Output single machine readable file with the whole report

[andersgs]

For instance:

MLST_REPORT_START ... MLST_REPORT_END ALN_START ... ALN_END

etc...

Or, in JSON format.

This will make it easier to parse the report into a LIMs system or into R.

[tseemann]

How would you want the JSON arranged?

sample:
   assay1: 
   assay2: 

or

assay:
   sample1: 
   sample2:

etc