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arq5x / bedtools

A powerful toolset for genome arithmetic.
http://code.google.com/p/bedtools/
GNU General Public License v2.0
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Update merge.rst #84

Open kzarns opened 11 years ago

kzarns commented 11 years ago

For sort, should chr9 be before chr10?

I Added a V to the end of the first sort criteria. V is for version. In this case V will sort the numeric section of the first field as a number so that chr9 comes before chr10. If the first field is just for grouping and the order of chr9 vs chr10 does not matter, then this can be left out.

arq5x commented 11 years ago

Well, version sort is not available for the default versions of many OS. I would rather assume -V is not present, but we could always make a note about the -V option in newer versions of coreutils.

brentp commented 11 years ago

Doesn't bedtools sort assume that it's NOT sorted in "natural" order and assumes that chr9 comes after chr10?