Fix mpileup -a bug#2229
Merged
Merged
Conversation
Caching the 2 references, and assuming if the first doesn't match then we must be using the second, turns out to be incorrect. It turns out our pileup code needs two (this ref and when using -a the last reference to finish up the sequence), plus bam_mplp64_auto uses two (current refence and potentially next reference if we're on the last record of that reference), and these two aren't necessarily the same pair. So our revised number of in-flight references is now 3, with better checking. Updated the test data to trigger the bug (under address sanitizer), to verify the fix works before the code changes were added. Fixes samtools#2227
daviesrob
pushed a commit
to daviesrob/samtools
that referenced
this pull request
Jul 10, 2025
Caching the 2 references, and assuming if the first doesn't match then we must be using the second, turns out to be incorrect. It turns out our pileup code needs two (this ref and when using -a the last reference to finish up the sequence), plus bam_mplp64_auto uses two (current refence and potentially next reference if we're on the last record of that reference), and these two aren't necessarily the same pair. So our revised number of in-flight references is now 3, with better checking. Updated the test data to trigger the bug (under address sanitizer), to verify the fix works before the code changes were added. Fixes samtools#2227
daviesrob
pushed a commit
to daviesrob/samtools
that referenced
this pull request
Mar 18, 2026
Caching the 2 references, and assuming if the first doesn't match then we must be using the second, turns out to be incorrect. It turns out our pileup code needs two (this ref and when using -a the last reference to finish up the sequence), plus bam_mplp64_auto uses two (current refence and potentially next reference if we're on the last record of that reference), and these two aren't necessarily the same pair. So our revised number of in-flight references is now 3, with better checking. Updated the test data to trigger the bug (under address sanitizer), to verify the fix works before the code changes were added. Fixes samtools#2227
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
2 participants
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.
Caching the 2 references, and assuming if the first doesn't match then we must be using the second, turns out to be incorrect.
It turns out our pileup code needs two (this ref and when using -a the last reference to finish up the sequence), plus bam_mplp64_auto uses two (current refence and potentially next reference if we're on the last record of that reference), and these two aren't necessarily the same pair. So our revised number of in-flight references is now 3, with better checking.
Updated the test data to trigger the bug (under address sanitizer), to verify the fix works before the code changes were added.
Fixes #2227