Fail to infer insert size distribution when no pairs are within boundaries (re issue 108) #141
Conversation
This file contains hidden or 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
Just as we set r.failed and return early if there are no high-quality read pairs at all, also do so if there are none within the calculated boundaries. This avoids returning avg=NAN std=NAN, which leads to malloc(INFINITY) and a crash; fixes lh3#108.
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Outdated suggestions cannot be applied.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.
@tillea's issue #108 appears to be caused by there being no sufficiently good pairs when calculating avg and std, leading to avg=NAN std=NAN and a later malloc failure when asked to malloc an insane amount of memory.
This suggested patch returns from
bsw2_stat()withr.failed = 1in this case, as in other cases of insufficient read pairs. I am not familiar enough with the implications of “failure to infer insert size distribution” to judge whether this is the best approach.