Allow RODs to specify that incomplete records are okay (i.e. that they allow optional fields)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1433 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java

@@ -63,6 +63,10 @@ public class SimpleIndelROD extends TabularROD implements Genotype, AllelicVaria
         return getFWDAlleles().get(0).length();
     }
 
+    public boolean allowIncompleteRecords() {
+        return true;
+    }
+
     public String toString() {
         StringBuffer sb = new StringBuffer();
         sb.append(getLocation().getContig() + "\t" + getLocation().getStart() + "\t");

java/src/org/broadinstitute/sting/gatk/refdata/TabularROD.java

@@ -163,6 +163,16 @@ public class TabularROD extends BasicReferenceOrderedDatum implements Map<String
         return readHeader(source);
     }
 
+    /**
+     * By default, all records (i.e. RODs) must contain the same number of fields as specified
+     * by the header.  Subclasses should override this method to disable this requirement.
+     *
+     * @return true if incomplete records are allowed; false otherwise
+     */
+    public boolean allowIncompleteRecords() {
+        return false;
+    }
+
     public static ArrayList<String> readHeader(final File source) throws FileNotFoundException {
         ArrayList<String> header = null;
         int linesLookedAt = 0;
@@ -308,7 +318,7 @@ public class TabularROD extends BasicReferenceOrderedDatum implements Map<String
         if ( parts.length == 0 || COMMENT_PATTERN.matcher(parts[0]).matches() || HEADER_PATTERN.matcher(parts[0]).matches() )
             return false;
 
-        if (header.size() != parts.length) {
+        if ( !allowIncompleteRecords() && header.size() != parts.length) {
             throw new IOException(String.format("Header length %d not equal to Tabular parts length %d", header.size(), parts.length));
         }