Open mikejiang opened 6 years ago
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
.h5
within existing fcs dir--no-data
to only parse meta infofcstool check-channel
--expected
to provide the expected channelsfcstool check-marker
fcstool check-time-channel
fcstool check-count
fcstool check-keyword
--expected
to provide the expected keywordsFor the single file
fcstool ls filename.h5
to quick browse content of fcs (similar to print(flowFrame)
in R)
fcstool ls -c
print channelsfcstool ls -m
print markersfcstool ls -k
print keywordsfcstool ls -d
print data valuesI 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.
@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