Disabling pipefail when the output is explicitely troncated #230
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
"grep -m 1" stop after the first found occurence. "samtools view" stop with an error if its output is closed. With pipefail, the samtools error is taken into account by the lumpyexpress script that immediately exits The error do not always occurs: if the information looked after by grep is at the end of the BAM file and samtools is able to complete before its output is closed, then no error occurs But we have several BAM files that triggered this error.
|
The travis-ci error does not seem to be due to my patch... |
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Outdated suggestions cannot be applied.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.
"grep -m 1" stop after the first found occurence.
"samtools view" stop with an error if its output is closed.
With pipefail, the samtools error is taken into account by the lumpyexpress script that immediately exits
The error do not always occurs:
if the information looked after by grep is at the end of the BAM file and samtools is able to complete before its output is closed, then no error occurs
But we have several BAM files that triggered this error.