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detect when a method doesn't return valid BedTool-supported output

Open daler opened this issue 11 years ago • 4 comments

BedTool.genome_coverage sometimes returns bedGraph-like output, sometimes not. In fact, by default, it doesn't return a valid BED-ish format file.

See #110, #111, #112.

note to future self: this prob needs yet another kwarg to bedtool._wraps, and you will need to go through BEDTools programs and args to work out which don't create valid output files.

daler avatar Aug 28 '14 19:08 daler

Perhaps at least add a note in the docs? Less confusing that way...

laserson avatar May 09 '17 18:05 laserson

Yep, good idea. Did you hit this with genome_coverage specifically or with another method?

daler avatar May 09 '17 18:05 daler

Just genome_coverage for me so far

laserson avatar May 09 '17 19:05 laserson

#213 adds some documentation. I will try implementing something like https://github.com/daler/pybedtools/issues/110#issuecomment-206426464, xref #167

daler avatar May 09 '17 21:05 daler