Hello, we are using Stranger in pipeline after https://github.com/Illumina/ExpansionHunter, and currently we have a problem.
If we want to use variant_catalog.json where there are no repeats with NormalMax/PathologicMin we are getting several warnings like:
WARNING Repeat number 1 (CSF1PO) is missing 'NormalMax'. Skipping..
and finally:
WARNING Could not find any repeat info
and program finishes with exit code 1 (due to this: https://github.com/Clinical-Genomics/stranger/blob/main/stranger/cli.py#L69-L71).
Is it possible to just warn about no repeat info and pass all input data to output (how it is done for skipped repeats)?
We can, of course, turn Stranger off for some variant_catalogs, but it will be easier for pipeline maintaining to simply not fail if there are nothing to do.
Or should we add some placeholders, like:
"NormalMax": "-",
"Disease": "-",
"PathologicMin": "-"What do you think, @dnil ?
Related to #76 (same problem origin)
Hello, we are using Stranger in pipeline after https://github.com/Illumina/ExpansionHunter, and currently we have a problem.
If we want to use
variant_catalog.jsonwhere there are no repeats withNormalMax/PathologicMinwe are getting several warnings like:and finally:
and program finishes with exit code 1 (due to this: https://github.com/Clinical-Genomics/stranger/blob/main/stranger/cli.py#L69-L71).
Is it possible to just warn about no repeat info and pass all input data to output (how it is done for skipped repeats)?
We can, of course, turn Stranger off for some variant_catalogs, but it will be easier for pipeline maintaining to simply not fail if there are nothing to do.
Or should we add some placeholders, like:
What do you think, @dnil ?
Related to #76 (same problem origin)