From e051311e8cf457f999eac4d618c47ae2ef431364 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 16 Dec 2009 17:58:41 +0000
Subject: [PATCH] Added convenience methods in RodVCF to pull out all of the
 VCF data from the VCFRecord (e.g. getID(), getSamples(), getInfoValues())

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2374 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/refdata/RodVCF.java            | 51 +++++++++++++++++++
 1 file changed, 51 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
index b9cd653ff..76201a0c8 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
@@ -13,6 +13,7 @@ import java.io.IOException;
 import java.util.Iterator;
 import java.util.List;
 import java.util.NoSuchElementException;
+import java.util.Map;
 
 
 /**
@@ -104,6 +105,11 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
         return mCurrentRecord.getType();
     }
 
+    public String getID() {
+        assertNotNull();
+        return mCurrentRecord.getID();
+    }
+
     /**
      * are we a SNP? If not we're a Indel/deletion
      *
@@ -166,6 +172,16 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
         return mCurrentRecord.getNegLog10PError();
     }
 
+    public double getQual() {
+        assertNotNull();
+        return mCurrentRecord.getQual();
+    }
+
+    public boolean hasAlternateAllele() {
+        assertNotNull();
+        return mCurrentRecord.hasAlternateAllele();
+    }
+
     /**
      * gets the alternate alleles.  This method should return all the alleles present at the location,
      * NOT including the reference base.  This is returned as a string list with no guarantee ordering
@@ -232,6 +248,11 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
         return mCurrentRecord.getReferenceForSNP();
     }
 
+    public boolean hasGenotypeData() {
+        assertNotNull();
+        return mCurrentRecord.hasGenotypeData();
+    }
+
     /**
      * get the genotype
      *
@@ -275,6 +296,36 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
         return mCurrentRecord.hasGenotype(x);
     }
 
+    public String[] getSampleNames() {
+        assertNotNull();
+        return mCurrentRecord.getSampleNames();
+    }
+
+    public Map<String, String> getInfoValues() {
+        assertNotNull();
+        return mCurrentRecord.getInfoValues();
+    }
+
+    public String[] getFilteringCodes() {
+        assertNotNull();
+        return mCurrentRecord.getFilteringCodes();
+    }
+
+    public boolean isFiltered() {
+        assertNotNull();
+        return mCurrentRecord.isFiltered();
+    }
+
+    public boolean hasFilteringCodes() {
+        assertNotNull();
+        return mCurrentRecord.hasFilteringCodes();
+    }
+
+    public String getFilterString() {
+        assertNotNull();
+        return mCurrentRecord.getFilterString();
+    }
+
     public VCFHeader getHeader() {
         return mReader.getHeader();
     }