Moving VF to vcf 4.0. Still need to fix genotype filters.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3777 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java

@@ -46,7 +46,7 @@ import java.util.*;
 /**
  * Filters variant calls using a number of user-selectable, parameterizable criteria.
  */
-@Requires(value={},referenceMetaData=@RMD(name="variant",type= ReferenceOrderedDatum.class))
+@Requires(value={},referenceMetaData=@RMD(name="variant", type=ReferenceOrderedDatum.class))
 @Reference(window=@Window(start=-50,stop=50))
 public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
 
@@ -84,7 +84,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
     private ArrayList<FiltrationContext> windowInitializer = new ArrayList<FiltrationContext>();
 
 
-    private void initializeVcfWriter(VCFRecord rec) {
+    private void initializeVcfWriter(VariantContext vc) {
         // setup the header fields
         Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
@@ -110,8 +110,8 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
             }
         }
 
-        writer = new VCFWriter(out);
+        writer = new VCFWriter(out, true);
-        writer.writeHeader(new VCFHeader(hInfo, new TreeSet<String>(Arrays.asList(rec.getSampleNames()))));
+        writer.writeHeader(new VCFHeader(hInfo, new TreeSet<String>(vc.getSampleNames())));
     }
 
     public void initialize() {
@@ -210,13 +210,13 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
 
         VariantContext filteredVC = new VariantContext(vc.getName(), vc.getLocation(), vc.getAlleles(), genotypes, vc.getNegLog10PError(), filters, vc.getAttributes());
 
-        writeVCF(VariantContextAdaptors.toVCF(filteredVC, context.getReferenceContext().getBase(), null, true, genotypeFilterExps.size() > 0));
+        writeVCF(filteredVC, context.getReferenceContext().getBase());
     }
 
-    private void writeVCF(VCFRecord rec) {
+    private void writeVCF(VariantContext vc, byte ref) {
         if ( writer == null )
-            initializeVcfWriter(rec);
+            initializeVcfWriter(vc);
-        writer.addRecord(rec);
+        writer.add(vc, new byte[]{ref});
     }
 
     public Integer reduce(Integer value, Integer sum) {

java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java

@@ -16,7 +16,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testNoAction() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("d2f0a3c6e598d9054de9ea7bd914a12d"));
+                Arrays.asList("d1aec615dba4d91991f4c67cadf3d56a"));
         executeTest("test no action", spec);
     }
 
@@ -24,7 +24,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testClusteredSnps() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -window 10 -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("4dad2ddfb74785c5c80c2a73709e543a"));
+                Arrays.asList("fa522e5b8c89c5a465ca03dd88bc2b8f"));
         executeTest("test clustered SNPs", spec);
     }
 
@@ -32,7 +32,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testMask() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -mask foo -B mask,VCF," + validationDataLocation + "vcfexample2.vcf -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("70fc964e73fda55ed3f2c0b0ae4bcec1"));
+                Arrays.asList("4d8a184417289c325410a5e545d9fc80"));
         executeTest("test mask", spec);
     }
 
@@ -40,7 +40,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilter1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("bde496530822a81197df31f5ecf98033"));
+                Arrays.asList("d48062f139d853a61e4f0bfb76bd695d"));
         executeTest("test filter #1", spec);
     }
 
@@ -48,7 +48,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilter2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("750f5076e906901dabec78f804f035fa"));
+                Arrays.asList("791f89c6da7bdde79913754d9ddb72eb"));
         executeTest("test filter #2", spec);
     }
 
@@ -56,7 +56,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilterWithSeparateNames() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --filterName ABF -filter 'AlleleBalance < 70.0' --filterName FSF -filter 'FisherStrand == 1.4' -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("7f876c9187948d27c0cd39f5a0395e0e"));
+                Arrays.asList("174caf880477f3edf68fe6722f227017"));
         executeTest("test filter with separate names #2", spec);
     }
 }