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detect when a method doesn't return valid BedTool-supported output #113

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daler opened this issue Aug 28, 2014 · 4 comments
Open

detect when a method doesn't return valid BedTool-supported output #113

daler opened this issue Aug 28, 2014 · 4 comments

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@daler
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daler commented Aug 28, 2014

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.

@laserson
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laserson commented May 9, 2017

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

@daler
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daler commented May 9, 2017

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

@laserson
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laserson commented May 9, 2017

Just genome_coverage for me so far

daler added a commit that referenced this issue May 9, 2017
@daler
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daler commented May 9, 2017

#213 adds some documentation. I will try implementing something like #110 (comment), xref #167

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