Make the mpileup BAM_CREF_SKIP filter optional. #2282
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
Mpileup removes alignments using the cigar ref skip operator ("N").
This was originally added in 2011 in samtools/samtools#d1643d6 with
the commit message of "fixed a bug in indel calling related to
unmapped and refskip reads".
Unfortunately I don't know what that bug was, but removing the code
shows it still works (at least for some data!). We need better
understanding of what's going on and why it was added, but this PR
makes it optional, keeping the default as before. Note there appears
to be no filtering of BAM_CREF_SKIP in indels-2.0 so the option would
be a nop there.
This is an alternative PR to samtools#2281. I've leave it to the project
maintainer as to what is preferable: removing the (no longer needed?)
filtering, or keeping the default behaviour identical and adding a new
option instead (which is safer, but possibly leads to accidental bad
calls due to not noticing a new option has appeared).
Fixes samtools#2277
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Outdated suggestions cannot be applied.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.
Mpileup removes alignments using the cigar ref skip operator ("N"). This was originally added in 2011 in samtools/samtools#d1643d6 with the commit message of "fixed a bug in indel calling related to unmapped and refskip reads".
Unfortunately I don't know what that bug was, but removing the code shows it still works (at least for some data!). We need better understanding of what's going on and why it was added, but this PR makes it optional, keeping the default as before. Note there appears to be no filtering of BAM_CREF_SKIP in indels-2.0 so the option would be a nop there.
This is an alternative PR to #2281. I've leave it to the project maintainer as to what is preferable: removing the (no longer needed?) filtering, or keeping the default behaviour identical and adding a new option instead (which is safer, but possibly leads to accidental bad calls due to not noticing a new option has appeared).
Fixes #2277