Parsing a Goby reads file

ReadsForeach.java

final String inputFilename = "input.compact-reads";
final MutableString sequence = new MutableString();
final ReadsReader reader =  new ReadsReader(new FileInputStream(inputFilename));

for (final Reads.ReadEntry readEntry : reader) {

     ReadsReader.decodeSequence(readEntry, sequence);
     System.out.printf("read-index: %d read-id: %s sequence: %s %n",
                        readEntry.getReadIndex(),
                        readEntry.hasReadIdentifier() ? readEntry.getReadIdentifier() : "",
                        sequence);
}

Demonstrate how to parse/iterate through a Goby .compact reads file.