df178b634c56","efc66ae3d036715b721f9bd35b65d556")
Arrays.asList("883ea7fd2b200c4b7fa95a4f7aa15931","7b1f5309c3d4f4aa7e9061f288dceb68")
);
executeTest("testTruePositiveMV", spec);
}
@ -67,7 +67,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
"-o %s"
),
2,
Arrays.asList("f9b0fae9fe1e0f09b883a292b0e70a12","398724bc1e65314cc5ee92706e05a3ee")
Arrays.asList("e812d62a3449b74b6948ee7deb8a0790","d00922496759e84c66a4b5e222e36997")
);
executeTest("testFalsePositiveMV", spec);
}
@ -86,7 +86,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
"-o %s"
),
2,
Arrays.asList("b8d1aa3789ce77b45430c62d13ee3006","a1a333e08fafb288cda0e7711909e1c3")
Arrays.asList("e3c572f933a40e1878a2cfa52049517a","60e4f0be344fb944ab3378f9ab27da64")
);
executeTest("testSpecialCases", spec);
}
@ -108,7 +108,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
"-o %s"
),
2,
Arrays.asList("7201ce7cc47db5840ac6b647709f7c33","c11b5e7cd7459d90d0160f917eff3b1e")
Arrays.asList("b42af3b73a2cb38cfc92f8047dd686b3","a69c3f9c005e852b44c29ab25e87ba0d")
);
executeTest("testPriorOption", spec);
}
@ -128,9 +128,30 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("398724bc1e65314cc5ee92706e05a3ee")
Arrays.asList("d00922496759e84c66a4b5e222e36997")
);
executeTest("testMVFileOption", spec);
}
//Test when running with the fatherAlleleFirst option
@Test
public void testFatherAlleleFirst() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T PhaseByTransmission",
"-NO_HEADER",
"-R " + b37KGReference,
"--variant " + TPTest,
"-ped "+ goodFamilyFile,
"-L 1:10109-10315",
"-mvf %s",
"-o %s",
"-fatherAlleleFirst"
),
2,
Arrays.asList("c158a3816357597543ef85c4478c41e8","4f8daca19c8f31bd87850c124f91e330")
);
executeTest("testFatherAlleleFirst", spec);
}
}