Gff3Writer provide a hook for providing a custom way to escape strings (

#1528)

The current implementation is valid according to the spec, but some downstream tools don't recognize UTF8 correctly.  This adds an overridable method that allows custom subclasses to do their own string escaping to deal with incompatible tools.

src/main/java/htsjdk/tribble/gff/Gff3Writer.java

@@ -68,9 +68,9 @@ private void tryToWrite(final String string) {
 
     private void writeFirstEightFields(final Gff3Feature feature) throws IOException {
         writeJoinedByDelimiter(Gff3Constants.FIELD_DELIMITER, this::tryToWrite, Arrays.asList(
-                encodeString(feature.getContig()),
-                encodeString(feature.getSource()),
-                encodeString(feature.getType()),
+                escapeString(feature.getContig()),
+                escapeString(feature.getSource()),
+                escapeString(feature.getType()),
                 Integer.toString(feature.getStart()),
                 Integer.toString(feature.getEnd()),
                 feature.getScore() < 0 ? Gff3Constants.UNDEFINED_FIELD_VALUE : Double.toString(feature.getScore()),
@@ -92,7 +92,7 @@ void writeKeyValuePair(final String key, final List<String> values) {
         try {
             tryToWrite(key);
             out.write(Gff3Constants.KEY_VALUE_SEPARATOR);
-            writeJoinedByDelimiter(Gff3Constants.VALUE_DELIMITER, v -> tryToWrite(encodeString(v)), values);
+            writeJoinedByDelimiter(Gff3Constants.VALUE_DELIMITER, v -> tryToWrite(escapeString(v)), values);
         } catch (final IOException ex) {
             throw new TribbleException("error writing out key value pair " + key + " " + values);
         }
@@ -123,6 +123,16 @@ public void addFeature(final Gff3Feature feature) throws IOException {
         out.write(Gff3Constants.END_OF_LINE_CHARACTER);
     }
 
+    /***
+     * escape a String.
+     * Default behavior is to call {@link #encodeString(String)}
+     * @param s the string to be escaped
+     * @return the escaped string
+     */
+    protected String escapeString(final String s) {
+        return encodeString(s);
+    }
+
     static String encodeString(final String s) {
         try {
             //URLEncoder.encode is hardcoded to change all spaces to +, but we want spaces left unchanged so have to do this