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--wmean not working #191

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brightgreendot opened this issue Aug 18, 2017 · 3 comments

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brightgreendot commented Aug 18, 2017

Hi guys,

I keep stumbling upon this error when trying to compute the weighted mean.

[xxx@node-head1 xxx]$ cat k9_bedmap.o441063

BEDMAP...
May use bedmap --help for more help.

Error: Unknown Operation: wmean. Program Error Detected.
May use bedmap --help for more help.

[xxx@node-head1 xxx]$ bedmap --version
bedmap
citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
version: 2.4.27 (typical)
authors: Shane Neph & Scott Kuehn

Any ideas? This is the command:

bedmap --bp-ovr 1 --echo --mean --wmean --delim '\t' $temp_d/Gene_coordinates.sorted.bed $temp_d/data.sorted.bed > $temp_d/Gene_coordinates_with_mean_score.bed

Thanks a lot!

sjneph self-assigned this

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sjneph commented Aug 18, 2017

That looks like a legit bug! I'm sorry for the troubles and thanks for reporting. We will release a source path soon.

sjneph added the bug label

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sjneph commented Aug 18, 2017

This has been fixed in commit 6eb937a
You can download and build v2p4p28 so that the --wmean option is available in bedmap. We expect to release binaries for this version of BEDOPS fairly soon. Again, thank you for pointing out this bug!

sjneph closed this as completed

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brightgreendot commented Aug 18, 2017

Nice! Thanks a lot!

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