}
}
// Open new file, using the fileIndex.
final File bfq1 = getOutputFile(this.outputPrefix , 1, fileIndex);
codec1 = new BinaryCodec(IOUtil.openFileForWriting(bfq1));
log.info("Now writing to file " + bfq1.getAbsolutePath());
if (pairedReads) {
final File bfq2 = getOutputFile(this.outputPrefix , 2, fileIndex);
codec2 = new BinaryCodec(IOUtil.openFileForWriting(bfq2));
log.info("Now writing to file " + bfq2.getAbsolutePath());
}
}