From 87aca647167a91430f867fd65554924b4513b73b Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 10 Sep 2010 21:16:03 +0000
Subject: [PATCH] Jumped the gun a bit on bam on-the-fly indexing -- Tim says
 it's not ready yet. Turned it off by default and added a property to turn it
 back on.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4254 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/io/storage/SAMFileWriterStorage.java |  2 +-
 .../SAMFileWriterArgumentTypeDescriptor.java  | 24 ++++++++++++++++++-
 .../gatk/io/stubs/SAMFileWriterStub.java      | 24 +++++++++++++++++++
 3 files changed, 48 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java b/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
index e20ac7675..d5507f626 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
@@ -52,7 +52,7 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
         this.file = file;
         SAMFileWriterFactory factory = new SAMFileWriterFactory();
         // Enable automatic index creation for pre-sorted BAMs.
-        if (stub.getFileHeader().getSortOrder().equals(SAMFileHeader.SortOrder.coordinate))
+        if (stub.getFileHeader().getSortOrder().equals(SAMFileHeader.SortOrder.coordinate) && stub.getIndexOnTheFly())
             factory.setCreateIndex(true);
         // Adjust max records in RAM.
         if(stub.getMaxRecordsInRam() != null)
diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
index 7a68f0cc1..c1a699fe0 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
@@ -48,6 +48,8 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
     private static final String COMPRESSION_FULLNAME = "bam_compression";
     private static final String COMPRESSION_SHORTNAME = "compress";
 
+    private static final String CREATE_INDEX_FULLNAME = "index_output_bam_on_the_fly";
+
     /**
      * The engine into which output stubs should be fed.
      */
@@ -76,7 +78,8 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
     @Override
     public List<ArgumentDefinition> createArgumentDefinitions( ArgumentSource source ) {
         return Arrays.asList( createBAMArgumentDefinition(source),
-                              createBAMCompressionArgumentDefinition(source) );
+                              createBAMCompressionArgumentDefinition(source),
+                              createWriteIndexArgumentDefinition(source));
     }
 
     @Override
@@ -104,6 +107,8 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
         if( compressionLevel != null )
             stub.setCompressionLevel(compressionLevel);
 
+        stub.setIndexOnTheFly(argumentIsPresent(createWriteIndexArgumentDefinition(source),matches));
+
         // WARNING: Side effects required by engine!
         parsingEngine.addTags(stub,getArgumentTags(matches));
         engine.addOutput(stub);
@@ -155,4 +160,21 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
                                        null,
                                        null );
     }
+
+    private ArgumentDefinition createWriteIndexArgumentDefinition(ArgumentSource source) {
+        Annotation annotation = this.getArgumentAnnotation(source);
+        return new ArgumentDefinition( ArgumentIOType.getIOType(annotation),
+                                       boolean.class,
+                                       CREATE_INDEX_FULLNAME,
+                                       null,
+                                       "Create a BAM index on-the-fly while writing the resulting file.",
+                                       false,
+                                       false,
+                                       false,
+                                       source.isHidden(),
+                                       null,
+                                       null,
+                                       null,
+                                       null );
+    }
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
index 12929214a..280888d76 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
@@ -37,6 +37,7 @@ import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 /**
  * A stub for routing and management of SAM file reading and writing.
@@ -71,6 +72,11 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
      */
     private Integer compressionLevel = null;
 
+    /**
+     * Should the GATK index the output BAM on-the-fly?
+     */
+    private boolean indexOnTheFly = false;
+
     /**
      * Should this BAM be presorted?
      */
@@ -155,6 +161,24 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
         this.compressionLevel = compressionLevel;
     }
 
+    /**
+     * Gets whether to index this output stream on-the-fly.
+     * @return True means create an index.  False means skip index creation.
+     */
+    public Boolean getIndexOnTheFly() {
+        return indexOnTheFly;
+    }
+
+    /**
+     * Controls whether to index this output stream on-the-fly.
+     * @param indexOnTheFly True means create an index.  False means skip index creation.
+     */
+    public void setIndexOnTheFly( boolean indexOnTheFly ) {
+        if(writeStarted)
+            throw new UserError("Attempted to index a BAM on the fly of a file with alignments already in it.");
+        this.indexOnTheFly = indexOnTheFly;
+    }
+
     /**
      * Whether the BAM file to create is actually presorted.
      * @return True if the BAM file is presorted.  False otherwise.