Recording source file names in output files, allowing output of intermediate results

src/main/java/CellFileReader.java

@@ -11,17 +11,19 @@ import java.util.List;
 
 public class CellFileReader {
 
+    private String filename;
     private List<Integer[]> distinctCells = new ArrayList<>();
 
     public CellFileReader(String filename) {
-
         if(!filename.matches(".*\\.csv")){
             filename = filename + ".csv";
         }
+        this.filename = filename;
 
         CSVFormat cellFileFormat = CSVFormat.Builder.create()
                 .setHeader("Alpha CDR3", "Beta CDR3", "Alpha CDR1", "Beta CDR1")
                 .setSkipHeaderRecord(true)
+                .setCommentMarker('#')
                 .build();
 
         try(//don't need to close reader bc of try-with-resources auto-closing
@@ -42,6 +44,8 @@ public class CellFileReader {
         }
     }
 
+    public String getFilename() { return filename;}
+
     public List<Integer[]> getCells(){
         return distinctCells;
     }