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Bugfixes on way to a working refactored VariantContext

This commit is contained in:
Mark DePristo 2011-11-15 16:42:50 -05:00
parent 2b2514dad2
commit 231c47c039
3 changed files with 5 additions and 7 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java
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@ -129,9 +129,8 @@ class PhasingUtils {
List<String> mergedIDs = new ArrayList<String>(); List<String> mergedIDs = new ArrayList<String>();
if ( vc1.hasID() ) mergedIDs.add(vc1.getID()); if ( vc1.hasID() ) mergedIDs.add(vc1.getID());
if ( vc2.hasID() ) mergedIDs.add(vc2.getID()); if ( vc2.hasID() ) mergedIDs.add(vc2.getID());
String mergedID = Utils.join(VCFConstants.ID_FIELD_SEPARATOR, mergedIDs); String mergedID = mergedIDs.isEmpty() ? VCFConstants.EMPTY_ID_FIELD : Utils.join(VCFConstants.ID_FIELD_SEPARATOR, mergedIDs);
// TODO -- FIX ID
VariantContext mergedVc = new VariantContext(mergedName, mergedID, vc1.getChr(), vc1.getStart(), vc2.getEnd(), mergeData.getAllMergedAlleles(), mergedGenotypes, mergedNegLog10PError, mergedFilters, mergedAttribs); VariantContext mergedVc = new VariantContext(mergedName, mergedID, vc1.getChr(), vc1.getStart(), vc2.getEnd(), mergeData.getAllMergedAlleles(), mergedGenotypes, mergedNegLog10PError, mergedFilters, mergedAttribs);
mergedAttribs = new HashMap<String, Object>(mergedVc.getAttributes()); mergedAttribs = new HashMap<String, Object>(mergedVc.getAttributes());

4
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
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@ -1126,9 +1126,11 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
private double negLog10PError; private double negLog10PError;
private Set<String> filters; private Set<String> filters;
private Map<String, Object> attributes; private Map<String, Object> attributes;
private String id;
public UnfinishedVariantContext(VariantContext vc) { public UnfinishedVariantContext(VariantContext vc) {
this.name = vc.getSource(); this.name = vc.getSource();
this.id = vc.getID();
this.contig = vc.getChr(); this.contig = vc.getChr();
this.start = vc.getStart(); this.start = vc.getStart();
this.stop = vc.getEnd(); this.stop = vc.getEnd();
@ -1140,7 +1142,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
} }
public VariantContext toVariantContext() { public VariantContext toVariantContext() {
return new VariantContext(name, VCFConstants.EMPTY_ID_FIELD, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes); return new VariantContext(name, id, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes);
} }
public GenomeLoc getLocation() { public GenomeLoc getLocation() {

5
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeCollection.java
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@ -70,9 +70,6 @@ public class GenotypeCollection implements List<Genotype> {
return new GenotypeCollection(nGenotypes, false); return new GenotypeCollection(nGenotypes, false);
} }
// todo -- differentiate between empty constructor and copy constructor
// todo -- create constructor (Genotype ... genotypes)
public static final GenotypeCollection create(final ArrayList<Genotype> genotypes) { public static final GenotypeCollection create(final ArrayList<Genotype> genotypes) {
return genotypes == null ? NO_GENOTYPES : new GenotypeCollection(genotypes, false); return genotypes == null ? NO_GENOTYPES : new GenotypeCollection(genotypes, false);
} }
@ -82,7 +79,7 @@ public class GenotypeCollection implements List<Genotype> {
} }
public static final GenotypeCollection copy(final GenotypeCollection toCopy) { public static final GenotypeCollection copy(final GenotypeCollection toCopy) {
return create(toCopy.genotypes); return create(new ArrayList<Genotype>(toCopy.genotypes));
} }
public static final GenotypeCollection copy(final Collection<Genotype> toCopy) { public static final GenotypeCollection copy(final Collection<Genotype> toCopy) {