Support for partial VCF writing

src/main/java/htsjdk/variant/variantcontext/writer/AsyncVariantContextWriter.java

@@ -53,4 +53,10 @@ public void writeHeader(final VCFHeader header) {
     public boolean checkError() {
         return false;
     }
+
+    @Override
+    public void setVcfHeader(VCFHeader header) {
+        this.underlyingWriter.setVcfHeader(header);
+    }
+
 }

src/main/java/htsjdk/variant/variantcontext/writer/BCF2Writer.java

@@ -221,6 +221,11 @@ public void close() {
         super.close();
     }
 
+    @Override
+    public void setVcfHeader(VCFHeader header) {
+        //no-op
+    }
+
     // --------------------------------------------------------------------------------
     //
     // implicit block

src/main/java/htsjdk/variant/variantcontext/writer/SortingVariantContextWriterBase.java

@@ -132,6 +132,11 @@ public synchronized void add(VariantContext vc) {
         emitSafeRecords();
     }
 
+    @Override
+    public void setVcfHeader(VCFHeader header) {
+        innerWriter.setVcfHeader(header);
+    }
+
     /**
      * Gets a string representation of this object.
      * @return a string representation of this object
@@ -199,4 +204,4 @@ public VCFRecord(VariantContext vc) {
             this.vc = vc;
         }
     }
-}
+}

src/main/java/htsjdk/variant/variantcontext/writer/VCFWriter.java

@@ -228,4 +228,10 @@ public void add(final VariantContext context) {
             throw new RuntimeIOException("Unable to write the VCF object to " + getStreamName(), e);
         }
     }
+
+    @Override
+    public void setVcfHeader(VCFHeader header) {
+        this.mHeader = doNotWriteGenotypes ? new VCFHeader(header.getMetaDataInSortedOrder()) : header;
+        this.vcfEncoder = new VCFEncoder(this.mHeader, this.allowMissingFieldsInHeader, this.writeFullFormatField);
+    }
 }

src/main/java/htsjdk/variant/variantcontext/writer/VariantContextWriter.java

@@ -49,4 +49,6 @@ public interface VariantContextWriter extends Closeable {
     public boolean checkError();
 
     public void add(VariantContext vc);
+
+    void setVcfHeader(VCFHeader header);
 }

src/test/java/htsjdk/variant/variantcontext/writer/VCFWriterUnitTest.java

@@ -26,10 +26,13 @@
 package htsjdk.variant.variantcontext.writer;
 
 import htsjdk.samtools.SAMSequenceDictionary;
+import htsjdk.samtools.util.BlockCompressedInputStream;
 import htsjdk.samtools.util.TestUtil;
 import htsjdk.tribble.AbstractFeatureReader;
 import htsjdk.tribble.FeatureReader;
 import htsjdk.tribble.Tribble;
+import htsjdk.tribble.readers.AsciiLineReader;
+import htsjdk.tribble.readers.AsciiLineReaderIterator;
 import htsjdk.tribble.util.TabixUtils;
 import htsjdk.variant.VariantBaseTest;
 import htsjdk.variant.variantcontext.Allele;
@@ -45,6 +48,7 @@
 import htsjdk.variant.vcf.VCFHeaderVersion;
 
 import java.io.File;
+import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.util.ArrayList;
@@ -133,6 +137,49 @@ public void testBasicWriteAndRead(final String extension) throws IOException {
 
     }
 
+    /** test, using the writer and reader, that we can output and input a VCF body without problems */
+    @Test(dataProvider = "vcfExtensionsDataProvider")
+    public void testWriteAndReadVCFBody(final String extension) throws IOException {
+        final File fakeVCFFile = File.createTempFile("testWriteAndReadVCFBody.", extension);
+        fakeVCFFile.deleteOnExit();
+        if (".vcf.gz".equals(extension)) {
+            new File(fakeVCFFile.getAbsolutePath() + ".tbi").deleteOnExit();
+        } else {
+            Tribble.indexFile(fakeVCFFile).deleteOnExit();
+        }
+        metaData = new HashSet<VCFHeaderLine>();
+        additionalColumns = new HashSet<String>();
+        final SAMSequenceDictionary sequenceDict = createArtificialSequenceDictionary();
+        final VCFHeader header = createFakeHeader(metaData, additionalColumns, sequenceDict);
+        final VariantContextWriter writer = new VariantContextWriterBuilder()
+                .setOutputFile(fakeVCFFile)
+                .setReferenceDictionary(sequenceDict)
+                .setOptions(EnumSet.of(Options.ALLOW_MISSING_FIELDS_IN_HEADER, Options.INDEX_ON_THE_FLY))
+                .build();
+        writer.setVcfHeader(header);
+        writer.add(createVC(header));
+        writer.add(createVC(header));
+        writer.close();
+
+        final VCFCodec codec = new VCFCodec();
+        codec.setVCFHeader(header, VCFHeaderVersion.VCF4_0);
+        AsciiLineReaderIterator iterator;
+        if (".vcf.gz".equals(extension)) {
+            iterator = new AsciiLineReaderIterator(new AsciiLineReader(new BlockCompressedInputStream(fakeVCFFile)));
+        } else {
+            iterator = new AsciiLineReaderIterator(new AsciiLineReader(new FileInputStream(fakeVCFFile)));
+        }
+        int counter = 0;
+        while(iterator.hasNext()) {
+            VariantContext context = codec.decode(iterator.next());
+            if (context != null) {
+                counter++;
+            }
+        }
+        Assert.assertEquals(counter, 2);
+
+    }
+
     /**
      * create a fake header of known quantity
      * @param metaData           the header lines