From e6d61197e68bbdb7d0be88f66ce08edf1a295d5f Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 22 Oct 2010 17:40:37 +0000
Subject: [PATCH] Disable OTF indexing when writing indices for temporary VCFs
 when running with -nt option.  When last I checked in, Ryan was seeing a ~25%
 speedup per shard by not indexing.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4556 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/io/storage/VCFWriterStorage.java     | 42 ++++++-------------
 1 file changed, 12 insertions(+), 30 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java b/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
index 183597069..3dd6fbf5b 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
@@ -32,7 +32,7 @@ public class VCFWriterStorage implements Storage<VCFWriterStorage>, VCFWriter {
     public VCFWriterStorage( VCFWriterStub stub )  {
         if ( stub.getFile() != null ) {
             this.file = stub.getFile();
-            writer = VCFWriterToFile(stub, stub.getFile());
+            writer = vcfWriterToFile(stub,stub.getFile(),true);
         }
         else if ( stub.getOutputStream() != null ) {
             this.file = null;
@@ -45,11 +45,12 @@ public class VCFWriterStorage implements Storage<VCFWriterStorage>, VCFWriter {
 
     /**
      * common initialization routine for multiple constructors
-     * @param stub
-     * @param file
+     * @param stub Stub to use when constructing the output file.
+     * @param file Target file into which to write VCF records.
+     * @param indexOnTheFly true to index the file on the fly.  NOTE: will be forced to false for compressed files.
      * @return A VCF writer for use with this class
      */
-    private StandardVCFWriter VCFWriterToFile(VCFWriterStub stub, File file) {
+    private StandardVCFWriter vcfWriterToFile(VCFWriterStub stub, File file, boolean indexOnTheFly) {
         try {
             if ( stub.isCompressed() )
                 stream = new BlockCompressedOutputStream(file);
@@ -60,18 +61,19 @@ public class VCFWriterStorage implements Storage<VCFWriterStorage>, VCFWriter {
             throw new UserException.CouldNotCreateOutputFile(file, "Unable to open target output stream", ex);
         }
 
-        return new StandardVCFWriter(file, this.stream, ! stub.isCompressed());
+        // The GATK/Tribble can't currently index block-compressed files on the fly.  Disable OTF indexing even if the user explicitly asked for it.
+        return new StandardVCFWriter(file, this.stream, indexOnTheFly && !stub.isCompressed());
     }
 
 
     /**
      * Constructs an object which will redirect into a different file.
      * @param stub Stub to use when synthesizing file / header info.
-     * @param file File into which to direct the output data.
+     * @param tempFile File into which to direct the output data.
      */
-    public VCFWriterStorage(VCFWriterStub stub, File file) {
-        this.file = file;
-        this.writer = VCFWriterToFile(stub, file);
+    public VCFWriterStorage(VCFWriterStub stub, File tempFile) {
+        this.file = tempFile;
+        this.writer = vcfWriterToFile(stub, file, false);
         writer.writeHeader(stub.getVCFHeader());
     }
 
@@ -95,30 +97,10 @@ public class VCFWriterStorage implements Storage<VCFWriterStorage>, VCFWriter {
         writer.close();
     }
 
-    /**
-     * Merges the stream backing up this temporary storage into the target.
-     * @param target Target stream for the temporary storage.  May not be null.
-     */
-//    public void mergeInto(VCFWriterStorage target) {
-//        PrintStream formattingTarget = new PrintStream(target.stream);
-//        try {
-//            BufferedReader reader = new BufferedReader(new FileReader(file));
-//            String line = reader.readLine();
-//            while ( line != null ) {
-//                if (!VCFHeaderLine.isHeaderLine(line))
-//                    formattingTarget.printf("%s%n",line);
-//                line = reader.readLine();
-//            }
-//
-//            reader.close();
-//        } catch (IOException e) {
-//            throw new UserException.CouldNotReadInputFile(file, "Error reading file in VCFWriterStorage: ", e);
-//        }
-//    }
     public void mergeInto(VCFWriterStorage target) {
         try {
             //System.out.printf("merging %s%n", file);
-            BasicFeatureSource<VariantContext> source = BasicFeatureSource.getFeatureSource(file.getAbsolutePath(), new VCFCodec());
+            BasicFeatureSource<VariantContext> source = BasicFeatureSource.getFeatureSource(file.getAbsolutePath(), new VCFCodec(), false);
             
             for ( VariantContext vc : source.iterator() ) {
                 target.writer.add(vc, vc.getReferenceBaseForIndel());