issue with providing filter options

[hudenise2]

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[lindenb]

What is it about ?

[hudenise2]

would you be able to elaborate on the syntax to precise options for biostar154220? I read the page you provide the link to (https://github.com/lindenb/jvarkit/blob/master/src/main/resources/javacc/com/github/lindenb/jvarkit/util/bio/samfilter/SamFilterParser.jj) but cannot manage to have my --filter options accepted

[lindenb]

but cannot manage to have my --filter options accepted

what did you try, what to you want ? the default should be ok.

[hudenise2]

I would like to filter when mapqlt is below a value. I tried --filter mapqlt 2 and --filter mapqlt 2. I'm trying --filter {maqplt 2} but not sure if correct.

[lindenb]

try --filter maplt(2)

[hudenise2]

Ok, will try, thank you

[hudenise2]

Dear Pierre, Here is the results of my test with your suggestion:

/tmp/1591170856.179631: line 8: syntax error near unexpected token (' /tmp/1591170856.179631: line 8:java -jar ../bin/jvarkit/biostar154220.jar -n 10 --filter mapqlt(0) -o fCotGobRNAAligned.out_Sorted2_thinned10f.bam --samoutputformat BAM fCotGobRNAAligned.out.bam'

Cheers Hubert

On 2 Jun 2020, at 17:48, Pierre Lindenbaum notifications@github.com wrote:

try --filter maplt(2)

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Hubert DENISE, PhD

Genome Data Analyst R.Durbin's group Department of Genetics University of Cambridge

[lindenb]

did you quote the argument 'mapq(2)' ?

[hudenise2]

No. Sorry did not understand that quotes were needed. It is running now, thanks Hubert

On 3 Jun 2020, at 09:31, Pierre Lindenbaum notifications@github.com wrote:

did you quote the argument 'mapq(2)' ?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/lindenb/jvarkit/issues/157#issuecomment-638046371, or unsubscribe https://github.com/notifications/unsubscribe-auth/AL6QK6UI2XGCHZGEY2VB7XLRUYC4PANCNFSM4NQ4N2XQ.

Hubert DENISE, PhD

Genome Data Analyst R.Durbin's group Department of Genetics University of Cambridge