FCS QC tool

[mikejiang]

@mimisikai , feel free to voice your opinion here on https://github.com/RGLab/cytoCL/blob/master/README.md since you have lots of first-hand experience (or frustrations) with this issue

[mikejiang]

For command line argument parsing, we could consider Boost.Program_options. And we could have a main command, say fcstool followed by the subcommands for all the different tasks. e.g.

• fcstool init
  • create new folder .h5 within existing fcs dir
  • parse all the fcs files into h5 so that all the subsequent tasks are performed on h5 with faster partial IO
  • with option --no-data to only parse meta info
• fcstool check-channel
  • perform channel QC
  • with option --expected to provide the expected channels
• fcstool check-marker
  • perform marker QC
• fcstool check-time-channel
  • perform time QC
• fcstool check-count
  • perform event count QC
• fcstool check-keyword
  • perform keyword QC
  • with option --expected to provide the expected keywords

[mikejiang]

For the single file

• fcstool ls filename.h5 to quick browse content of fcs (similar to print(flowFrame) in R)
  • fcstool ls -c print channels
  • fcstool ls -m print markers
  • fcstool ls -k print keywords
  • fcstool ls -d print data values

[jacobpwagner]

I ran in to an issue with some FCS files that is relevant to fcstool check -m:

$PnS is optional in FCS 3.0 and 3.1, and $PnN is also optional in FCS 3.0, so checking channel/marker names should take that in to account in terms of checks and output.