Compress outputs in IlluminaBasecallsToFastq

I have added COMPRESS_OUTPUTS command line parameter to IlluminaBasecallsToFastq so that it can generate compressed FASTQ files (with file extension .fastq.gz). This saves temporary disk space and the need for a separate compression step. Hope this is useful for someone else as well and that it can be merged to the master Picard branch.

/Nicklas

That would be fine with me, though I don't know how to best control that via the parameter... I looked at the COMPRESS_OUTPUTS functionality in ExtractIlluminaBarcodes and made something similar, but I can't seem to find any place which uses bz2 or bfq. Would it be possible to define an enum with the 3 compression options and use that for the COMPRESS_OUTPUTS parameter?