Additional sanity checking: make sure the user can't alter the header / compression level / presorted state of a file to which SAMRecords have already been written.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2562 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -34,6 +34,7 @@ import java.io.File;
 import org.broadinstitute.sting.gatk.io.OutputTracker;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.StingException;
 
 /**
  * A stub for routing and management of SAM file reading and writing.
@@ -74,6 +75,13 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
      */
     private OutputTracker outputTracker = null;
 
+    /**
+     * Has the write started?  If so, throw an exception if someone tries to
+     * change write parameters to the file (compression level, presorted flag,
+     * header, etc).
+     */
+    private boolean writeStarted = false;
+
     /**
      * Create a new stub given the requested SAM file and compression level.
      * @param engine source of header data, maybe other data about input files.
@@ -113,6 +121,8 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
      * @param compressionLevel The suggested compression level.
      */
     public void setCompressionLevel( Integer compressionLevel ) {
+        if(writeStarted)
+            throw new StingException("User attempted to change the compression level of a file with alignments already in it.");        
         this.compressionLevel = compressionLevel;
     }
 
@@ -129,6 +139,8 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
      * @param presorted True if the BAM file is presorted.  False otherwise.
      */
     public void setPresorted(boolean presorted) {
+        if(writeStarted)
+            throw new StingException("User attempted to change the presorted state of a file with alignments already in it.");
         this.presorted = presorted;
     }
 
@@ -145,6 +157,8 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
      * @param header The header to write.
      */
     public void writeHeader(SAMFileHeader header) {
+        if(writeStarted)
+            throw new StingException("User attempted to change the header of a file with alignments already in it.");
         this.headerOverride = header;
     }
 
@@ -152,6 +166,7 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
      * @{inheritDoc}
      */
     public void addAlignment( SAMRecord alignment ) {
+        writeStarted = true;
         outputTracker.getStorage(this).addAlignment(alignment);
     }