fix: store CL BAM tag as scalar integer for samtools filtering#91
Open
jayhesselberth wants to merge 2 commits into
Open
fix: store CL BAM tag as scalar integer for samtools filtering#91jayhesselberth wants to merge 2 commits into
jayhesselberth wants to merge 2 commits into
Conversation
The CL (charging likelihood) tag was stored as a byte array (B:C,[220]) because it was copied verbatim from Remora's ML tag. This prevented filtering with `samtools view -d CL:>=200`. Converting to a scalar integer (CL:i:220) enables standard samtools tag filtering. - Add --to-scalar flag to transfer_tags.py for array-to-scalar conversion - Update transfer_bam_tags rule to pass --to-scalar CL - Update get_charging_table.py to handle both scalar and array CL values - Add tests for scalar conversion and backward compatibility
jayhesselberth
force-pushed
the
fix/cl-tag-scalar
branch
from
b59b43c to
9fe69df
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Summary
B:C,[220]) because it was copied verbatim from Remora's ML tag. This prevented filtering withsamtools view -d CL:>=200.--to-scalarflag totransfer_tags.pythat converts single-element array tags to scalar integers (CL:i:220) during transfer.get_charging_table.pyto handle both scalar int (new) and array (legacy) CL values for backward compatibility.Test plan
--to-scalarconversion intest_transfer_tags.pytest_get_charging_table.pypixi run dry-runpassessamtools view -d 'CL:>=200' bam/final/sample/sample.bam | head🤖 Generated with Claude Code