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Insert the ROD filename into MongoDB as part of the primary key

This commit is contained in:
Joel Thibault 2012-04-10 11:48:37 -04:00
parent bb8a6e9b0a
commit 1f7c628796
2 changed files with 12 additions and 3 deletions
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12
public/java/src/org/broadinstitute/sting/gatk/walkers/InsertRODsWalker.java
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@ -18,6 +18,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.File;
import java.io.PrintStream; import java.io.PrintStream;
/** /**
@ -38,6 +39,8 @@ public class InsertRODsWalker extends RodWalker<Integer, Integer> {
protected Mongo mongo; protected Mongo mongo;
protected DBCollection mongoCollection; protected DBCollection mongoCollection;
private String RODFileName;
@Override @Override
public void initialize() public void initialize()
{ {
@ -46,15 +49,20 @@ public class InsertRODsWalker extends RodWalker<Integer, Integer> {
DB mongoDb = mongo.getDB(MONGO_DB_NAME); DB mongoDb = mongo.getDB(MONGO_DB_NAME);
mongoCollection = mongoDb.getCollection(MONGO_VC_COLLECTION); mongoCollection = mongoDb.getCollection(MONGO_VC_COLLECTION);
RODFileName = input.getSource();
int lastSep = RODFileName.lastIndexOf(File.separator);
RODFileName = RODFileName.substring(lastSep + 1);
// set up indices // set up indices
mongoCollection.ensureIndex("location"); mongoCollection.ensureIndex("location");
mongoCollection.ensureIndex("sample"); mongoCollection.ensureIndex("sample");
mongoCollection.ensureIndex("sourceROD");
mongoCollection.ensureIndex("contig"); mongoCollection.ensureIndex("contig");
mongoCollection.ensureIndex("start"); mongoCollection.ensureIndex("start");
mongoCollection.ensureIndex("stop"); mongoCollection.ensureIndex("stop");
// set up primary key // set up primary key
mongoCollection.ensureIndex(new BasicDBObject("location", 1).append("sample", 1), new BasicDBObject("unique", 1)); mongoCollection.ensureIndex(new BasicDBObject("location", 1).append("sample", 1).append("sourceROD", 1), new BasicDBObject("unique", 1));
} }
catch (MongoException e) {} catch (MongoException e) {}
@ -82,7 +90,7 @@ public class InsertRODsWalker extends RodWalker<Integer, Integer> {
for ( Feature feature : tracker.getValues(Feature.class, context.getLocation()) ) { for ( Feature feature : tracker.getValues(Feature.class, context.getLocation()) ) {
if ( feature instanceof VariantContext ) { if ( feature instanceof VariantContext ) {
VariantContext vc = (VariantContext) feature; VariantContext vc = (VariantContext) feature;
for (BasicDBObject vcForMongo : vc.toMongoDB()) { for (BasicDBObject vcForMongo : vc.toMongoDB(RODFileName)) {
mongoCollection.insert(vcForMongo); mongoCollection.insert(vcForMongo);
} }
} }

3
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
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@ -1221,7 +1221,7 @@ public class VariantContext implements Feature { // to enable tribble integratio
this.getGenotypes()); this.getGenotypes());
} }
public List<BasicDBObject> toMongoDB() { public List<BasicDBObject> toMongoDB(String sourceROD) {
List<BasicDBObject> vcDocs = new ArrayList<BasicDBObject>(); List<BasicDBObject> vcDocs = new ArrayList<BasicDBObject>();
for (Genotype genotype : this.getGenotypes()) { for (Genotype genotype : this.getGenotypes()) {
BasicDBObject vcDoc = new BasicDBObject(); BasicDBObject vcDoc = new BasicDBObject();
@ -1233,6 +1233,7 @@ public class VariantContext implements Feature { // to enable tribble integratio
vcDoc.put("error", this.getLog10PError()); vcDoc.put("error", this.getLog10PError());
vcDoc.put("sample", genotype.getSampleName()); vcDoc.put("sample", genotype.getSampleName());
vcDoc.put("source", this.getSource()); vcDoc.put("source", this.getSource());
vcDoc.put("sourceROD", sourceROD);
vcDoc.put("type", this.getType().toString()); vcDoc.put("type", this.getType().toString());
Integer alleleIndex = 0; Integer alleleIndex = 0;