SAM TLEN should be 0 when either read is unmapped #373
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
this_rid/this_pos will be copied from r_prev(=r_next)'s values when this read is unmapped (i.e., r is NULL). In this case, we can write RNEXT as '=' but should not calculate TLEN from these placeholder values. Similarly when the mate is unmapped (i.e., r_next is NULL). Fixes lh3#365.
|
Thanks! |
# for free
to join this conversation on GitHub.
Already have an account?
# 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Outdated suggestions cannot be applied.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.
Don't compute
tlenwhen eitherrorr_nextindicates unmapped. Fixes #365.(Compiled, but I have not rigorously tested this.)