fixes for GSA-199: Need easier way to write binary outputs to standard output. GLF and VCF now have stream constructors, and can get dumped to standard out.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1818 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java

@@ -101,7 +101,8 @@ public class UnifiedGenotyper extends LocusWalker<List<GenotypeCall>, Integer> {
                                                   "UnifiedGenotyper",
                                                   this.getToolkit().getArguments().referenceFile.getName());
         else
-            writer = GenotypeWriterFactory.create(VAR_FORMAT, GenomeAnalysisEngine.instance.getSAMFileHeader(), out);
+            writer = GenotypeWriterFactory.create(VAR_FORMAT, GenomeAnalysisEngine.instance.getSAMFileHeader(), out, "UnifiedGenotyper",
+                                                  this.getToolkit().getArguments().referenceFile.getName());
 
         gcm = GenotypeCalculationModelFactory.makeGenotypeCalculation(UAC, samples, writer, logger);
     }

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

@@ -46,10 +46,14 @@ public class GenotypeWriterFactory {
         }
     }
 
-    public static GenotypeWriter create(GENOTYPE_FORMAT format, SAMFileHeader header, PrintStream destination) {
+    public static GenotypeWriter create(GENOTYPE_FORMAT format, SAMFileHeader header, PrintStream destination, String source, String referenceName ) {
         switch (format) {
             case GELI:
                 return new GeliTextWriter(destination);
+            case GLF:
+                return new GLFWriter(header.toString(), destination);
+            case VCF:
+                return new VCFGenotypeWriterAdapter(source, referenceName, destination);
             default:
                 throw new StingException("Genotype writer to " + format.toString() + " to standard output is not implemented");
         }

java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java

@@ -10,6 +10,7 @@ import org.broadinstitute.sting.utils.genotype.*;
 
 import java.io.DataOutputStream;
 import java.io.File;
+import java.io.OutputStream;
 import java.util.Arrays;
 import java.util.List;
 /*
@@ -73,6 +74,20 @@ public class GLFWriter implements GenotypeWriter {
         this.writeHeader();
     }
 
+    /**
+     * The public constructor for creating a GLF object
+     *
+     * @param headerText the header text (currently unclear what the contents are)
+     * @param writeTo    the location to write to
+     */
+    public GLFWriter(String headerText, OutputStream writeTo) {
+        this.headerText = headerText;
+        outputBinaryCodec = new BinaryCodec(writeTo);
+        outputBinaryCodec.setOutputFileName(writeTo.toString());
+        this.writeHeader();
+    }
+
+
     /**
      * add a point genotype to the GLF writer
      *

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

@@ -8,11 +8,8 @@ import org.broadinstitute.sting.utils.genotype.ReadBacked;
 import org.broadinstitute.sting.utils.genotype.SampleBacked;
 
 import java.io.File;
-import java.util.Arrays;
+import java.io.OutputStream;
-import java.util.ArrayList;
+import java.util.*;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
 
 
 /**
@@ -31,13 +28,21 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
     private final Map<String, String> mSampleNames = new HashMap<String, String>();
     private boolean mInitialized = false;
     private final File mFile;
+    private final OutputStream mStream;
 
     public VCFGenotypeWriterAdapter(String source, String referenceName, File writeTo) {
         mReferenceName = referenceName;
         mSource = source;
         mFile = writeTo;
+        mStream = null;
     }
 
+    public VCFGenotypeWriterAdapter(String source, String referenceName, OutputStream writeTo) {
+        mReferenceName = referenceName;
+        mSource = source;
+        mFile = null;
+        mStream = writeTo;
+    }
 
     /**
      * initialize this VCF writer
@@ -45,7 +50,7 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
      * @param genotypes the genotypes
      * @param file      the file location to write to
      */
-    private void lazyInitialize(List<Genotype> genotypes, File file) {
+    private void lazyInitialize(List<Genotype> genotypes, File file, OutputStream stream) {
         Map<String, String> hInfo = new HashMap<String, String>();
         List<String> sampleNames = getSampleNames(genotypes);
 
@@ -55,6 +60,9 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
 
         // setup the sample names
         mHeader = new VCFHeader(hInfo, sampleNames);
+        if (mFile == null)
+            mWriter = new VCFWriter(mHeader, stream);
+        else
             mWriter = new VCFWriter(mHeader, file);
         mInitialized = true;
     }
@@ -111,7 +119,7 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
     @Override
     public void addMultiSampleCall(List<Genotype> genotypes) {
         if (!mInitialized)
-            lazyInitialize(genotypes, mFile);
+            lazyInitialize(genotypes, mFile, mStream);
 
 
         VCFParamters params = new VCFParamters();

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

@@ -1,10 +1,14 @@
 package org.broadinstitute.sting.utils.genotype.vcf;
 
 
+import org.broadinstitute.sting.utils.StingException;
+
 import java.io.*;
 import java.nio.charset.Charset;
 
-/** this class writers VCF files */
+/**
+ * this class writers VCF files
+ */
 public class VCFWriter {
 
     // the VCF header we're storing
@@ -21,16 +25,30 @@ public class VCFWriter {
      * @param location the file location to write to
      */
     public VCFWriter(VCFHeader header, File location) {
-        this.mHeader = header;
+        FileOutputStream output;
-        Charset utf8 = Charset.forName("UTF-8");
         try {
-            mWriter = new BufferedWriter(
+            output = new FileOutputStream(location);
-                    new OutputStreamWriter(
-                            new FileOutputStream(location),
-                            utf8));
         } catch (FileNotFoundException e) {
-            throw new RuntimeException("Unable to create VCF file: " + location, e);
+            throw new RuntimeException("Unable to create VCF file at location: " + location);
         }
+        initialize(header, output);
+    }
+
+
+    /**
+     * create a VCF writer, given a VCF header and a file to write to
+     *
+     * @param header   the VCF header
+     * @param location the file location to write to
+     */
+    public VCFWriter(VCFHeader header, OutputStream location) {
+        initialize(header, location);
+    }
+
+    private void initialize(VCFHeader header, OutputStream location) {
+        this.mHeader = header;
+        mWriter = new BufferedWriter(
+                new OutputStreamWriter(location));
         try {
             // write the header meta-data out
             for (String metadata : header.getMetaData().keySet()) {
@@ -71,8 +89,9 @@ public class VCFWriter {
     }
 
 
-
+    /**
-    /** attempt to close the VCF file */
+     * attempt to close the VCF file
+     */
     public void close() {
         try {
             mWriter.flush();