Adds BARCODES_DIR parameter to IlluminaBasecallsToFastq and
IlluminaBasecallsToSam so that they can use the barcode files from
ExtractIlluminaBarcodes when it has been run with OUTPUT_DIR different
from the BASECALLS_DIR parameter.

The use case is that the BASECALLS_DIR directory is read-only and the
barcode files can't be written to that directory and the other tools are
useless if they can't read the barcode files from a different directory.
Merge pull request #15 from nnordborg/barcodes-dir

Add BARCODES_DIR parameter to IlluminaBasecallsToFastq and IlluminaBasecallsToSam