setMaxRecordsInRam now a member of StingSAMFileWriter.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4138 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java

@@ -22,4 +22,10 @@ public interface StingSAMFileWriter extends SAMFileWriter {
      * @param presorted True if the BAM file is presorted.  False otherwise.
      */    
     public void setPresorted(boolean presorted);
+
+    /**
+     * Set how many records in RAM the BAM file stores when sorting on-the-fly.
+     * @param maxRecordsInRam Max number of records in RAM.
+     */
+    public void setMaxRecordsInRam(int maxRecordsInRam);
 }

java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java

@@ -49,14 +49,18 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
 
     public SAMFileWriterStorage( SAMFileWriterStub stub, File file ) {
         this.file = file;
+        SAMFileWriterFactory factory = new SAMFileWriterFactory();
+        if(stub.getMaxRecordsInRam() != null)
+            factory.setMaxRecordsInRam(stub.getMaxRecordsInRam());
+
         if(stub.getSAMFile() != null) {
             if( stub.getCompressionLevel() != null )
-                this.writer = new SAMFileWriterFactory().makeBAMWriter( stub.getFileHeader(), stub.isPresorted(), file, stub.getCompressionLevel() );
+                this.writer = factory.makeBAMWriter( stub.getFileHeader(), stub.isPresorted(), file, stub.getCompressionLevel() );
             else
-                this.writer = new SAMFileWriterFactory().makeBAMWriter( stub.getFileHeader(), stub.isPresorted(), file );
+                this.writer = factory.makeBAMWriter( stub.getFileHeader(), stub.isPresorted(), file );
         }
         else if(stub.getSAMOutputStream() != null){
-            this.writer = new SAMFileWriterFactory().makeSAMWriter( stub.getFileHeader(), stub.isPresorted(), stub.getSAMOutputStream());
+            this.writer = factory.makeSAMWriter( stub.getFileHeader(), stub.isPresorted(), stub.getSAMOutputStream());
         }
         else
             throw new StingException("Unable to write to SAM file; neither a target file nor a stream has been specified");

java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java

@@ -75,6 +75,12 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
      */
     private boolean presorted = true;
 
+    /**
+     * How many records should the BAM writer store in RAM while
+     * sorting the BAM on-the-fly?
+     */
+    private Integer maxRecordsInRam = null;
+
     /**
      * Connects this stub with an external stream capable of serving the
      * requests of the consumer of this stub.
@@ -166,6 +172,24 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
         this.presorted = presorted;
     }
 
+    /**
+     * Get the maximum number of reads to hold in RAM when sorting a BAM on-the-fly.
+     * @return Max records in RAM, or null if unset.
+     */
+    public Integer getMaxRecordsInRam() {
+        return this.maxRecordsInRam;
+    }
+
+    /**
+     * Sets the maximum number of reads to hold in RAM when sorting a BAM on-the-fly.
+     * @param maxRecordsInRam Max number of records in RAM.
+     */
+    public void setMaxRecordsInRam(int maxRecordsInRam) {
+        if(writeStarted)
+            throw new StingException("User attempted to change the max records in RAM of a file with alignments already in it.");
+        this.maxRecordsInRam = maxRecordsInRam;
+    }
+
     /**
      * Registers the given streamConnector with this stub.
      * @param outputTracker The connector used to provide an appropriate stream.