functions for setting gentoype records and alternate bases; function for getting all rods implementing VCF

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2611 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java

@@ -479,6 +479,12 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
         mGenotypeRecords.add(mGenotypeRecord);
     }
 
+    public void setGenotypeRecords(List<VCFGenotypeRecord> records) {
+        mGenotypeRecords.clear();
+        for ( VCFGenotypeRecord g : records )
+            addGenotypeRecord(g);
+    }
+
     /**
      * add an alternate base to our alternate base list.  All bases are uppercased
      * before being added to the list.
@@ -489,6 +495,12 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
         if (!mAlts.contains(base)) mAlts.add(base);
     }
 
+    public void setAlternateBases(List<VCFGenotypeEncoding> bases) {
+        mAlts.clear();
+        for ( VCFGenotypeEncoding e : bases )
+            addAlternateBase(e);
+    }
+
     /**
      * add an info field to the record
      *

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java

@@ -19,6 +19,18 @@ public class VCFUtils {
      */
     private VCFUtils() { }
 
+    public static Set<ReferenceOrderedData> getRodVCFs(GenomeAnalysisEngine toolkit) {
+        Set<ReferenceOrderedData> vcfs = new HashSet<ReferenceOrderedData>();
+
+        for ( ReferenceOrderedDataSource source : toolkit.getRodDataSources() ) {
+            ReferenceOrderedData rod = source.getReferenceOrderedData();
+            if ( rod.getType().equals(RodVCF.class) ) {
+                vcfs.add(rod);
+            }
+        }
+
+        return vcfs;
+    }
 
     /**
      * Gets the header fields from all VCF rods input by the user