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.
Add html upload to the build not just shtml.
Merge remote-tracking branch 'origin/master'
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