From b125571a98d5a1961d3b3eca0b45ec04d291cd13 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 29 Dec 2009 16:11:11 +0000
Subject: [PATCH] Intermediate check in: transfer responsibility of wrapping
 the GenotypeWriter around the output stream to the output management code. 
 Currently, will not work when neither -varout nor -vf are specified, but
 should work in all other cases.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2463 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../io/storage/GenotypeWriterStorage.java     | 11 ++++++-
 .../gatk/io/stubs/GLFGenotypeWriterStub.java  | 10 ++++++
 .../io/stubs/GeliTextGenotypeWriterStub.java  | 10 ++++++
 .../GenotypeWriterArgumentTypeDescriptor.java | 16 +++++----
 .../gatk/io/stubs/GenotypeWriterStub.java     | 33 +++++++++++++++++--
 .../gatk/io/stubs/VCFGenotypeWriterStub.java  | 10 ++++++
 .../walkers/genotyper/UnifiedGenotyper.java   |  7 ----
 7 files changed, 80 insertions(+), 17 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/GenotypeWriterStorage.java b/java/src/org/broadinstitute/sting/gatk/io/storage/GenotypeWriterStorage.java
index 54fd534e9..62418b183 100755
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/GenotypeWriterStorage.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/GenotypeWriterStorage.java
@@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.io.stubs.GenotypeWriterStub;
 import org.broadinstitute.sting.utils.genotype.*;
 import org.broadinstitute.sting.utils.genotype.vcf.*;
 import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.StingException;
 
 /**
  * Provides temporary storage for GenotypeWriters.
@@ -43,6 +44,7 @@ import org.broadinstitute.sting.utils.SampleUtils;
  */
 public abstract class GenotypeWriterStorage<T extends GenotypeWriter> implements GenotypeWriter, Storage<T> {
     protected final File file;
+    protected final PrintStream stream;
     protected final GenotypeWriter writer;
 
     /**
@@ -52,7 +54,13 @@ public abstract class GenotypeWriterStorage<T extends GenotypeWriter> implements
      */
     public GenotypeWriterStorage( GenotypeWriterStub stub ) {
         this.file = stub.getFile();
-        writer = GenotypeWriterFactory.create(stub.getFormat(), file);
+        this.stream = stub.getOutputStream();
+        if(file != null)
+            writer = GenotypeWriterFactory.create(stub.getFormat(), file);
+        else if(stream != null)
+            writer = GenotypeWriterFactory.create(stub.getFormat(), stream);
+        else
+            throw new StingException("Unable to create target to which to write; storage was provided with neither a file nor a stream.");
     }
 
     /**
@@ -62,6 +70,7 @@ public abstract class GenotypeWriterStorage<T extends GenotypeWriter> implements
      */
     public GenotypeWriterStorage( GenotypeWriterStub stub, File file ) {
         this.file = file;
+        this.stream = null;
         writer = GenotypeWriterFactory.create(stub.getFormat(), file);
         Set<String> samples = SampleUtils.getSAMFileSamples(stub.getSAMFileHeader());
         GenotypeWriterFactory.writeHeader(writer, stub.getSAMFileHeader(), samples, new HashSet<VCFHeaderLine>());
diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/GLFGenotypeWriterStub.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/GLFGenotypeWriterStub.java
index a898553e7..1f540bf19 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/GLFGenotypeWriterStub.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/GLFGenotypeWriterStub.java
@@ -6,6 +6,7 @@ import org.broadinstitute.sting.utils.genotype.glf.GLFRecord;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 
 import java.io.File;
+import java.io.PrintStream;
 
 /**
  * Stub providing a passthrough for GLF files.
@@ -23,6 +24,15 @@ public class GLFGenotypeWriterStub extends GenotypeWriterStub<GLFGenotypeWriter>
         super(engine,genotypeFile);
     }
 
+    /**
+     * Construct a new stub with the given engine and target stream.
+     * @param engine The engine, for extracting command-line arguments, etc.
+     * @param genotypeStream Target stream into which to write genotyping data.
+     */
+    public GLFGenotypeWriterStub(GenomeAnalysisEngine engine, PrintStream genotypeStream) {
+        super(engine,genotypeStream);
+    }
+
     /**
      * Gets the format of this stub.  We may want to discontinue use of this method and rely on instanceof comparisons.
      * @return GLF always.
diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/GeliTextGenotypeWriterStub.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/GeliTextGenotypeWriterStub.java
index 915901bee..1af3c7651 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/GeliTextGenotypeWriterStub.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/GeliTextGenotypeWriterStub.java
@@ -5,6 +5,7 @@ import org.broadinstitute.sting.utils.genotype.GenotypeWriterFactory;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 
 import java.io.File;
+import java.io.PrintStream;
 
 import net.sf.samtools.SAMFileHeader;
 import edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods;
@@ -25,6 +26,15 @@ public class GeliTextGenotypeWriterStub extends GenotypeWriterStub<GeliGenotypeW
         super(engine,genotypeFile);
     }
 
+    /**
+     * Construct a new stub with the given engine and target stream.
+     * @param engine The engine, for extracting command-line arguments, etc.
+     * @param genotypeStream Target stream into which to write genotyping data.
+     */
+    public GeliTextGenotypeWriterStub(GenomeAnalysisEngine engine, PrintStream genotypeStream) {
+        super(engine,genotypeStream);
+    }
+
     /**
      * Gets the format of this stub.  We may want to discontinue use of this method and rely on instanceof comparisons.
      * @return GELI always.
diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/GenotypeWriterArgumentTypeDescriptor.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/GenotypeWriterArgumentTypeDescriptor.java
index 2c051e285..ed32e793b 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/GenotypeWriterArgumentTypeDescriptor.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/GenotypeWriterArgumentTypeDescriptor.java
@@ -67,10 +67,11 @@ public class GenotypeWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
      */
     @Override
     public Object parse( ArgumentSource source, Class type, ArgumentMatches matches )  {
+        // Get the filename for the genotype file, if it exists.  If not, we'll need to send output to out.
         String writerFileName = getArgumentValue(createGenotypeFileArgumentDefinition(source),matches);
-        if(writerFileName == null)
-            throw new StingException("Genotype format was supplied, but no file was supplied to contain the genotype info..");
+        File writerFile = writerFileName != null ? new File(writerFileName) : null;
 
+        // Get the format of the genotype object, if it exists.
         String genotypeFormatText = getArgumentValue(createGenotypeFormatArgumentDefinition(source),matches);
         GenotypeWriterFactory.GENOTYPE_FORMAT genotypeFormat = GenotypeWriterFactory.GENOTYPE_FORMAT.VCF;
         if(genotypeFormatText != null) {
@@ -82,19 +83,22 @@ public class GenotypeWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
             }            
         }
 
+        // Create a stub for the given object.
         GenotypeWriterStub stub = null;
         switch(genotypeFormat) {
             case GELI:
-                stub = new GeliTextGenotypeWriterStub(engine, new File(writerFileName));
+                stub = (writerFile != null) ? new GeliTextGenotypeWriterStub(engine, writerFile) : new GeliTextGenotypeWriterStub(engine,System.out);
                 break;
             case GELI_BINARY:
-                stub = new GeliBinaryGenotypeWriterStub(engine, new File(writerFileName));
+                if(writerFile == null)
+                    throw new StingException("Geli binary files cannot be output to the console.");
+                stub = new GeliBinaryGenotypeWriterStub(engine, writerFile);
                 break;
             case GLF:
-                stub = new GLFGenotypeWriterStub(engine, new File(writerFileName));
+                stub = (writerFile != null) ? new GLFGenotypeWriterStub(engine, writerFile) : new GLFGenotypeWriterStub(engine,System.out);
                 break;
             case VCF:
-                stub = new VCFGenotypeWriterStub(engine, new File(writerFileName));
+                stub = (writerFile != null) ? new VCFGenotypeWriterStub(engine, writerFile) : new VCFGenotypeWriterStub(engine,System.out);
                 break;
             default:
                 throw new StingException("Unable to create stub for file format " + genotypeFormat);
diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/GenotypeWriterStub.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/GenotypeWriterStub.java
index 94658aa45..1ef6648bc 100755
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/GenotypeWriterStub.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/GenotypeWriterStub.java
@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.io.stubs;
 
 import java.io.File;
+import java.io.PrintStream;
 import java.util.List;
 
 import org.broadinstitute.sting.gatk.io.OutputTracker;
@@ -50,11 +51,17 @@ public abstract class GenotypeWriterStub<T extends GenotypeWriter> implements St
     private final GenomeAnalysisEngine engine;
 
     /**
-     * The file that this stub should write to.  Should be passed along to
-     * whatever happens to create the StreamConnector.
+     * The file that this stub should write to.  Should be mutually
+     * exclusive with genotypeStream.
      */
     private final File genotypeFile;
 
+    /**
+     * The output stream to which stub data should be written.  Will be
+     * mutually exclusive with genotypeFile.
+     */
+    private final PrintStream genotypeStream;
+
     /**
      * Connects this stub with an external stream capable of serving the
      * requests of the consumer of this stub.
@@ -69,16 +76,36 @@ public abstract class GenotypeWriterStub<T extends GenotypeWriter> implements St
     public GenotypeWriterStub(GenomeAnalysisEngine engine,File genotypeFile) {
         this.engine = engine;
         this.genotypeFile = genotypeFile;
+        this.genotypeStream = null;
+    }
+
+    /**
+     * Create a new stub given the requested file.
+     * @param engine        GATK engine.
+     * @param genotypeStream  stream to (ultimately) write.
+     */
+    public GenotypeWriterStub(GenomeAnalysisEngine engine,PrintStream genotypeStream) {
+        this.engine = engine;
+        this.genotypeFile = null;
+        this.genotypeStream = genotypeStream;
     }
 
     /**
      * Retrieves the file to (ultimately) be created.
-     * @return The file.  Must not be null.
+     * @return The file.  Can be null if genotypeStream is not.
      */
     public File getFile() {
         return genotypeFile;
     }
 
+    /**
+     * Retrieves the output stearm to which to (ultimately) write.
+     * @return The file.  Can be null if genotypeFile is not.
+     */
+    public PrintStream getOutputStream() {
+        return genotypeStream;
+    }
+
     /**
      * Retrieves the header to use when creating the new file.
      * @return header to use when creating the new file.
diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFGenotypeWriterStub.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFGenotypeWriterStub.java
index 75ca245e8..fa03cc340 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFGenotypeWriterStub.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFGenotypeWriterStub.java
@@ -7,6 +7,7 @@ import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 
 import java.io.File;
+import java.io.PrintStream;
 import java.util.Set;
 
 /**
@@ -25,6 +26,15 @@ public class VCFGenotypeWriterStub extends GenotypeWriterStub<VCFGenotypeWriter>
         super(engine,genotypeFile);
     }
 
+    /**
+     * Construct a new stub with the given engine and target stream.
+     * @param engine The engine, for extracting command-line arguments, etc.
+     * @param genotypeStream Target stream into which to write genotyping data.
+     */
+    public VCFGenotypeWriterStub(GenomeAnalysisEngine engine, PrintStream genotypeStream) {
+        super(engine,genotypeStream);
+    }
+
     /**
      * Gets the format of this stub.  We may want to discontinue use of this method and rely on instanceof comparisons.
      * @return VCF always.
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 2e70fe6da..5525f50db 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -118,13 +118,6 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
                 throw new IllegalArgumentException("For technical reasons, the VERBOSE argument cannot be used with multiple threads");
         }
 
-        // set up the writer manually if it needs to use the output stream
-        if ( writer == null && out != null ) {
-            logger.warn("For technical reasons, VCF format must be used when writing to standard out.");
-            logger.warn("Specify an output file if you would like to use a different output format.");
-            writer = GenotypeWriterFactory.create(GenotypeWriterFactory.GENOTYPE_FORMAT.VCF, out);
-        }
-
         // get all of the unique sample names - unless we're in POOLED mode, in which case we ignore the sample names
         if ( UAC.genotypeModel != GenotypeCalculationModel.Model.POOLED ) {
             // if we're supposed to assume a single sample, do so