-s parameter fails to convert scan data

[tomas-pluskal]

Hi,
the -s parameter introduced after the discussion in #99 does not work in the latest version 1.3.4. (I have not tested previous releases so I don't know if it worked in the past and got broken at some point)

A simple test: I use a 15MB .raw file called a.raw.
After running ThermoRawFileParser.exe -i a.raw I get a complete mzML file a.mzML with comparable size (~10 MB).
When I run ThermoRawFileParser.exe -s -i a.raw > a.mzML the output file is tiny (~3 KB) and contains only the mzML header but no scan data.

[nielshulstaert]

Hi Tomas thanks for reporting this, I'll have a look and get back to you.

[caetera]

Hi Tomas, thank you for reporting. The cause of the error is likely because since 1.3.3 the default output format is indexed mzML, it is not possible to index piped output and thus TRFP crashes (I am actually surprised it does not spit any error or exception it does not throw any error since the logging is silenced in piped output).
In future, -s should imply regular mzML, as quick work around, please, try using -f=1 (regular mzML)

[nielshulstaert]

Yes indeed I was looking for a fix but I didn't find one yet. @caetera indeed we need to at least mention it in de help output. As mentioned, it does work for all the other output formats, including the metadata.

[tomas-pluskal]

I can confirm it works fine with the -f=1 parameter.

[caetera]

Closed in 410ff00.
STDOUT (-s) always forces plain mzML instead of indexed mzML