Writing calls to standard out now works again (it got broken when we introduced parallelization)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2446 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -130,6 +130,13 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
             //     logger.debug("SAMPLE: " + sample);
         }
 
+        // 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);
+        }
+
         // initialize the verbose writer
         if ( VERBOSE != null ) {
             try {

java/src/org/broadinstitute/sting/utils/genotype/geli/GeliTextWriter.java

@@ -52,6 +52,7 @@ public class GeliTextWriter implements GeliGenotypeWriter {
     public void writeHeader(final SAMFileHeader fileHeader) {
         // ignore the SAM header; the geli text header is fixed.
         mWriter.println(headerLine);        
+        mWriter.flush();  // necessary so that writing to an output stream will work
     }
 
     /**
@@ -102,10 +103,12 @@ public class GeliTextWriter implements GeliGenotypeWriter {
                                       posteriors[7],
                                       posteriors[8],
                                       posteriors[9]));
+        mWriter.flush();  // necessary so that writing to an output stream will work
     }
 
     public void addGenotypeLikelihoods(GenotypeLikelihoods gl) {
         mWriter.println(gl.toString());
+        mWriter.flush();  // necessary so that writing to an output stream will work
     }
 
     /**
@@ -119,6 +122,7 @@ public class GeliTextWriter implements GeliGenotypeWriter {
 
     /** finish writing, closing any open files. */
     public void close() {
+        mWriter.flush();
         mWriter.close();
     }
 

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

@@ -71,6 +71,7 @@ public class VCFWriter {
                 for (String field : header.getGenotypeSamples()) b.append(field + FIELD_SEPERATOR);
             }
             mWriter.write(b.toString() + "\n");
+            mWriter.flush();  // necessary so that writing to an output stream will work
         }
         catch (IOException e) {
             throw new RuntimeException("IOException writing the VCF header", e);
@@ -89,6 +90,7 @@ public class VCFWriter {
         String vcfString = record.toStringEncoding(mHeader);
         try {
             mWriter.write(vcfString + "\n");
+            mWriter.flush();  // necessary so that writing to an output stream will work
         } catch (IOException e) {
             throw new RuntimeException("Unable to write the VCF object to a file");
         }