Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Fixed
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Labels:None
Description
Allow BED detail as another option for saving selected annotations.
If gene name and description values are missing, insert "NA" in missing fields.
To test: open TAIR10, save track as bed, then as bed detail - ensure that the bed detail file has 'gene name' as an option in Annotations>label. Select a subset of genes, repeat above as "Save selected annotations"
Open Bos Taurus, repeat all of the above. The bed detail files should have "N/A" displayed when label is set to gene name.
Attachments
Issue Links
- relates to
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BUG-622 File format issues
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- Closed
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Activity
Currently if a file is a bed detail and you chose to save as a bed, it saves as bed detail - is this the correct behavior? Or is it supposed to actually save as a bed when you ask it to, and a bed detail when you ask it to? Or will it always default to bed detail?
Fixed in r13276.
It would always output the selected format.
bed detail is not saving properly for a bed detail file... (no data in it)
open TAIR10 and the LL juncs. Select 1or 2 annot, and chose save selected. For LL Jun file, save as bed or save as bed detail works. But for TAIR10, bed works fine, but bed detail does not.
If user selects "bed detail" and the annotations have no "gene name" or "description" fields, values "NA" (not available) should be inserted in fields 13 and 14.
A typo creeped in. Fixed in r13287.
If source sym is of type bed detail then it would output bed detail other wise it would output bed.
Do you want it to force output bed detail all time?
Note: Bed detail might be used in other places like Galaxy.