Merged
Conversation
For single bp reads, there is an ambiguity in the SAM format ``` read001 0 ref 1 255 1M * 0 0 A * ``` The read above could have a QV value of `*`, or no QV values at all. Since htslib [sets a sentinel value of 255](https://github.com/samtools/htslib/blob/b14fffb4b5689696723634a20b85219be92f9d06/sam.c#L3029-L3030) in this case, it can lead to overflow in downstream operations.
evolvedmicrobe
force-pushed
the
nd/no_ambiguity
branch
from
f72c7e0 to
e509e24
Compare
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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
For single bp reads, there is an ambiguity in the SAM format
The read above could have a QV value of
*, or no QV values at all. Since htslib sets a sentinel value of 255 in this case, it can lead to overflow in downstream operations. Since we pass in aqualarray for alignment, we can know it's not ambiguous and set the value back to it's correct value.