Fix fastp hanging forever on invalid input files #469
Merged
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Outdated suggestions cannot be applied.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.
root cause: the processor does no longer process reads because one of the input files is at EOF while the other still contains reads. When the difference in reads is sufficiently large, the mechanism that pauses a reader when the processor is too far behind kicks in and blocks the reader forever since the processor will no longer process reads.
This will only happen on invalid input. This patch causes fastp to exit with an error when the input is invalid.
This fixes issues like #455, possibly #448, #425, #410, #400, #378, #340 (partial), #333, ...