search

asntech / intervene

Intervene: a tool for intersection and visualization of multiple genomic region and gene sets
http://intervene.rtfd.io/
Other
132 stars 28 forks source link

bedtools intersect options #3

Closed adomingues closed 6 years ago

adomingues commented 6 years ago

Feature suggestion as discussed via email with credits to @asntech .

It seems from looking at the source code that the genomic regions overlap is calculated using pybedtools intersect default settings which counts as intersection any regions that overlap by at least 1 bp. Could please consider

  1. adding a note to the Docs, and/or
  2. consider adding an option to, for instance, consider an overlap only regions matching 100 %? The perfect solution would be to an option, where user will be able to list any of the arguments available for bedtool’s intersect command. Something like this: --bedtool-options f=0.8,r=true,etc

The default is perfectly sensible, but it might lead to unexpected results for those not aware of it.

asntech commented 6 years ago

Thanks @adomingues for the recomendation. Please try the latest release on GitHub now.

asntech commented 6 years ago

This option is now available in version v0.6.1 through pip