Fixed UG parallelization bug. Better integration test to catch this in the future.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3432 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/io/storage/GenotypeWriterStorage.java

@@ -27,9 +27,7 @@ package org.broadinstitute.sting.gatk.io.storage;
 
 import java.io.*;
 import java.util.Set;
-import java.util.HashSet;
 
-import org.broad.tribble.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.gatk.io.stubs.GenotypeWriterStub;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.genotype.*;
@@ -73,8 +71,7 @@ public abstract class GenotypeWriterStorage<T extends GenotypeWriter> implements
         this.stream = null;
         writer = GenotypeWriterFactory.create(stub.getFormat(), file);
         Set<String> samples = SampleUtils.getSAMFileSamples(stub.getSAMFileHeader());
-        // TODO: this line is a problem, creating with an empty hashset eliminates any genotype FORMAT fields in the calls (besides GT)
+        GenotypeWriterFactory.writeHeader(writer, stub.getSAMFileHeader(), samples, null);
-        GenotypeWriterFactory.writeHeader(writer, stub.getSAMFileHeader(), samples, new HashSet<VCFHeaderLine>());
     }
 
     public void addCall(VariantContext vc, String refAllele) {

java/src/org/broadinstitute/sting/utils/genotype/GenotypeWriterFactory.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.utils.genotype;
 
 import net.sf.samtools.SAMFileHeader;
 import org.broad.tribble.vcf.VCFHeaderLine;
+import org.broad.tribble.vcf.VCFGenotypeRecord;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.genotype.geli.*;
 import org.broadinstitute.sting.utils.genotype.glf.*;
@@ -10,6 +11,7 @@ import org.broadinstitute.sting.utils.genotype.vcf.*;
 import java.io.File;
 import java.io.PrintStream;
 import java.util.Set;
+import java.util.HashSet;
 
 
 /**
@@ -65,6 +67,8 @@ public class GenotypeWriterFactory {
                                    Set<VCFHeaderLine> headerInfo) {
         // VCF
         if ( writer instanceof VCFGenotypeWriter ) {
+            if ( headerInfo == null )
+                headerInfo = new HashSet<VCFHeaderLine>(VCFGenotypeRecord.getSupportedHeaderStrings());
             ((VCFGenotypeWriter)writer).writeHeader(sampleNames, headerInfo);
         }
         // GELI 

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

@@ -35,7 +35,7 @@ public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter {
     private VALIDATION_STRINGENCY validationStringency = VALIDATION_STRINGENCY.STRICT;
 
     // allowed genotype format strings
-    private List<String> allowedGenotypeFormatStrings;
+    private List<String> allowedGenotypeFormatStrings = null;
 
     public VCFGenotypeWriterAdapter(File writeTo) {
         if (writeTo == null) throw new RuntimeException("VCF output file must not be null");
@@ -59,18 +59,22 @@ public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter {
         // set up the header fields
         Set<VCFHeaderLine> hInfo = new TreeSet<VCFHeaderLine>();
         hInfo.add(new VCFHeaderLine(VCFHeader.FILE_FORMAT_KEY, VCFHeader.VCF_VERSION));
-        hInfo.addAll(headerInfo);
+
-        
+        // set up the allowed genotype format fields
+        if ( headerInfo != null ) {
+            for ( VCFHeaderLine field : headerInfo ) {
+                hInfo.add(field);
+                if ( field instanceof VCFFormatHeaderLine) {
+                    if ( allowedGenotypeFormatStrings == null )
+                        allowedGenotypeFormatStrings = new ArrayList<String>();
+                    allowedGenotypeFormatStrings.add(((VCFFormatHeaderLine)field).getName());
+                }
+            }
+        }
+
         // set up the sample names
         mHeader = new VCFHeader(hInfo, mSampleNames);
         mWriter.writeHeader(mHeader);
-
-        // set up the allowed genotype format fields
-        allowedGenotypeFormatStrings = new ArrayList<String>();
-        for ( VCFHeaderLine field : headerInfo ) {
-            if ( field instanceof VCFFormatHeaderLine)
-                allowedGenotypeFormatStrings.add(((VCFFormatHeaderLine)field).getName());
-        }
     }
 
     /** finish writing, closing any open files. */

java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -57,15 +57,23 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
     // --------------------------------------------------------------------------------------------------------------
     //
-    // testing joint estimation model
+    // testing parallelization
     //
     // --------------------------------------------------------------------------------------------------------------
+
     @Test
     public void testParallelization() {
-        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+        String md5 = "638911a5d7b155076afc79a3d3f50548";
-                "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,400,000 -nt 4", 1,
+
-                Arrays.asList("60bf51595eda646f5ccf0b0bf5db95d8"));
+        WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
-        executeTest("test parallelization", spec);
+                "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000", 1,
+                Arrays.asList(md5));
+        executeTest("test parallelization (single thread)", spec1);
+
+        WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
+                "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000 -nt 2", 1,
+                Arrays.asList(md5));
+        executeTest("test parallelization (multithread)", spec2);
     }
 
     // --------------------------------------------------------------------------------------------------------------