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Handle multiple samples/genotypes per location 

TODO: sample selection
This commit is contained in:
Joel Thibault 2012-04-10 11:50:02 -04:00
parent 1f7c628796
commit 4bdfeacdaa
1 changed files with 49 additions and 42 deletions
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91
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -563,44 +563,17 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
query.put("contig", contig); query.put("contig", contig);
query.put("start", start); query.put("start", start);
query.put("stop", stop); query.put("stop", stop);
//query.put("sample", "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;
Collection<Genotype> genotypes = new ArrayList<Genotype>();
while(cursor.hasNext()) { while(cursor.hasNext()) {
DBObject result = cursor.next(); result = cursor.next();
String source = (String)result.get("source");
ArrayList<Allele> alleles = new ArrayList<Allele>();
BasicDBObject allelesInDb = (BasicDBObject)result.get("alleles");
for (Object alleleInDb : allelesInDb.values()) {
String rawAllele = (String)alleleInDb;
boolean isRef = rawAllele.contains("*");
String allele = rawAllele.replace("*", "");
alleles.add(Allele.create(allele, isRef));
}
VariantContextBuilder builder = new VariantContextBuilder(source, contig, start, stop, alleles);
String id = (String)result.get("id");
String sample = (String)result.get("sample"); String sample = (String)result.get("sample");
Double error = (Double)result.get("error");
Map<String, Object> attributes = new TreeMap<String, Object>();
BasicDBList attrsInDb = (BasicDBList)result.get("attributes");
for (Object attrInDb : attrsInDb) {
BasicDBObject attrKVP = (BasicDBObject)attrInDb;
String key = (String)attrKVP.get("key");
Object value = attrKVP.get("value");
attributes.put(key, value);
}
Set<String> filters = new HashSet<String>();
BasicDBObject filtersInDb = (BasicDBObject)result.get("filters");
if (filtersInDb != null) {
for (Object filterInDb : filtersInDb.values()) {
filters.add((String)filterInDb);
}
}
BasicDBObject genotypeInDb = (BasicDBObject)result.get("genotype"); BasicDBObject genotypeInDb = (BasicDBObject)result.get("genotype");
Double genotypeError = (Double)genotypeInDb.get("error"); Double genotypeError = (Double)genotypeInDb.get("error");
@ -624,17 +597,51 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
} }
Genotype genotype = new Genotype(sample, genotypeAlleles, genotypeError); Genotype genotype = new Genotype(sample, genotypeAlleles, genotypeError);
genotype = Genotype.modifyAttributes(genotype, genotypeAttributes); genotypes.add(Genotype.modifyAttributes(genotype, genotypeAttributes));
builder.id(id);
builder.log10PError(error);
builder.genotypes(genotype);
builder.attributes(attributes);
builder.filters(filters);
vcs.add(builder.make());
} }
// TODO: handle result == null
ArrayList<Allele> alleles = new ArrayList<Allele>();
BasicDBObject allelesInDb = (BasicDBObject)result.get("alleles");
for (Object alleleInDb : allelesInDb.values()) {
String rawAllele = (String)alleleInDb;
boolean isRef = rawAllele.contains("*");
String allele = rawAllele.replace("*", "");
alleles.add(Allele.create(allele, isRef));
}
Map<String, Object> attributes = new TreeMap<String, Object>();
BasicDBList attrsInDb = (BasicDBList)result.get("attributes");
for (Object attrInDb : attrsInDb) {
BasicDBObject attrKVP = (BasicDBObject)attrInDb;
String key = (String)attrKVP.get("key");
Object value = attrKVP.get("value");
attributes.put(key, value);
}
Set<String> filters = new HashSet<String>();
BasicDBObject filtersInDb = (BasicDBObject)result.get("filters");
if (filtersInDb != null) {
for (Object filterInDb : filtersInDb.values()) {
filters.add((String)filterInDb);
}
}
String source = (String)result.get("source");
String id = (String)result.get("id");
Double error = (Double)result.get("error");
VariantContextBuilder builder = new VariantContextBuilder(source, contig, start, stop, alleles);
builder.id(id);
builder.log10PError(error);
builder.genotypes(genotypes);
builder.attributes(attributes);
builder.filters(filters);
vcs.add(builder.make());
return vcs; return vcs;
} }