From 41392f8ff531fd1a2e4e404ce3f6b9d6f8c7acdc Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sat, 16 Jan 2010 20:19:43 +0000
Subject: [PATCH] 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
---
 .../sting/utils/genotype/vcf/VCFRecord.java        | 14 +++++++++++++-
 .../sting/utils/genotype/vcf/VCFUtils.java         | 12 ++++++++++++
 2 files changed, 25 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
index e24245fd5..439e2a257 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
@@ -283,7 +283,7 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
     }
     
     public VARIANT_TYPE getType() {
-        if ( !hasAlternateAllele() )
+        if ( ! hasAlternateAllele() )
             return VARIANT_TYPE.REFERENCE;
 
         VCFGenotypeEncoding.TYPE type = mAlts.get(0).getType();
@@ -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
      *
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
index 46d7de6ac..0ef038ba6 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
+++ b/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