Adds COMPRESS_OUTPUTS parameter to IlluminaBasecallsToFastq so that it
can generate compressed FASTQ files (with file extension .fastq.gz).
Default is false.
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.
Avoid logging a NullPointerException if IlluminaBasecallsToFastq is
started with FORCE_GC=false.

GC timer write to the 'log' instead of directly to System.out. There is
really no reason to handle this information differently than other
logging.
Merge pull request #15 from nnordborg/barcodes-dir

Add BARCODES_DIR parameter to IlluminaBasecallsToFastq and IlluminaBasecallsToSam
Merge pull request #14 from nnordborg/gc-timer-npe

FORCE_GC=false causes NPE in log
Clarify what a "non-PF read" is.
Merge pull request #17 from marcelm/master

Clarify what a "non-PF read" is.
Merge pull request #13 from nnordborg/compress-outputs

Compress outputs in IlluminaBasecallsToFastq
Control size of sorting collection with MAX_RECORDS_IN_RAM
Merge pull request #20 from broadinstitute/aw_elc_rec_in_ram

Control size of sorting collection with MAX_RECORDS_IN_RAM
Add a single CLP entry point for all picard command line programs.
Add Reflections Library and update PicardCommandLine
Remove Reflections in lieu of using an annotations processor at compile and ServiceLoader at runtime.
Added annotation processor jar.
Converting Picard CLPs to go through PicardCommandLine.  Updating unit tests to use this too.
Finished converting Picard CLPs to go through PicardCommandLine.  Updated all unit tests to use the PicardCommandLine.instanceMain() methodology in order to better test command line usage.