Bedtools genomeCoverageBed cannot find 'zero_regions'

[hexylena]

For version 2.22.0 of genomeCoverageBed, I see the Cheetah error NotFound: cannot find 'zero_regions'. This is because it lacks the $report prefix on the conditional variables.

Additionally the validator for unspecified_build seems odd, I had to hack that out to get it to function.

[hexylena]

Will make a PR once it's tested.

[bgruening]

Seems so, also for scale

[hexylena]

yep, adding test cases for it now.

[blankenberg]

See also #54

[hexylena]

@blankenberg thanks for that--that should've been merged a while ago. Now that I'm using the tools I suppose I'm qualified to review that PR! Merged, I'll push test cases once I figure out how genomecov will get the results I expect out of it.

[mtayeb]

Has this issue been resolved? I'm still getting this error using a small bacterial genome BAM with a custom build from a FASTA file in Galaxy. Not sure what release of the toolset is the newest in Galaxy.

[hexylena]

It'll be in the test tool shed, I don't think anyone pushdd to the MTS yet.
12. mar. 2015 10.42 skrev "cheezemeister" notifications@github.com:

Has this issue been resolved? I'm still getting this error using a small
bacterial genome BAM with a custom build from a FASTA file in Galaxy.

—
Reply to this email directly or view it on GitHub
#57 (comment)
.