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Skip locations with no genotypes instead of throwing a NPE

This commit is contained in:
Joel Thibault 2012-04-10 16:55:01 -04:00
parent 4bdfeacdaa
commit 7ed0ee7ed0
1 changed files with 39 additions and 39 deletions
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78
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -600,48 +600,48 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
genotypes.add(Genotype.modifyAttributes(genotype, genotypeAttributes));
}
// 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);
if (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());
}
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;
}