fix: allow empty seqeunce in BAM record in perbase only-depth
#92
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
Handle empty sequences in BAM record when generating a pileup to fix an out of bound error in `perbase only-depth` when a BAM record does not have an associated sequence (`*` in sequence column in SAM format). Fixes: sstadick#91
sstadick
added a commit
that referenced
this pull request
Dec 11, 2025
- Add 3 tests for empty SEQ records in base-depth pileup code path - Bump version to 1.2.0 - Add changelog entry for PR #92 - Add README note about empty SEQ handling 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
sstadick
added a commit
to ghuls/perbase
that referenced
this pull request
Dec 11, 2025
- Add 3 tests for empty SEQ records in base-depth pileup code path - Bump version to 1.2.0 - Add changelog entry for PR sstadick#92 - Add README note about empty SEQ handling
- Add 3 tests for empty SEQ records in base-depth pileup code path - Bump version to 1.2.0 - Add changelog entry for PR sstadick#92 - Add README note about empty SEQ handling
sstadick
force-pushed
the
fix_empty_sequence
branch
from
b6cc640 to
f5cfac8
Compare
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Outdated suggestions cannot be applied.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.
Handle empty sequences in BAM record when generating a pileup to fix an out of bound error in
perbase only-depthwhen a BAM record does not have an associated sequence (*in sequence column in SAM format).Fixes: #91