Store entire PG record in intermediate files

[dkj]

At the moment I think we're storing just the command line in the intermediate files i.e. filter and calibration table files. If we flip software version between creating these files and applying them then we'll be putting the wrong version for the first stage in the BAM headers we produce. So..., let's just bung the @pg BAM header for the first stage in the intermediate files ready to be pulled out and used when annotating the the BAM header in the second stage (careful with the PP field).