[Bioc-devel] Fwd: flowCore: read.FCS() broken since recent update!

[Kieran O'Neill]

Hi Mike

Would it not make more sense for flowCore to assume the byte offset is
zero if it is left blank? Josef Spidlen (first author of the FCS 3.0
standard) has said to me that he thinks there are many FCS files out
there which have this issue, so this "fix" broken flowCore's
functionality for many people.

Cheers,
Kieran

On 14 June 2012 11:01, Mike <wjiang2 at fhcrc.org> wrote:
> Kieran,
>
> I looked at your FCS, it has empty keyword value which does not conform to
> FCS 3.0 standard:
> "3.2.9 Keywords and keyword values must have lengths greater than zero.
> "(http://murphylab.cbi.cmu.edu/FCSAPI/FCS3.html).
>
> Particularly, this occurs at $ENDSTEXT keyword-value pairs
> :"\\$ENDSTEXT\\\\$ETIM..."
> Which is "byte offset to end of the supplemental TEXT segment" and really
> shouldn't be empty (normally it is put as "0")
>
> And "\\" is used as delimiter here, FCS 3.0 allows delimiter appears in the
> keyword value or keyword name as long as it is " immediately followed by a
> second delimiter". So the characters "\\\\" after "$ENDSTEXT" keyword is
> misunderstood as part of "$ETIM" by the parser here, which further messed up
> the parsing of subsequent string. That is why the parser is reporting error.
>
> Originally,flowCore did not handle this delimiter issue properly. It might
> read FCS successfully with the incorrect keyword values without notifying
> the user. Now,we thought it may be helpful to throw the error and let user
> know the issue with the TEXT segment of FCS.
>
> I have attached the TEXT Segment of your FCS file.
>
> Let me know if you have questions.
>
> Thanks,
> Mike
>
>
> On 06/13/2012 12:41 PM, Kieran O'Neill wrote:
>
> Hi there
>
> I'm writing because I have found that the current version of flowCore
> (1.22.0) no longer reads some of my FCS files. I was using it without
> difficulty up until a few months ago, but when I tried to read it with the
> current version, it failed with the following error:
>
> Error in fcs_text_parse(txt) : ERROR! no end found
>
> I have attached a single FCS file as an example.
>
> read.FCS() still works on most other FCS files I have. It is only the files
> from this particular cytometer that appear to no longer work.
>
> Best,
> Kieran
>