Deleted MutableVariantContext
-- All methods that used this capable now use VariantContext directly instead
This commit is contained in:
Mark DePristo
parent
b11c535527
commit
077397cb4b
|
|
@ -39,7 +39,6 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
|
|||
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
|
||||
import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
|
||||
import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
|
||||
import org.broadinstitute.sting.utils.variantcontext.MutableVariantContext;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
|
||||
|
||||
|
|
@ -466,9 +465,7 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
|
|||
|
||||
if (vcfWriter != null && writeVariant) {
|
||||
if (!vcComp.hasAttribute("callStatus")) {
|
||||
MutableVariantContext mvc = new MutableVariantContext(vcComp);
|
||||
mvc.putAttribute("callStatus", call.isCalledAlt(callConf) ? "ALT" : "REF" );
|
||||
vcfWriter.add(mvc);
|
||||
vcfWriter.add(VariantContext.modifyAttribute(vcComp, "callStatus", call.isCalledAlt(callConf) ? "ALT" : "REF"));
|
||||
}
|
||||
else
|
||||
vcfWriter.add(vcComp);
|
||||
|
|
|
|||
|
|
@ -1,212 +0,0 @@
|
|||
package org.broadinstitute.sting.utils.variantcontext;
|
||||
|
||||
|
||||
import java.util.Collection;
|
||||
import java.util.Map;
|
||||
import java.util.Set;
|
||||
import java.util.TreeMap;
|
||||
|
||||
/**
|
||||
* Mutable version of VariantContext
|
||||
*
|
||||
* @author depristo
|
||||
*/
|
||||
public class MutableVariantContext extends VariantContext {
|
||||
// ---------------------------------------------------------------------------------------------------------
|
||||
//
|
||||
// constructors
|
||||
//
|
||||
// ---------------------------------------------------------------------------------------------------------
|
||||
|
||||
public MutableVariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Collection<Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
|
||||
super(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes);
|
||||
}
|
||||
|
||||
public MutableVariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, GenotypeMap genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
|
||||
super(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes);
|
||||
}
|
||||
|
||||
public MutableVariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles) {
|
||||
super(source, contig, start, stop, alleles, NO_GENOTYPES, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null);
|
||||
}
|
||||
|
||||
public MutableVariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Collection<Genotype> genotypes) {
|
||||
super(source, contig, start, stop, alleles, genotypes, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null);
|
||||
}
|
||||
|
||||
public MutableVariantContext(VariantContext parent) {
|
||||
super(parent.getSource(), parent.contig, parent.start, parent.stop, parent.getAlleles(), parent.getGenotypes(), parent.getNegLog10PError(), parent.getFilters(), parent.getAttributes(), parent.getReferenceBaseForIndel());
|
||||
}
|
||||
|
||||
/**
|
||||
* Sets the alleles segregating in this context to the collect of alleles. Each of which must be unique according
|
||||
* to equals() in Allele. Validate() should be called when you are done modifying the context.
|
||||
*
|
||||
* @param alleles
|
||||
*/
|
||||
public void setAlleles(Collection<Allele> alleles) {
|
||||
this.alleles.clear();
|
||||
for ( Allele a : alleles )
|
||||
addAllele(a);
|
||||
}
|
||||
|
||||
/**
|
||||
* Adds allele to the segregating allele list in this context to the collection of alleles. The new
|
||||
* allele must be be unique according to equals() in Allele.
|
||||
* Validate() should be called when you are done modifying the context.
|
||||
*
|
||||
* @param allele
|
||||
*/
|
||||
public void addAllele(Allele allele) {
|
||||
final boolean allowDuplicates = false; // used to be a parameter
|
||||
|
||||
type = null;
|
||||
|
||||
for ( Allele a : alleles ) {
|
||||
if ( a.basesMatch(allele) && ! allowDuplicates )
|
||||
throw new IllegalArgumentException("Duplicate allele added to VariantContext" + this);
|
||||
}
|
||||
|
||||
// we are a novel allele
|
||||
alleles.add(allele);
|
||||
}
|
||||
|
||||
public void clearGenotypes() {
|
||||
genotypes = GenotypeMap.create();
|
||||
}
|
||||
|
||||
/**
|
||||
* Adds this single genotype to the context, not allowing duplicate genotypes to be added
|
||||
* @param genotype
|
||||
*/
|
||||
public void addGenotypes(Genotype genotype) {
|
||||
putGenotype(genotype.getSampleName(), genotype, false);
|
||||
}
|
||||
|
||||
/**
|
||||
* Adds these genotypes to the context, not allowing duplicate genotypes to be added
|
||||
* @param genotypes
|
||||
*/
|
||||
public void addGenotypes(Collection<Genotype> genotypes) {
|
||||
for ( Genotype g : genotypes ) {
|
||||
addGenotype(g);
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Adds these genotype to the context, not allowing duplicate genotypes to be added.
|
||||
* @param genotypes
|
||||
*/
|
||||
public void addGenotypes(Map<String, Genotype> genotypes) {
|
||||
for ( Map.Entry<String, Genotype> elt : genotypes.entrySet() ) {
|
||||
addGenotype(elt.getValue());
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Adds these genotypes to the context.
|
||||
*
|
||||
* @param genotypes
|
||||
*/
|
||||
public void putGenotypes(Map<String, Genotype> genotypes) {
|
||||
for ( Map.Entry<String, Genotype> g : genotypes.entrySet() )
|
||||
putGenotype(g.getKey(), g.getValue());
|
||||
}
|
||||
|
||||
/**
|
||||
* Adds these genotypes to the context.
|
||||
*
|
||||
* @param genotypes
|
||||
*/
|
||||
public void putGenotypes(Collection<Genotype> genotypes) {
|
||||
for ( Genotype g : genotypes )
|
||||
putGenotype(g);
|
||||
}
|
||||
|
||||
/**
|
||||
* Adds this genotype to the context, throwing an error if it's already bound.
|
||||
*
|
||||
* @param genotype
|
||||
*/
|
||||
public void addGenotype(Genotype genotype) {
|
||||
addGenotype(genotype.getSampleName(), genotype);
|
||||
}
|
||||
|
||||
/**
|
||||
* Adds this genotype to the context, throwing an error if it's already bound.
|
||||
*
|
||||
* @param genotype
|
||||
*/
|
||||
public void addGenotype(String sampleName, Genotype genotype) {
|
||||
putGenotype(sampleName, genotype, false);
|
||||
}
|
||||
|
||||
/**
|
||||
* Adds this genotype to the context.
|
||||
*
|
||||
* @param genotype
|
||||
*/
|
||||
public void putGenotype(Genotype genotype) {
|
||||
putGenotype(genotype.getSampleName(), genotype);
|
||||
}
|
||||
|
||||
/**
|
||||
* Adds this genotype to the context.
|
||||
*
|
||||
* @param genotype
|
||||
*/
|
||||
public void putGenotype(String sampleName, Genotype genotype) {
|
||||
putGenotype(sampleName, genotype, true);
|
||||
}
|
||||
|
||||
private void putGenotype(String sampleName, Genotype genotype, boolean allowOverwrites) {
|
||||
if ( hasGenotype(sampleName) && ! allowOverwrites )
|
||||
throw new IllegalStateException("Attempting to overwrite sample->genotype binding: " + sampleName + " this=" + this);
|
||||
|
||||
if ( ! sampleName.equals(genotype.getSampleName()) )
|
||||
throw new IllegalStateException("Sample name doesn't equal genotype.getSample(): " + sampleName + " genotype=" + genotype);
|
||||
|
||||
this.genotypes.put(sampleName, genotype);
|
||||
}
|
||||
|
||||
/**
|
||||
* Removes the binding from sampleName to genotype. If this doesn't exist, throws an IllegalArgumentException
|
||||
* @param sampleName
|
||||
*/
|
||||
public void removeGenotype(String sampleName) {
|
||||
if ( ! this.genotypes.containsKey(sampleName) )
|
||||
throw new IllegalArgumentException("Sample name isn't contained in genotypes " + sampleName + " genotypes =" + genotypes);
|
||||
|
||||
this.genotypes.remove(sampleName);
|
||||
}
|
||||
|
||||
/**
|
||||
* Removes genotype from the context. If this doesn't exist, throws an IllegalArgumentException
|
||||
* @param genotype
|
||||
*/
|
||||
public void removeGenotype(Genotype genotype) {
|
||||
removeGenotype(genotype.getSampleName());
|
||||
}
|
||||
|
||||
// todo -- add replace genotype routine
|
||||
|
||||
// ---------------------------------------------------------------------------------------------------------
|
||||
//
|
||||
// InferredGeneticContext mutation operators
|
||||
//
|
||||
// ---------------------------------------------------------------------------------------------------------
|
||||
|
||||
public void setSource(String source) { commonInfo.setName(source); }
|
||||
public void addFilter(String filter) { commonInfo.addFilter(filter); }
|
||||
public void addFilters(Collection<String> filters) { commonInfo.addFilters(filters); }
|
||||
public void clearFilters() { commonInfo.clearFilters(); }
|
||||
public void setFilters(Collection<String> filters) { commonInfo.setFilters(filters); }
|
||||
public void setAttributes(Map<String, ?> map) { commonInfo.setAttributes(map); }
|
||||
public void clearAttributes() { commonInfo.clearAttributes(); }
|
||||
public void putAttribute(String key, Object value) { commonInfo.putAttribute(key, value); }
|
||||
public void removeAttribute(String key) { commonInfo.removeAttribute(key); }
|
||||
public void putAttributes(Map<String, ?> map) { commonInfo.putAttributes(map); }
|
||||
public void setNegLog10PError(double negLog10PError) { commonInfo.setNegLog10PError(negLog10PError); }
|
||||
public void putAttribute(String key, Object value, boolean allowOverwrites) { commonInfo.putAttribute(key, value, allowOverwrites); }
|
||||
public void setID(String id) { putAttribute(ID_KEY, id, true); }
|
||||
}
|
||||
|
|
@ -399,6 +399,12 @@ public class VariantContext implements Feature { // to enable tribble intergrati
|
|||
return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, attributes, vc.getReferenceBaseForIndel(), true);
|
||||
}
|
||||
|
||||
public static VariantContext modifyAttribute(VariantContext vc, final String key, final Object value) {
|
||||
Map<String, Object> attributes = new HashMap<String, Object>(vc.getAttributes());
|
||||
attributes.put(key, value);
|
||||
return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, attributes, vc.getReferenceBaseForIndel(), true);
|
||||
}
|
||||
|
||||
public static VariantContext modifyReferencePadding(VariantContext vc, Byte b) {
|
||||
return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, vc.getAttributes(), b, true);
|
||||
}
|
||||
|
|
@ -407,6 +413,10 @@ public class VariantContext implements Feature { // to enable tribble intergrati
|
|||
return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.genotypes, negLog10PError, filters, attributes, vc.getReferenceBaseForIndel(), true);
|
||||
}
|
||||
|
||||
public static VariantContext modifyID(final VariantContext vc, final String id) {
|
||||
return modifyAttribute(vc, ID_KEY, id);
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------------------------------------------
|
||||
//
|
||||
// Selectors
|
||||
|
|
|
|||
|
|
@ -11,10 +11,7 @@ import org.testng.annotations.DataProvider;
|
|||
import org.testng.annotations.Test;
|
||||
import org.testng.Assert;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.Collections;
|
||||
import java.util.List;
|
||||
import java.util.*;
|
||||
|
||||
|
||||
public class VariantContextUnitTest extends BaseTest {
|
||||
|
|
@ -402,29 +399,26 @@ public class VariantContextUnitTest extends BaseTest {
|
|||
List<Allele> alleles = Arrays.asList(Aref, T, del);
|
||||
Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10);
|
||||
Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10);
|
||||
MutableVariantContext vc = new MutableVariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1,g2));
|
||||
|
||||
VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1,g2));
|
||||
|
||||
Assert.assertTrue(vc.isNotFiltered());
|
||||
Assert.assertFalse(vc.isFiltered());
|
||||
Assert.assertEquals(0, vc.getFilters().size());
|
||||
|
||||
vc.addFilter("BAD_SNP_BAD!");
|
||||
Set<String> filters = new HashSet<String>(Arrays.asList("BAD_SNP_BAD!"));
|
||||
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1,g2), VariantContext.NO_NEG_LOG_10PERROR, filters, null);
|
||||
|
||||
Assert.assertFalse(vc.isNotFiltered());
|
||||
Assert.assertTrue(vc.isFiltered());
|
||||
Assert.assertEquals(1, vc.getFilters().size());
|
||||
|
||||
vc.addFilters(Arrays.asList("REALLY_BAD_SNP", "CHRIST_THIS_IS_TERRIBLE"));
|
||||
filters = new HashSet<String>(Arrays.asList("BAD_SNP_BAD!", "REALLY_BAD_SNP", "CHRIST_THIS_IS_TERRIBLE"));
|
||||
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1,g2), VariantContext.NO_NEG_LOG_10PERROR, filters, null);
|
||||
|
||||
Assert.assertFalse(vc.isNotFiltered());
|
||||
Assert.assertTrue(vc.isFiltered());
|
||||
Assert.assertEquals(3, vc.getFilters().size());
|
||||
|
||||
vc.clearFilters();
|
||||
|
||||
Assert.assertTrue(vc.isNotFiltered());
|
||||
Assert.assertFalse(vc.isFiltered());
|
||||
Assert.assertEquals(0, vc.getFilters().size());
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
|
|||
|
|
@ -245,13 +245,13 @@ public class VariantContextUtilsUnitTest extends BaseTest {
|
|||
|
||||
@Test(dataProvider = "simplemergersiddata")
|
||||
public void testRSIDMerge(SimpleMergeRSIDTest cfg) {
|
||||
final VariantContext snpVC1 = makeVC("snpvc1", Arrays.asList(Aref, T));
|
||||
VariantContext snpVC1 = makeVC("snpvc1", Arrays.asList(Aref, T));
|
||||
final List<VariantContext> inputs = new ArrayList<VariantContext>();
|
||||
|
||||
for ( final String id : cfg.inputs ) {
|
||||
MutableVariantContext vc = new MutableVariantContext(snpVC1);
|
||||
if ( ! id.equals(".") ) vc.setID(id);
|
||||
inputs.add(vc);
|
||||
if ( id.equals(".") )
|
||||
snpVC1 = VariantContext.modifyID(snpVC1, id);
|
||||
inputs.add(snpVC1);
|
||||
}
|
||||
|
||||
final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
|
||||
|
|
|
|||
Loading…
Reference in New Issue