Can't open FCS files that were created using HistoCAT

[dtelad11]

Describe the bug
When trying to use flowCore::read.FCS with an FCS file that was created using HistoCAT, I get the following error:

Error in readFCSgetPar(x, paste("$P", 1:nrpar, "B", sep = "")) : 
  Parameter(s) $P1B not contained in 'x'
Parameter(s) $P2B not contained in 'x'
Parameter(s) $P3B not contained in 'x'
Parameter(s) $P4B not contained in 'x'
Parameter(s) $P5B not contained in 'x'
Parameter(s) $P6B not contained in 'x'
Parameter(s) $P7B not contained in 'x'
Parameter(s) $P8B not contained in 'x'
Parameter(s) $P9B not contained in 'x'
Parameter(s) $P10B not contained in 'x'
Parameter(s) $P11B not contained in 'x'
Parameter(s) $P12B not contained in 'x'
Parameter(s) $P13B not contained in 'x'
Parameter(s) $P14B not contained in 'x'
Parameter(s) $P15B not contained in 'x'
Parameter(s) $P16B not contained in 'x'
Parameter(s) $P17B not contained in 'x'
Parameter(s) $P18B not contained in 'x'
Parameter(s) $P19B not contained in 'x'
Parameter(s) $P20B not contained in 'x'
Parameter(s) $P21B not contained in 'x'
Parameter(s) $P22B not contained in 'x'
Parameter(s) $P23B not contained in 'x'
Parameter(s) $P24B not contained in 'x'
Parameter(s) $P25B not contained in 'x'

To Reproduce
Just run

fcs <- flowCore::read.FCS("filename.fcs")

Where filename.fcs was exported from HistoCAT.

Expected behavior

I expected the file to import normally.

Additional context

I have an example file I could share. Please contact me at el.ad.david.amir@gmail.com and I'll send it to you. Once we figure it out I'm happy to contact HistoCAT and explain the issue to them, hopefully they can fix it on their end.

[gfinak]

The error is due to the FCS file being malformed.
There is no keyword for parameter $P1B, instead these are named "1B" and so forth.

[dtelad11]

Thank you. I will reach out to HistoCAT.

[DenisSch]

I will follow up on this in the next few days! Thank you!

[DenisSch]

I can not reproduce the error in histoCAT so far. Please share the histoCAT's "sessionData"

The parameters should be included:
https://github.com/BodenmillerGroup/histoCAT/blob/bb14e391ce98ae61aaf22df0f055a4df9990b78a/histoCAT/3rdParty/fca_fcs/fca_writefcs.m#L24

[gfinak]

I'll keep this open until someone, maybe @dtelad11 , can reproduce this. We were just handed a malformed FCS file. flowCore et al. never touched the file.

[dtelad11]

Since this is a HistoCAT issue (rather than a flowCore issue) I think you can safely close this, no?