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Can have multiple variants at a location

This commit is contained in:
Joel Thibault 2012-04-17 12:50:36 -04:00
parent 11ed8e61c9
commit 3198ce5471
1 changed files with 18 additions and 9 deletions
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27
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -567,15 +567,17 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
query.put("sample", new BasicDBObject("$ne", "NA12878")); // TODO: remove kluge query.put("sample", new BasicDBObject("$ne", "NA12878")); // TODO: remove kluge
DBCursor cursor = mongoCollection.find(query); DBCursor cursor = mongoCollection.find(query);
DBObject result = null; Map<String,DBObject> results = new HashMap<String,DBObject>();
Map<String,ArrayList<Genotype>> genotypes = new HashMap<String,ArrayList<Genotype>>();
Collection<Genotype> genotypes = new ArrayList<Genotype>();
while(cursor.hasNext()) { while(cursor.hasNext()) {
result = cursor.next(); DBObject oneResult = cursor.next();
String sample = (String)result.get("sample"); String type = (String)oneResult.get("type");
results.put(type, oneResult);
BasicDBObject genotypeInDb = (BasicDBObject)result.get("genotype"); String sample = (String)oneResult.get("sample");
BasicDBObject genotypeInDb = (BasicDBObject)oneResult.get("genotype");
Double genotypeError = (Double)genotypeInDb.get("error"); Double genotypeError = (Double)genotypeInDb.get("error");
ArrayList<Allele> genotypeAlleles = new ArrayList<Allele>(); ArrayList<Allele> genotypeAlleles = new ArrayList<Allele>();
@ -597,10 +599,17 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
} }
Genotype genotype = new Genotype(sample, genotypeAlleles, genotypeError); Genotype genotype = new Genotype(sample, genotypeAlleles, genotypeError);
genotypes.add(Genotype.modifyAttributes(genotype, genotypeAttributes));
if (!genotypes.containsKey(type))
genotypes.put(type, new ArrayList<Genotype>());
Collection<Genotype> genotypesByType = genotypes.get(type);
genotypesByType.add(Genotype.modifyAttributes(genotype, genotypeAttributes));
} }
if (result != null) { for (String type : results.keySet()) {
DBObject result = results.get(type);
ArrayList<Allele> alleles = new ArrayList<Allele>(); ArrayList<Allele> alleles = new ArrayList<Allele>();
BasicDBObject allelesInDb = (BasicDBObject)result.get("alleles"); BasicDBObject allelesInDb = (BasicDBObject)result.get("alleles");
for (Object alleleInDb : allelesInDb.values()) { for (Object alleleInDb : allelesInDb.values()) {
@ -635,7 +644,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
builder.id(id); builder.id(id);
builder.log10PError(error); builder.log10PError(error);
builder.genotypes(genotypes); builder.genotypes(genotypes.get(type));
builder.attributes(attributes); builder.attributes(attributes);
builder.filters(filters); builder.filters(filters);