From dc62685a2f3aa5e40f42e4f8a9a67a6007c811f8 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 2 Mar 2011 01:50:42 +0000
Subject: [PATCH] For Ryan: force creation of BAM index when no reads are
 present in the BAM file.  Temporary fix until Picard changes the behavior of
 indexing.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5351 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/io/storage/SAMFileWriterStorage.java | 45 ++++++++++++++++---
 1 file changed, 40 insertions(+), 5 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 6460a1ab8..d2d9d94aa 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
@@ -29,8 +29,11 @@ import net.sf.samtools.*;
 import net.sf.samtools.util.CloseableIterator;
 
 import java.io.*;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
 
 import net.sf.samtools.util.RuntimeIOException;
+import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.ConstrainedMateFixingSAMFileWriter;
@@ -45,6 +48,8 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
     private final File file;
     private SAMFileWriter writer;
 
+    private static Logger logger = Logger.getLogger(SAMFileWriterStorage.class);
+
     public SAMFileWriterStorage( SAMFileWriterStub stub ) {
         this(stub,stub.getSAMFile());   
     }
@@ -66,10 +71,7 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
                 factory.setCreateIndex(false);
 
             try {
-                if( stub.getCompressionLevel() != null )
-                    this.writer = factory.makeBAMWriter( stub.getFileHeader(), stub.isPresorted(), file, stub.getCompressionLevel() );
-                else
-                    this.writer = factory.makeBAMWriter( stub.getFileHeader(), stub.isPresorted(), file );
+                this.writer = createBAMWriter(factory,stub.getFileHeader(),stub.isPresorted(),file,stub.getCompressionLevel());
             }
             catch(RuntimeIOException ex) {
                 throw new UserException.CouldNotCreateOutputFile(file,"file could not be created",ex);
@@ -116,4 +118,37 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
         }
     }
 
-}
\ No newline at end of file
+    private SAMFileWriter createBAMWriter(final SAMFileWriterFactory factory,
+                                 final SAMFileHeader header,
+                                 final boolean presorted,
+                                 final File outputFile,
+                                 final Integer compressionLevel) {
+        SAMFileWriter writer;
+        if(compressionLevel != null)
+            writer = factory.makeBAMWriter(header, presorted, outputFile, compressionLevel);
+        else
+            writer = factory.makeBAMWriter(header, presorted, outputFile);
+
+        // mhanna - 1 Mar 2011 - temporary hack until Picard generates an index file for empty BAMs --
+        //                     - do a pre-initialization of the BAM file.
+        try {
+            Method prepareToWriteAlignmentsMethod = writer.getClass().getDeclaredMethod("prepareToWriteAlignments");
+            if(prepareToWriteAlignmentsMethod != null) {
+                prepareToWriteAlignmentsMethod.setAccessible(true);
+                prepareToWriteAlignmentsMethod.invoke(writer);
+            }
+        }
+        catch(NoSuchMethodException ex) {
+            logger.info("Unable to call prepareToWriteAlignments method; this should be reviewed when Picard is updated.");
+        }
+        catch(IllegalAccessException ex) {
+            logger.info("Unable to access prepareToWriteAlignments method; this should be reviewed when Picard is updated.");
+        }
+        catch(InvocationTargetException ex) {
+            logger.info("Unable to invoke prepareToWriteAlignments method; this should be reviewed when Picard is updated.");
+        }
+
+        return writer;
+    }
+
+}