Handle broken pipes #30
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Make the main function handle broken pipes and cleanup; fixes for pipe handling for igblast context manager and subprocess
This reaches back out from the unit testing to run a bash script to check this behavior. Not sure if this would scale reasonably if there are many more of these, but at least it's tested somewhere (and this test currently fails on dev but should pass here)
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
If igseq's stdout is closed (such as from another process working with its output) this will try to gracefully handle the closed pipe, including for an igblastn subprocess. Fixes #20. I think.