Nice error when passing non-GAM file to vg filter #4779
Merged
+15
−3
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Changelog Entry
To be copied to the draft changelog by merger:
vg filtergives a clean error when passing files that don't look like GAMsDescription
A long-term minor annoyance of mine: if you accidentally pass a valid non-GAM file (e.g. a TSV) to
vg filterit would try to read it as a GAM and then very verbosely and confusingly crash. This change checks whether the filename ends with.gam. If not, a short and readable error is printed. Standard input works as before since that can't be easily checked.