Add more logging

Author: bbimber

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

@@ -161,6 +161,7 @@ else if (SequenceUtil.FILETYPE.cram.getFileType().isType(so.getFile()))
                             SequenceAnalysisService.get().getExpectedBamOrCramIndex(so.getFile()).delete();
                             so.getFile().delete();
 
+                            ctx.getLogger().debug("Replacing original file:  " + so.getFile().getPath());
                             FileUtils.moveFile(outputFile, so.getFile());
                             FileUtils.moveFile(new File(outputFile.getPath() + ".crai"), new File(so.getFile() + ".crai"));
                         }
@@ -169,6 +170,10 @@ else if (SequenceUtil.FILETYPE.cram.getFileType().isType(so.getFile()))
                             throw new PipelineJobException(e);
                         }
                     }
+                    else
+                    {
+                        throw new PipelineJobException("Unknown file type: " + so.getFile().getPath());
+                    }
                 }
                 else
                 {