Make the set of VariantContextAdaptors dynamic so that Andrey's MafFeature can
continue to exist and live in playground (and thus outside of the normal release / git release branch). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5909 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna
parent
44cb7e4980
commit
6cc84c3ce2
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@ -1,5 +1,6 @@
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package org.broadinstitute.sting.gatk.refdata;
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import org.broad.tribble.Feature;
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import org.broad.tribble.dbsnp.DbSNPFeature;
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import org.broad.tribble.gelitext.GeliTextFeature;
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import org.broad.tribble.hapmap.HapMapFeature;
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@ -12,6 +13,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
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import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
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import org.broadinstitute.sting.playground.gatk.features.maf.MafFeature;
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import org.broadinstitute.sting.utils.classloader.PluginManager;
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import java.util.*;
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@ -36,14 +38,13 @@ public class VariantContextAdaptors {
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//
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// --------------------------------------------------------------------------------------------------------------
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private static Map<Class, VCAdaptor> adaptors = new HashMap<Class, VCAdaptor>();
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private static Map<Class<? extends Feature>,VCAdaptor> adaptors = new HashMap<Class<? extends Feature>,VCAdaptor>();
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static {
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adaptors.put(DbSNPFeature.class, new DBSnpAdaptor());
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adaptors.put(HapMapFeature.class, new HapMapAdaptor());
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adaptors.put(GeliTextFeature.class, new GeliTextAdaptor());
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adaptors.put(VariantContext.class, new VariantContextAdaptor());
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adaptors.put(MafFeature.class, new MafAdaptor());
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PluginManager<VCAdaptor> vcAdaptorManager = new PluginManager<VCAdaptor>(VCAdaptor.class);
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List<VCAdaptor> adaptorInstances = vcAdaptorManager.createAllTypes();
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for(VCAdaptor adaptor: adaptorInstances)
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adaptors.put(adaptor.getAdaptableFeatureType(),adaptor);
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}
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public static boolean canBeConvertedToVariantContext(Object variantContainingObject) {
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@ -51,8 +52,13 @@ public class VariantContextAdaptors {
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}
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/** generic superclass */
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private static abstract class VCAdaptor {
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abstract VariantContext convert(String name, Object input, ReferenceContext ref);
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public interface VCAdaptor {
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/**
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* Gets the type of feature that this adaptor can 'adapt' into a VariantContext.
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* @return Type of adaptable feature. Must be a Tribble feature class.
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*/
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Class<? extends Feature> getAdaptableFeatureType();
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VariantContext convert(String name, Object input, ReferenceContext ref);
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}
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public static VariantContext toVariantContext(String name, Object variantContainingObject, ReferenceContext ref) {
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@ -68,10 +74,17 @@ public class VariantContextAdaptors {
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// From here below you can add adaptor classes for new rods (or other types) to convert to VC
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//
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// --------------------------------------------------------------------------------------------------------------
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private static class VariantContextAdaptor implements VCAdaptor {
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/**
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* 'Null' adaptor; adapts variant contexts to variant contexts.
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* @return VariantContext.
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*/
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@Override
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public Class<? extends Feature> getAdaptableFeatureType() { return VariantContext.class; }
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private static class VariantContextAdaptor extends VCAdaptor {
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// already a VC, just cast and return it
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VariantContext convert(String name, Object input, ReferenceContext ref) {
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@Override
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public VariantContext convert(String name, Object input, ReferenceContext ref) {
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return (VariantContext)input;
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}
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}
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@ -82,8 +95,16 @@ public class VariantContextAdaptors {
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//
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// --------------------------------------------------------------------------------------------------------------
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private static class DBSnpAdaptor extends VCAdaptor {
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VariantContext convert(String name, Object input, ReferenceContext ref) {
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private static class DBSnpAdaptor implements VCAdaptor {
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/**
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* Converts non-VCF formatted dbSNP records to VariantContext.
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* @return DbSNPFeature.
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*/
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@Override
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public Class<? extends Feature> getAdaptableFeatureType() { return DbSNPFeature.class; }
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@Override
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public VariantContext convert(String name, Object input, ReferenceContext ref) {
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DbSNPFeature dbsnp = (DbSNPFeature)input;
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if ( ! Allele.acceptableAlleleBases(DbSNPHelper.getReference(dbsnp)) )
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return null;
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@ -128,7 +149,14 @@ public class VariantContextAdaptors {
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//
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// --------------------------------------------------------------------------------------------------------------
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private static class GeliTextAdaptor extends VCAdaptor {
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private static class GeliTextAdaptor implements VCAdaptor {
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/**
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* Converts Geli text records to VariantContext.
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* @return GeliTextFeature.
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*/
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@Override
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public Class<? extends Feature> getAdaptableFeatureType() { return GeliTextFeature.class; }
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/**
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* convert to a Variant Context, given:
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* @param name the name of the ROD
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@ -146,7 +174,8 @@ public class VariantContextAdaptors {
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* @param ref the reference context
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* @return a VariantContext object
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*/
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VariantContext convert(String name, Object input, ReferenceContext ref) {
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@Override
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public VariantContext convert(String name, Object input, ReferenceContext ref) {
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GeliTextFeature geli = (GeliTextFeature)input;
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if ( ! Allele.acceptableAlleleBases(String.valueOf(geli.getRefBase())) )
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return null;
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@ -195,7 +224,14 @@ public class VariantContextAdaptors {
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//
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// --------------------------------------------------------------------------------------------------------------
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private static class HapMapAdaptor extends VCAdaptor {
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private static class HapMapAdaptor implements VCAdaptor {
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/**
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* Converts HapMap records to VariantContext.
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* @return HapMapFeature.
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*/
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@Override
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public Class<? extends Feature> getAdaptableFeatureType() { return HapMapFeature.class; }
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/**
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* convert to a Variant Context, given:
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* @param name the name of the ROD
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@ -213,7 +249,8 @@ public class VariantContextAdaptors {
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* @param ref the reference context
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* @return a VariantContext object
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*/
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VariantContext convert(String name, Object input, ReferenceContext ref) {
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@Override
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public VariantContext convert(String name, Object input, ReferenceContext ref) {
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if ( ref == null )
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throw new UnsupportedOperationException("Conversion from HapMap to VariantContext requires a reference context");
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@ -281,120 +318,4 @@ public class VariantContextAdaptors {
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return vc;
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}
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}
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private static class MafAdaptor extends VCAdaptor {
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/**
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* convert to a Variant Context, given:
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* @param name the name of the ROD
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* @param input the Rod object, in this case a MafFeature
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* @return a VariantContext object
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*/
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// VariantContext convert(String name, Object input) {
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// return convert(name, input, null);
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// }
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/**
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* convert to a Variant Context, given:
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* @param name the name of the ROD
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* @param input the Rod object, in this case a MafFeature
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* @param ref the reference context
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* @return a VariantContext object
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*/
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VariantContext convert(String name, Object input, ReferenceContext ref) {
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if ( ref == null )
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throw new UnsupportedOperationException("Conversion from MAF to VariantContext requires a reference context, null received");
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MafFeature maf = (MafFeature)input;
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if ( ! Allele.acceptableAlleleBases(maf.getRefBases()) )
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return null;
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List<Allele> alleles = new ArrayList<Allele>();
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Allele refAllele = Allele.create(maf.getRefBases(), true);
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// add the reference allele:
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alleles.add(refAllele);
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// add all of the alt alleles
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for ( String alt : maf.getAllNonRefAlleleList() ) {
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if ( ! Allele.acceptableAlleleBases(alt) ) {
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//System.out.printf("Excluding dbsnp record %s%n", dbsnp);
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return null;
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}
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alleles.add(Allele.create(alt, false));
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}
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// make a mapping from sample to genotype
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String normalSample = maf.getNormalSampleId();
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String tumorSample = maf.getTumorSampleId();
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// String[] genotypeStrings = hapmap.getGenotypes();
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Map<String, Genotype> genotypes = new HashMap<String, Genotype>(2);
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addGenotype(genotypes, normalSample, maf.getObservedNormalAlleleList(),maf.getRefBases());
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addGenotype(genotypes,tumorSample,maf.getObservedTumorAlleleList(),maf.getRefBases());
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HashMap<String, Object> attrs = new HashMap<String, Object>(10);
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// fill attributes:
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if ( maf.getHugoGeneSymbol() != null && ! maf.getHugoGeneSymbol().equals("Unknown"))
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attrs.put("Gene",maf.getHugoGeneSymbol());
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if ( maf.isSomatic() ) {
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attrs.put(VCFConstants.SOMATIC_KEY,true);
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attrs.put("SS","Somatic");
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} else {
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attrs.put("SS","Germline");
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}
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if ( maf.getVariantClassification() != null ) {
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switch(maf.getVariantClassification()) {
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case Intergenic: attrs.put("VC","Genomic"); break;
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case Intron: attrs.put("VC","Intron"); break;
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case Noncoding_transcript: attrs.put("VC","Noncoding_transcript"); break;
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case UTR3: attrs.put("VC","3'UTR"); break;
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case UTR5: attrs.put("VC","5'UTR"); break;
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case Flank5: attrs.put("VC","5'flank"); break;
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case Promoter: attrs.put("VC","5'flank"); break;
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case De_novo_start: attrs.put("VC","De_novo_start"); break;
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case De_novo_start_out_of_frame: attrs.put("VC","De_novo_start_out_of_frame"); break;
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case Silent: attrs.put("VC","Silent"); break;
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case Missense: attrs.put("VC","Missense"); break;
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case Nonsense: attrs.put("VC","Nonsense"); break;
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case Splice_site: attrs.put("VC","Splice_site"); break;
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case miRNA: attrs.put("VC","miRNA"); break;
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case Frameshift: attrs.put("VC","Frameshift"); break;
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case Inframe: attrs.put("VC","Inframe"); break;
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case Stop_deletion: attrs.put("VC","Stop_codon_deletion");
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case Unclassified: attrs.put("VC","Unclassified");
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default:
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}
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}
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attrs.put("VT",maf.getType());
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// attrs.put(VariantContext.ID_KEY, hapmap.getName());
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int end = maf.getEnd();
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VariantContext vc = new VariantContext(name, maf.getChr(), maf.getStart(), end, alleles,
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genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attrs);
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return vc;
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}
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private void addGenotype(Map<String,Genotype> dest, String sampleId, List<String> alleles, String refAllele) {
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List<Allele> myAlleles = new ArrayList<Allele>(2);
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boolean success = true;
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for ( String a : alleles ) {
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if ( a.isEmpty() || a.contains("N") || a.contains(".")) return; // bad allele found
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myAlleles.add(Allele.create(a,refAllele.equals(a)));
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}
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dest.put(sampleId, new Genotype(sampleId,myAlleles));
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}
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}
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}
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@ -26,6 +26,12 @@
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package org.broadinstitute.sting.playground.gatk.features.maf;
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import org.broad.tribble.Feature;
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import org.broad.tribble.util.variantcontext.Allele;
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import org.broad.tribble.util.variantcontext.Genotype;
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import org.broad.tribble.util.variantcontext.VariantContext;
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import org.broad.tribble.vcf.VCFConstants;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
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import org.broadinstitute.sting.utils.exceptions.StingException;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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@ -264,3 +270,125 @@ public class MafFeature implements Feature {
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}
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}
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class MafAdaptor implements VariantContextAdaptors.VCAdaptor {
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/**
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* Converts Maf features to VariantContext.
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* @return MafFeature.
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*/
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@Override
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public Class<? extends Feature> getAdaptableFeatureType() { return MafFeature.class; }
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/**
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* convert to a Variant Context, given:
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* @param name the name of the ROD
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* @param input the Rod object, in this case a MafFeature
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* @return a VariantContext object
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*/
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// VariantContext convert(String name, Object input) {
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// return convert(name, input, null);
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// }
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/**
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* convert to a Variant Context, given:
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* @param name the name of the ROD
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* @param input the Rod object, in this case a MafFeature
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* @param ref the reference context
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* @return a VariantContext object
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*/
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@Override
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public VariantContext convert(String name, Object input, ReferenceContext ref) {
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if ( ref == null )
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throw new UnsupportedOperationException("Conversion from MAF to VariantContext requires a reference context, null received");
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MafFeature maf = (MafFeature)input;
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if ( ! Allele.acceptableAlleleBases(maf.getRefBases()) )
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return null;
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List<Allele> alleles = new ArrayList<Allele>();
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Allele refAllele = Allele.create(maf.getRefBases(), true);
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// add the reference allele:
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alleles.add(refAllele);
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// add all of the alt alleles
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for ( String alt : maf.getAllNonRefAlleleList() ) {
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if ( ! Allele.acceptableAlleleBases(alt) ) {
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//System.out.printf("Excluding dbsnp record %s%n", dbsnp);
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return null;
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}
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alleles.add(Allele.create(alt, false));
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}
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// make a mapping from sample to genotype
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String normalSample = maf.getNormalSampleId();
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String tumorSample = maf.getTumorSampleId();
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// String[] genotypeStrings = hapmap.getGenotypes();
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Map<String, Genotype> genotypes = new HashMap<String, Genotype>(2);
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addGenotype(genotypes, normalSample, maf.getObservedNormalAlleleList(),maf.getRefBases());
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addGenotype(genotypes,tumorSample,maf.getObservedTumorAlleleList(),maf.getRefBases());
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HashMap<String, Object> attrs = new HashMap<String, Object>(10);
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// fill attributes:
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if ( maf.getHugoGeneSymbol() != null && ! maf.getHugoGeneSymbol().equals("Unknown"))
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attrs.put("Gene",maf.getHugoGeneSymbol());
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if ( maf.isSomatic() ) {
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attrs.put(VCFConstants.SOMATIC_KEY,true);
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attrs.put("SS","Somatic");
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} else {
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attrs.put("SS","Germline");
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}
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if ( maf.getVariantClassification() != null ) {
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switch(maf.getVariantClassification()) {
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case Intergenic: attrs.put("VC","Genomic"); break;
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case Intron: attrs.put("VC","Intron"); break;
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case Noncoding_transcript: attrs.put("VC","Noncoding_transcript"); break;
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case UTR3: attrs.put("VC","3'UTR"); break;
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case UTR5: attrs.put("VC","5'UTR"); break;
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case Flank5: attrs.put("VC","5'flank"); break;
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case Promoter: attrs.put("VC","5'flank"); break;
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case De_novo_start: attrs.put("VC","De_novo_start"); break;
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case De_novo_start_out_of_frame: attrs.put("VC","De_novo_start_out_of_frame"); break;
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case Silent: attrs.put("VC","Silent"); break;
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case Missense: attrs.put("VC","Missense"); break;
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case Nonsense: attrs.put("VC","Nonsense"); break;
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case Splice_site: attrs.put("VC","Splice_site"); break;
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case miRNA: attrs.put("VC","miRNA"); break;
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case Frameshift: attrs.put("VC","Frameshift"); break;
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case Inframe: attrs.put("VC","Inframe"); break;
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case Stop_deletion: attrs.put("VC","Stop_codon_deletion");
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case Unclassified: attrs.put("VC","Unclassified");
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default:
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}
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}
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attrs.put("VT",maf.getType());
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// attrs.put(VariantContext.ID_KEY, hapmap.getName());
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int end = maf.getEnd();
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VariantContext vc = new VariantContext(name, maf.getChr(), maf.getStart(), end, alleles,
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genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attrs);
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return vc;
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}
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private void addGenotype(Map<String,Genotype> dest, String sampleId, List<String> alleles, String refAllele) {
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List<Allele> myAlleles = new ArrayList<Allele>(2);
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boolean success = true;
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for ( String a : alleles ) {
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if ( a.isEmpty() || a.contains("N") || a.contains(".")) return; // bad allele found
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myAlleles.add(Allele.create(a,refAllele.equals(a)));
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}
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dest.put(sampleId, new Genotype(sampleId,myAlleles));
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}
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}
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@ -35,6 +35,7 @@ import org.reflections.scanners.SubTypesScanner;
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import org.reflections.util.ConfigurationBuilder;
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import org.slf4j.LoggerFactory;
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import java.lang.reflect.Constructor;
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import java.lang.reflect.Method;
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import java.net.URL;
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import java.net.URLClassLoader;
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@ -249,10 +250,11 @@ public class PluginManager<PluginType> {
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* @param pluginType type of the plugin to create.
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* @return The plugin object if created; null otherwise.
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*/
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@SuppressWarnings("unchecked")
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public PluginType createByType(Class pluginType) {
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public PluginType createByType(Class<? extends PluginType> pluginType) {
|
||||
try {
|
||||
return ((Class<? extends PluginType>) pluginType).newInstance();
|
||||
Constructor<? extends PluginType> noArgsConstructor = pluginType.getDeclaredConstructor((Class[])null);
|
||||
noArgsConstructor.setAccessible(true);
|
||||
return noArgsConstructor.newInstance();
|
||||
} catch (Exception e) {
|
||||
throw new DynamicClassResolutionException(pluginType, e);
|
||||
}
|
||||
|
|
@ -265,11 +267,7 @@ public class PluginManager<PluginType> {
|
|||
public List<PluginType> createAllTypes() {
|
||||
List<PluginType> instances = new ArrayList<PluginType>();
|
||||
for ( Class<? extends PluginType> c : getPlugins() ) {
|
||||
try {
|
||||
instances.add(c.newInstance());
|
||||
} catch (Exception e) {
|
||||
throw new DynamicClassResolutionException(c, e);
|
||||
}
|
||||
instances.add(createByType(c));
|
||||
}
|
||||
return instances;
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue