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Add alleles to the primary key

This commit is contained in:
Joel Thibault 2012-04-17 16:21:46 -04:00
parent 3198ce5471
commit 221ce9c3d6
2 changed files with 2 additions and 5 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/walkers/InsertRODsWalker.java
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@ -62,8 +62,7 @@ public class InsertRODsWalker extends RodWalker<Integer, Integer> {
mongoCollection.ensureIndex("stop"); mongoCollection.ensureIndex("stop");
// set up primary key // set up primary key
mongoCollection.ensureIndex(new BasicDBObject("location", 1).append("sample", 1).append("sourceROD", 1), new BasicDBObject("unique", 1)); mongoCollection.ensureIndex(new BasicDBObject("location", 1).append("sample", 1).append("sourceROD", 1).append("alleles", 1), new BasicDBObject("unique", 1));
} }
catch (MongoException e) {} catch (MongoException e) {}
catch (java.net.UnknownHostException e) {} catch (java.net.UnknownHostException e) {}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -562,9 +562,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
BasicDBObject query = new BasicDBObject(); BasicDBObject query = new BasicDBObject();
query.put("contig", contig); query.put("contig", contig);
query.put("start", start); query.put("start", start);
query.put("stop", stop); // can't know stop location for deletions from reference
//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);
Map<String,DBObject> results = new HashMap<String,DBObject>(); Map<String,DBObject> results = new HashMap<String,DBObject>();