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this.allele, getAlleles(), and getAltAlleles() now return List not set 

-- Changes associated code throughout the codebase
-- Updated necessary (but minimal) UnitTests to reflect new behavior
-- Much better makealleles() function in VC.java that enforces a lot of key constraints in VC
This commit is contained in:
Mark DePristo 2011-10-09 11:45:55 -07:00
parent 822654b119
commit 46e7370128
12 changed files with 55 additions and 59 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
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@ -47,7 +47,7 @@ public class AlleleBalanceBySample extends GenotypeAnnotation implements Experim
if (!g.isHet())
return null;
Set<Allele> altAlleles = vc.getAlternateAlleles();
Collection<Allele> altAlleles = vc.getAlternateAlleles();
if ( altAlleles.size() == 0 )
return null;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
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@ -33,6 +33,7 @@ import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.PrintStream;
import java.util.List;
import java.util.Map;
import java.util.Set;
@ -76,7 +77,7 @@ public abstract class AlleleFrequencyCalculationModel implements Cloneable {
*/
protected abstract void getLog10PNonRef(RefMetaDataTracker tracker,
ReferenceContext ref,
Map<String, Genotype> GLs, Set<Allele> Alleles,
Map<String, Genotype> GLs, List<Allele> Alleles,
double[] log10AlleleFrequencyPriors,
double[] log10AlleleFrequencyPosteriors);

9
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
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@ -29,19 +29,14 @@ import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.SimpleTimer;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import sun.reflect.generics.reflectiveObjects.NotImplementedException;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;
import java.util.*;
public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
//
@ -58,7 +53,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
public void getLog10PNonRef(RefMetaDataTracker tracker,
ReferenceContext ref,
Map<String, Genotype> GLs, Set<Allele>alleles,
Map<String, Genotype> GLs, List<Allele> alleles,
double[] log10AlleleFrequencyPriors,
double[] log10AlleleFrequencyPosteriors) {
final int numAlleles = alleles.size();

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java
View File

@ -54,7 +54,7 @@ public class GridSearchAFEstimation extends AlleleFrequencyCalculationModel {
protected void getLog10PNonRef(RefMetaDataTracker tracker,
ReferenceContext ref,
Map<String, Genotype> GLs, Set<Allele>alleles,
Map<String, Genotype> GLs, List<Allele> alleles,
double[] log10AlleleFrequencyPriors,
double[] log10AlleleFrequencyPosteriors) {
initializeAFMatrix(GLs);

4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -423,7 +423,7 @@ public class UnifiedGenotyperEngine {
int endLoc = calculateEndPos(vc.getAlleles(), vc.getReference(), loc);
Set<Allele> myAlleles = vc.getAlleles();
Set<Allele> myAlleles = new HashSet<Allele>(vc.getAlleles());
// strip out the alternate allele if it's a ref call
if ( bestAFguess == 0 && UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY ) {
myAlleles = new HashSet<Allele>(1);
@ -447,7 +447,7 @@ public class UnifiedGenotyperEngine {
return new VariantCallContext(vcCall, confidentlyCalled(phredScaledConfidence, PofF));
}
private int calculateEndPos(Set<Allele> alleles, Allele refAllele, GenomeLoc loc) {
private int calculateEndPos(Collection<Allele> alleles, Allele refAllele, GenomeLoc loc) {
// TODO - temp fix until we can deal with extended events properly
// for indels, stop location is one more than ref allele length
boolean isSNP = true, hasNullAltAllele = false;

5
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
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@ -10,6 +10,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.Collection;
import java.util.Set;
/**
@ -142,8 +143,8 @@ public class ValidationReport extends VariantEvaluator implements StandardEval {
public boolean haveDifferentAltAlleles(VariantContext eval, VariantContext comp) {
Set<Allele> evalAlts = eval.getAlternateAlleles();
Set<Allele> compAlts = comp.getAlternateAlleles();
Collection<Allele> evalAlts = eval.getAlternateAlleles();
Collection<Allele> compAlts = comp.getAlternateAlleles();
if ( evalAlts.size() != compAlts.size() ) {
return true;
} else {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
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@ -237,7 +237,7 @@ public class VariantValidationAssessor extends RodWalker<VariantContext,Integer>
infoMap.put("HomVarPct", String.format("%.1f", 100.0*homVarProp));
infoMap.put("HetPct", String.format("%.1f", 100.0*hetProp));
infoMap.put("HW", String.format("%.2f", hwScore));
Set<Allele> altAlleles = vContext.getAlternateAlleles();
Collection<Allele> altAlleles = vContext.getAlternateAlleles();
int altAlleleCount = altAlleles.size() == 0 ? 0 : vContext.getChromosomeCount(altAlleles.iterator().next());
if ( !isViolation && altAlleleCount > 0 )
numTrueVariants++;

71
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
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@ -181,7 +181,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
protected Type type = null;
/** A set of the alleles segregating in this context */
protected LinkedHashSet<Allele> alleles = null;
final protected List<Allele> alleles;
/** A mapping from sampleName -> genotype objects for all genotypes associated with this context */
protected Map<String, Genotype> genotypes = null;
@ -355,7 +355,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
if ( alleles == null ) { throw new IllegalArgumentException("Alleles cannot be null"); }
// we need to make this a LinkedHashSet in case the user prefers a given ordering of alleles
this.alleles = alleleCollectionToSet(new LinkedHashSet<Allele>(), alleles);
this.alleles = makeAlleles(alleles);
if ( genotypes == null ) { genotypes = NO_GENOTYPES; }
@ -445,7 +445,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @param alleles the set of allele segregating alleles at this site. Must include those in genotypes, but may be more
* @return vc subcontext
*/
public VariantContext subContextFromGenotypes(Collection<Genotype> genotypes, Set<Allele> alleles) {
public VariantContext subContextFromGenotypes(Collection<Genotype> genotypes, Collection<Allele> alleles) {
return new VariantContext(getSource(), contig, start, stop, alleles, genotypes != null ? genotypeCollectionToMap(new TreeMap<String, Genotype>(), genotypes) : null, getNegLog10PError(), filtersWereApplied() ? getFilters() : null, getAttributes(), getReferenceBaseForIndel());
}
@ -687,17 +687,6 @@ public class VariantContext implements Feature { // to enable tribble intergrati
return ref;
}
/** Private helper routine that grabs the reference allele but doesn't throw an error if there's no such allele */
// private Allele getReferenceWithoutError() {
// for ( Allele allele : getAlleles() ) {
// if ( allele.isReference() ) {
// return allele;
// }
// }
//
// return null;
// }
/**
* @return true if the context is strictly bi-allelic
@ -754,7 +743,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
*
* @return the set of alleles
*/
public Set<Allele> getAlleles() { return alleles; }
public List<Allele> getAlleles() { return alleles; }
/**
* Gets the alternate alleles. This method should return all the alleles present at the location,
@ -763,14 +752,8 @@ public class VariantContext implements Feature { // to enable tribble intergrati
*
* @return the set of alternate alleles
*/
public Set<Allele> getAlternateAlleles() {
LinkedHashSet<Allele> altAlleles = new LinkedHashSet<Allele>();
for ( Allele allele : alleles ) {
if ( allele.isNonReference() )
altAlleles.add(allele);
}
return Collections.unmodifiableSet(altAlleles);
public List<Allele> getAlternateAlleles() {
return alleles.subList(1, alleles.size());
}
/**
@ -797,14 +780,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @throws IllegalArgumentException if i is invalid
*/
public Allele getAlternateAllele(int i) {
int n = 0;
for ( Allele allele : alleles ) {
if ( allele.isNonReference() && n++ == i )
return allele;
}
throw new IllegalArgumentException("Requested " + i + " alternative allele but there are only " + n + " alternative alleles " + this);
return alleles.get(i+1);
}
/**
@ -813,8 +789,8 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* regardless of ordering. Otherwise returns false.
*/
public boolean hasSameAlternateAllelesAs ( VariantContext other ) {
Set<Allele> thisAlternateAlleles = getAlternateAlleles();
Set<Allele> otherAlternateAlleles = other.getAlternateAlleles();
List<Allele> thisAlternateAlleles = getAlternateAlleles();
List<Allele> otherAlternateAlleles = other.getAlternateAlleles();
if ( thisAlternateAlleles.size() != otherAlternateAlleles.size() ) {
return false;
@ -1121,7 +1097,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
if ( !hasGenotypes() )
return;
Set<Allele> reportedAlleles = getAlleles();
List<Allele> reportedAlleles = getAlleles();
Set<Allele> observedAlleles = new HashSet<Allele>();
observedAlleles.add(getReference());
for ( Genotype g : getGenotypes().values() ) {
@ -1371,17 +1347,34 @@ public class VariantContext implements Feature { // to enable tribble intergrati
}
// protected basic manipulation routines
private static LinkedHashSet<Allele> alleleCollectionToSet(LinkedHashSet<Allele> dest, Collection<Allele> alleles) {
for ( Allele a : alleles ) {
for ( Allele b : dest ) {
private static List<Allele> makeAlleles(Collection<Allele> alleles) {
final List<Allele> alleleList = new ArrayList<Allele>(alleles.size());
boolean sawRef = false;
for ( final Allele a : alleles ) {
for ( final Allele b : alleleList ) {
if ( a.equals(b, true) )
throw new IllegalArgumentException("Duplicate allele added to VariantContext: " + a);
}
dest.add(a);
// deal with the case where the first allele isn't the reference
if ( a.isReference() ) {
if ( sawRef )
throw new IllegalArgumentException("Alleles for a VariantContext must contain a single reference allele: " + alleles);
alleleList.add(0, a);
sawRef = true;
}
else
alleleList.add(a);
}
return dest;
if ( alleleList.isEmpty() )
throw new IllegalArgumentException("Cannot create a VariantContext with an empty allele list");
if ( alleleList.get(0).isNonReference() )
throw new IllegalArgumentException("Alleles for a VariantContext must contain a single reference allele: " + alleles);
return alleleList;
}
public static Map<String, Genotype> genotypeCollectionToMap(Map<String, Genotype> dest, Collection<Genotype> genotypes) {

2
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
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@ -666,7 +666,7 @@ public class VariantContextUtils {
return merged;
}
private static final boolean hasPLIncompatibleAlleles(final Set<Allele> alleleSet1, final Set<Allele> alleleSet2) {
private static final boolean hasPLIncompatibleAlleles(final Collection<Allele> alleleSet1, final Collection<Allele> alleleSet2) {
final Iterator<Allele> it1 = alleleSet1.iterator();
final Iterator<Allele> it2 = alleleSet2.iterator();

4
public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java
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@ -70,7 +70,7 @@ public class DiffableReaderUnitTest extends BaseTest {
private static void testLeaf(DiffNode rec, String field, Object expected) {
DiffElement value = rec.getElement(field);
Assert.assertNotNull(value, "Expected to see leaf named " + field + " in rec " + rec);
Assert.assertEquals(value.getValue().getValue(), expected, "Expected to leaf named " + field + " to have value " + expected + " in rec " + rec);
Assert.assertEquals(value.getValue().getValue(), expected, "Expected to see leaf named " + field + " to have value " + expected + " in rec " + rec + " but got instead " + value.getValue().getValue());
}
@Test(enabled = true, dependsOnMethods = "testPluggableDiffableReaders")
@ -95,7 +95,7 @@ public class DiffableReaderUnitTest extends BaseTest {
testLeaf(rec1, "POS", 2646);
testLeaf(rec1, "ID", "rs62635284");
testLeaf(rec1, "REF", Allele.create("G", true));
testLeaf(rec1, "ALT", new HashSet<Allele>(Arrays.asList(Allele.create("A"))));
testLeaf(rec1, "ALT", Arrays.asList(Allele.create("A")));
testLeaf(rec1, "QUAL", 0.15);
testLeaf(rec1, "FILTER", Collections.<Object>emptySet());
testLeaf(rec1, "AC", "2");

8
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
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@ -13,6 +13,7 @@ import org.testng.Assert;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
@ -261,11 +262,16 @@ public class VariantContextUnitTest extends BaseTest {
new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(delRef, del));
}
@Test (expectedExceptions = IllegalStateException.class)
@Test (expectedExceptions = IllegalArgumentException.class)
public void testBadConstructorArgs3() {
new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(del));
}
@Test (expectedExceptions = IllegalArgumentException.class)
public void testBadConstructorArgs4() {
new VariantContext("test", insLoc, insLocStart, insLocStop, Collections.<Allele>emptyList());
}
@Test (expectedExceptions = IllegalArgumentException.class)
public void testBadConstructorArgsDuplicateAlleles1() {
new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(Aref, T, T));

2
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java
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@ -439,7 +439,7 @@ public class VariantContextUtilsUnitTest extends BaseTest {
new MergeGenotypesTest("PerserveAlleles", "1,2",
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)),
makeVC("2", Arrays.asList(Aref, C), makeG("s2", Aref, C, 2)),
makeVC("3", Arrays.asList(Aref, C, T), makeG("s1", Aref, T, 1), makeG("s2", Aref, C, 2)));
makeVC("3", Arrays.asList(Aref, T, C), makeG("s1", Aref, T, 1), makeG("s2", Aref, C, 2)));
new MergeGenotypesTest("TakeGenotypePartialOverlap-1,2", "1,2",
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)),