diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/Allele.java b/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/Allele.java index f6e5a062f..418c2f483 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/Allele.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/Allele.java @@ -206,7 +206,6 @@ public class Allele { * @return the segregating bases */ public byte[] getBases() { return bases; } - // todo -- can we make this immutable? /** * @param other the other allele diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/MutableVariantContext.java b/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/MutableVariantContext.java index 59bb6877e..72c08e862 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/MutableVariantContext.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/MutableVariantContext.java @@ -18,7 +18,6 @@ public class MutableVariantContext extends VariantContext { // // --------------------------------------------------------------------------------------------------------- - // todo -- add remaining context constructors public MutableVariantContext(String name, GenomeLoc loc, Collection alleles, Collection genotypes, double negLog10PError, Set filters, Map attributes) { super(name, loc, alleles, genotypes, negLog10PError, filters, attributes); } diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/TestVariantContextWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/TestVariantContextWalker.java index c204638ac..81022549e 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/TestVariantContextWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/TestVariantContextWalker.java @@ -15,40 +15,41 @@ public class TestVariantContextWalker extends RodWalker { if ( ref == null ) return 0; else { - RODRecordList dbsnpList = tracker.getTrackData("dbsnp", null); - - if (dbsnpList != null) { - // do dbSNP conversion - int n = 0; - for (ReferenceOrderedDatum d : dbsnpList) { - rodDbSNP dbsnpRecord = (rodDbSNP)d; - if ( dbsnpRecord.getLocation().getStart() == context.getLocation().getStart() ) { - VariantContext vc = VariantContextAdaptors.convertToVariantContext("dbsnp", dbsnpRecord); - if ( vc != null ) { - n++; - System.out.printf("%s%n", vc); - } - } - } - - return n; - } - - RODRecordList vcfList = tracker.getTrackData("vcf", null); - if (vcfList != null) { - // do vcf conversion - int n = 0; - for (ReferenceOrderedDatum d : vcfList) { - RodVCF vcfRecord = (RodVCF)d; - VariantContext vc = VariantContextAdaptors.convertToVariantContext("vcf", vcfRecord); - if ( vc != null ) { - n++; - System.out.printf("%s%n", vc); - } - } - - return n; - } + // todo -- this should just invoke the new RefMetaDataConverter, and print out all of the info +// RODRecordList dbsnpList = tracker.getTrackData("dbsnp", null); +// +// if (dbsnpList != null) { +// // do dbSNP conversion +// int n = 0; +// for (ReferenceOrderedDatum d : dbsnpList) { +// rodDbSNP dbsnpRecord = (rodDbSNP)d; +// if ( dbsnpRecord.getLocation().getStart() == context.getLocation().getStart() ) { +// VariantContext vc = VariantContextAdaptors.convertToVariantContext("dbsnp", dbsnpRecord); +// if ( vc != null ) { +// n++; +// System.out.printf("%s%n", vc); +// } +// } +// } +// +// return n; +// } +// +// RODRecordList vcfList = tracker.getTrackData("vcf", null); +// if (vcfList != null) { +// // do vcf conversion +// int n = 0; +// for (ReferenceOrderedDatum d : vcfList) { +// RodVCF vcfRecord = (RodVCF)d; +// VariantContext vc = VariantContextAdaptors.convertToVariantContext("vcf", vcfRecord); +// if ( vc != null ) { +// n++; +// System.out.printf("%s%n", vc); +// } +// } +// +// return n; +// } return 0; } diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContext.java b/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContext.java index 0b633ef51..0ffc5ef9b 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContext.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContext.java @@ -34,6 +34,9 @@ import java.util.*; * It's also easy to create subcontexts based on selected genotypes. * * == Working with Variant Contexts == + * By default, VariantContexts are immutable. In order to access (in the rare circumstances where you need them) + * setter routines, you need to create MutableVariantContexts and MutableGenotypes. + * * === Some example data === * * Allele A, Aref, T, Tref; @@ -71,19 +74,19 @@ import java.util.*; * Here's an example of a A/T polymorphism with the A being reference: * * 
- * VariantContext vc = new VariantContext(snpLoc, Arrays.asList(Aref, T));
+ * VariantContext vc = new VariantContext(name, snpLoc, Arrays.asList(Aref, T));
  *
* * If you want to create a non-variant site, just put in a single reference allele * * 
- * VariantContext vc = new VariantContext(snpLoc, Arrays.asList(Aref));
+ * VariantContext vc = new VariantContext(name, snpLoc, Arrays.asList(Aref));
  *
* * A deletion is just as easy: * * 
- * VariantContext vc = new VariantContext(delLoc, Arrays.asList(ATCref, del));
+ * VariantContext vc = new VariantContext(name, delLoc, Arrays.asList(ATCref, del));
  *
* * The only 2 things that distinguishes between a insertion and deletion are the reference allele @@ -92,7 +95,7 @@ import java.util.*; * a 1-bp GenomeLoc (at say 20). * * 
- * VariantContext vc = new VariantContext(insLoc, Arrays.asList(delRef, ATC));
+ * VariantContext vc = new VariantContext("name", insLoc, Arrays.asList(delRef, ATC));
  *
* * ==== Converting rods and other data structures to VCs ==== @@ -100,7 +103,7 @@ import java.util.*; * You can convert many common types into VariantContexts using the general function: * * 
- * VariantContextAdaptors.convertToVariantContext(myObject)
+ * VariantContextAdaptors.convertToVariantContext(name, myObject)
  *
* * dbSNP and VCFs, for example, can be passed in as myObject and a VariantContext corresponding to that @@ -112,12 +115,10 @@ import java.util.*; * * 
  * List alleles = Arrays.asList(Aref, T);
- * VariantContext vc = new VariantContext(snpLoc, alleles);
- *
  * Genotype g1 = new Genotype(Arrays.asList(Aref, Aref), "g1", 10);
  * Genotype g2 = new Genotype(Arrays.asList(Aref, T), "g2", 10);
  * Genotype g3 = new Genotype(Arrays.asList(T, T), "g3", 10);
- * vc.addGenotypes(Arrays.asList(g1, g2, g3));
+ * VariantContext vc = new VariantContext(snpLoc, alleles, Arrays.asList(g1, g2, g3));
  *
* * At this point we have 3 genotypes in our context, g1-g3. @@ -200,19 +201,50 @@ public class VariantContext { validate(); } + /** + * Create a new VariantContext + * + * @param name + * @param loc + * @param alleles + * @param genotypes + * @param negLog10PError + * @param filters + * @param attributes + */ public VariantContext(String name, GenomeLoc loc, Collection alleles, Collection genotypes, double negLog10PError, Set filters, Map attributes) { this(name, loc, alleles, genotypeCollectionToMap(new HashMap(), genotypes), negLog10PError, filters, attributes); } + /** + * Create a new variant context without genotypes and no Perror, no filters, and no attributes + * @param name + * @param loc + * @param alleles + */ public VariantContext(String name, GenomeLoc loc, Collection alleles) { this(name, loc, alleles, NO_GENOTYPES, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null); } + /** + * Create a new variant context without genotypes and no Perror, no filters, and no attributes + * @param name + * @param loc + * @param alleles + */ public VariantContext(String name, GenomeLoc loc, Collection alleles, Collection genotypes) { this(name, loc, alleles, genotypes, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null); } - // todo -- add clone method + /** + * Copy constructor + * + * @param other the VariantContext to copy + */ + public VariantContext(VariantContext other) { + this(other.getName(), other.getLocation(), other.getAlleles(), other.getGenotypes(), other.getNegLog10PError(), other.getFilters(), other.getAttributes()); + } + // --------------------------------------------------------------------------------------------------------- // diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContextAdaptors.java b/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContextAdaptors.java index fe5210c2c..6c10d7b5f 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContextAdaptors.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContextAdaptors.java @@ -2,60 +2,116 @@ package org.broadinstitute.sting.oneoffprojects.variantcontext; import org.broadinstitute.sting.gatk.refdata.rodDbSNP; import org.broadinstitute.sting.gatk.refdata.RodVCF; -import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord; import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeEncoding; import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord; import java.util.*; - +/** + * A terrible but temporary approach to converting objects to VariantContexts. If you want to add a converter, + * you need to create a adaptor object here and register a converter from your class to this object. When tribble arrives, + * we'll use a better approach. + * + * @author depristo@broadinstitute.org + */ public class VariantContextAdaptors { - public static boolean canBeConvertedToVariantContext(String name, Object variantContainingObject) { - return convertToVariantContext(name, variantContainingObject) != null; + // -------------------------------------------------------------------------------------------------------------- + // + // Generic support routines. Do not modify + // + // -------------------------------------------------------------------------------------------------------------- + + private static Map adaptors = new HashMap(); + + static { + adaptors.put(rodDbSNP.class, new RodDBSnpAdaptor()); + adaptors.put(RodVCF.class, new RodVCFAdaptor()); + adaptors.put(VCFRecord.class, new VCFRecordAdaptor()); } - public static VariantContext convertToVariantContext(String name, Object variantContainingObject) { - if ( variantContainingObject instanceof rodDbSNP ) - return dbsnpToVariantContext(name, (rodDbSNP)variantContainingObject); - else if ( variantContainingObject instanceof RodVCF ) - return vcfToVariantContext(name, ((RodVCF)variantContainingObject).getRecord()); - else if ( variantContainingObject instanceof VCFRecord ) - return vcfToVariantContext(name, (VCFRecord)variantContainingObject); - else + public static boolean canBeConvertedToVariantContext(Object variantContainingObject) { + return adaptors.containsKey(variantContainingObject.getClass()); +// return convertToVariantContext(name, variantContainingObject) != null; + } + + /** generic superclass */ + private static abstract class VCAdaptor { + abstract VariantContext convert(String name, Object input); + } + + public static VariantContext toVariantContext(String name, Object variantContainingObject) { + if ( ! adaptors.containsKey(variantContainingObject.getClass()) ) return null; - //throw new IllegalArgumentException("Cannot convert object " + variantContainingObject + " of class " + variantContainingObject.getClass() + " to a variant context"); - + else { + return adaptors.get(variantContainingObject.getClass()).convert(name, variantContainingObject); + } } - private static VariantContext dbsnpToVariantContext(String name, rodDbSNP dbsnp) { - if ( dbsnp.isSNP() || dbsnp.isIndel() || dbsnp.varType.contains("mixed") ) { - // add the reference allele - if ( ! Allele.acceptableAlleleBases(dbsnp.getReference()) ) { - //System.out.printf("Excluding dbsnp record %s%n", dbsnp); - return null; - } + // -------------------------------------------------------------------------------------------------------------- + // + // From here below you can add adaptor classes for new rods (or other types) to convert to VCF + // + // -------------------------------------------------------------------------------------------------------------- - List alleles = new ArrayList(); - Allele refAllele = new Allele(dbsnp.getReference(), true); - alleles.add(refAllele); - // add all of the alt alleles - for ( String alt : dbsnp.getAlternateAlleleList() ) { - if ( ! Allele.acceptableAlleleBases(alt) ) { + + // -------------------------------------------------------------------------------------------------------------- + // + // dbSNP to VariantContext + // + // -------------------------------------------------------------------------------------------------------------- + + private static class RodDBSnpAdaptor extends VCAdaptor { + VariantContext convert(String name, Object input) { + rodDbSNP dbsnp = (rodDbSNP)input; + if ( dbsnp.isSNP() || dbsnp.isIndel() || dbsnp.varType.contains("mixed") ) { + // add the reference allele + if ( ! Allele.acceptableAlleleBases(dbsnp.getReference()) ) { //System.out.printf("Excluding dbsnp record %s%n", dbsnp); return null; } - alleles.add(new Allele(alt, false)); - } - VariantContext vc = new VariantContext(name, dbsnp.getLocation(), alleles); - vc.validate(); - return vc; - } else - return null; // can't handle anything else + List alleles = new ArrayList(); + Allele refAllele = new Allele(dbsnp.getReference(), true); + alleles.add(refAllele); + + // add all of the alt alleles + for ( String alt : dbsnp.getAlternateAlleleList() ) { + if ( ! Allele.acceptableAlleleBases(alt) ) { + //System.out.printf("Excluding dbsnp record %s%n", dbsnp); + return null; + } + alleles.add(new Allele(alt, false)); + } + + VariantContext vc = new VariantContext(name, dbsnp.getLocation(), alleles); + vc.validate(); + return vc; + } else + return null; // can't handle anything else + } } + // -------------------------------------------------------------------------------------------------------------- + // + // VCF to VariantContext + // + // -------------------------------------------------------------------------------------------------------------- + + private static class RodVCFAdaptor extends VCAdaptor { + VariantContext convert(String name, Object input) { + return vcfToVariantContext(name, ((RodVCF)input).getRecord()); + } + } + + private static class VCFRecordAdaptor extends VCAdaptor { + VariantContext convert(String name, Object input) { + return vcfToVariantContext(name, (VCFRecord)input); + } + } + + private static VariantContext vcfToVariantContext(String name, VCFRecord vcf) { if ( vcf.isSNP() || vcf.isIndel() ) { // add the reference allele @@ -74,6 +130,7 @@ public class VariantContextAdaptors { alleles.add(refAllele); for ( String alt : vcf.getAlternateAlleleList() ) { if ( ! Allele.acceptableAlleleBases(alt) ) { + // todo -- cleanup System.out.printf("Excluding vcf record %s%n", vcf); return null; } diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContextUtils.java index 98e0e9cd0..b2ec1a6f7 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContextUtils.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContextUtils.java @@ -2,25 +2,40 @@ package org.broadinstitute.sting.oneoffprojects.variantcontext; import java.util.*; import org.apache.commons.jexl.*; -import org.broadinstitute.sting.oneoffprojects.variantcontext.varianteval2.VariantEvaluator; import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.Utils; public class VariantContextUtils { - /** */ - public static class MatchExp { + /** + * A simple but common wrapper for matching VariantContext objects using JEXL expressions + */ + public static class JexlVCMatchExp { public String name; - public String expStr; public Expression exp; - public MatchExp(String name, String str, Expression exp) { + /** + * Create a new matcher expression with name and JEXL expression exp + * @param name + * @param exp + */ + public JexlVCMatchExp(String name, Expression exp) { this.name = name; this.exp = exp; } } - public static List initializeMatchExps(String[] names, String[] exps) { + /** + * Method for creating JexlVCMatchExp from input walker arguments names and exps. These two arrays contain + * the name associated with each JEXL expression. initializeMatchExps will parse each expression and return + * a list of JexlVCMatchExp, in order, that correspond to the names and exps. These are suitable input to + * match() below. + * + * @param names + * @param exps + * @return + */ + public static List initializeMatchExps(String[] names, String[] exps) { if ( names == null || exps == null ) throw new StingException("BUG: neither names nor exps can be null: names " + names + " exps=" + exps ); @@ -33,8 +48,17 @@ public class VariantContextUtils { return VariantContextUtils.initializeMatchExps(map); } - public static List initializeMatchExps(Map names_and_exps) { - List exps = new ArrayList(); + /** + * Method for creating JexlVCMatchExp from input walker arguments mapping from names to exps. These two arrays contain + * the name associated with each JEXL expression. initializeMatchExps will parse each expression and return + * a list of JexlVCMatchExp, in order, that correspond to the names and exps. These are suitable input to + * match() below. + * + * @param names_and_exps + * @return + */ + public static List initializeMatchExps(Map names_and_exps) { + List exps = new ArrayList(); for ( Map.Entry elt : names_and_exps.entrySet() ) { String name = elt.getKey(); @@ -42,8 +66,8 @@ public class VariantContextUtils { if ( name == null || expStr == null ) throw new IllegalArgumentException("Cannot create null expressions : " + name + " " + expStr); try { - Expression filterExpression = ExpressionFactory.createExpression(expStr); - exps.add(new MatchExp(name, expStr, filterExpression)); + Expression exp = ExpressionFactory.createExpression(expStr); + exps.add(new JexlVCMatchExp(name, exp)); } catch (Exception e) { throw new StingException("Invalid expression used (" + expStr + "). Please see the JEXL docs for correct syntax."); } @@ -52,11 +76,27 @@ public class VariantContextUtils { return exps; } - public static boolean match(VariantContext vc, MatchExp exp) { + /** + * Returns true if exp match VC. See collection<> version for full docs. + * @param vc + * @param exp + * @return + */ + public static boolean match(VariantContext vc, JexlVCMatchExp exp) { return match(vc,Arrays.asList(exp)).get(exp); } - public static Map match(VariantContext vc, Collection exps) { + /** + * Matches each JexlVCMatchExp exp against the data contained in vc, and returns a map from these + * expressions to true (if they matched) or false (if they didn't). This the best way to apply JEXL + * expressions to VariantContext records. Use initializeMatchExps() to create the list of JexlVCMatchExp + * expressions. + * + * @param vc + * @param exps + * @return + */ + public static Map match(VariantContext vc, Collection exps) { // todo -- actually, we should implement a JEXL context interface to VariantContext, // todo -- which just looks up the values assigned statically here. Much better approach @@ -93,8 +133,8 @@ public class VariantContextUtils { jContext.setVars(infoMap); try { - Map resultMap = new HashMap(); - for ( MatchExp e : exps ) { + Map resultMap = new HashMap(); + for ( JexlVCMatchExp e : exps ) { resultMap.put(e, (Boolean)e.exp.evaluate(jContext)); } return resultMap; @@ -110,9 +150,7 @@ public class VariantContextUtils { } } - - - private static final String UNIQUIFIED_SUFFIX = ".unique"; +// private static final String UNIQUIFIED_SUFFIX = ".unique"; /** * @param other another variant context diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/varianteval2/VariantEval2Walker.java b/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/varianteval2/VariantEval2Walker.java index 561086f15..1c00f7d83 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/varianteval2/VariantEval2Walker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/varianteval2/VariantEval2Walker.java @@ -86,9 +86,9 @@ public class VariantEval2Walker extends RodWalker { private class EvaluationContext extends HashMap> { // useful for typing public String trackName, contextName; - VariantContextUtils.MatchExp selectExp; + VariantContextUtils.JexlVCMatchExp selectExp; - public EvaluationContext(String trackName, String contextName, VariantContextUtils.MatchExp selectExp) { + public EvaluationContext(String trackName, String contextName, VariantContextUtils.JexlVCMatchExp selectExp) { this.trackName = trackName; this.contextName = contextName; this.selectExp = selectExp; @@ -117,11 +117,11 @@ public class VariantEval2Walker extends RodWalker { public void initialize() { determineAllEvalations(); - List selectExps = VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS); + List selectExps = VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS); for ( ReferenceOrderedDataSource d : this.getToolkit().getRodDataSources() ) { if ( d.getName().startsWith("eval") ) { - for ( VariantContextUtils.MatchExp e : selectExps ) { + for ( VariantContextUtils.JexlVCMatchExp e : selectExps ) { addNewContext(d.getName(), d.getName() + "." + e.name, e); } addNewContext(d.getName(), d.getName() + ".all", null); @@ -171,7 +171,7 @@ public class VariantEval2Walker extends RodWalker { return evals; } - private void addNewContext(String trackName, String contextName, VariantContextUtils.MatchExp selectExp) { + private void addNewContext(String trackName, String contextName, VariantContextUtils.JexlVCMatchExp selectExp) { EvaluationContext group = new EvaluationContext(trackName, contextName, selectExp); for ( String filteredName : Arrays.asList(RAW_SET_NAME, RETAINED_SET_NAME, FILTERED_SET_NAME) ) { @@ -288,7 +288,7 @@ public class VariantEval2Walker extends RodWalker { if ( rodList != null ) { for ( ReferenceOrderedDatum rec : rodList.getRecords() ) { if ( rec.getLocation().getStart() == context.getLocation().getStart() ) { - VariantContext vc = VariantContextAdaptors.convertToVariantContext(name, rec); + VariantContext vc = VariantContextAdaptors.toVariantContext(name, rec); if ( vc != null ) { return vc; } diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java index 0c7cea819..8045f1c8a 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java @@ -47,7 +47,7 @@ public class SNPDensity extends RefWalker, SNPDe if (vcfList != null) { for (ReferenceOrderedDatum d : vcfList) { RodVCF vcfRecord = (RodVCF)d; - vc = VariantContextAdaptors.convertToVariantContext("eval", vcfRecord); + vc = VariantContextAdaptors.toVariantContext("eval", vcfRecord); break; } }