Avoid NPE when importing BAM as reads

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceNormalizationTask.java

@@ -341,7 +341,10 @@ public RecordedActionSet run() throws PipelineJobException
                             fp.file1 = p.first;
                             fp.file2 = p.second;
                             getHelper().getFileManager().addIntermediateFile(fp.file1);
-                            getHelper().getFileManager().addIntermediateFile(fp.file2);
+                            if (fp.file2 != null)
+                            {
+                                getHelper().getFileManager().addIntermediateFile(fp.file2);
+                            }
                         }
 
                         //NOTE: continue to normalize sequence, in case the BAM-derived data has non-standard encoding