[WIP] Add single variant to existing sample #828
Draft
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
The library is by nlohmann and is composed of a single json.hpp header file.
The function joins a vector of strings into a single string using a delineator string as a separator.
The function writes a VCF files for the given HTSlib header and records. The function can write a .vcf or .vcf.gz file and a corresponding .tbi index file can be optionally generated.
This method returns the sample id (row index) for the given sample name.
These are utilites for working with individual variants that aren't necessarily affiliated with a VCF file or have been ingested. Currently these utilities are composed of a Variant class that is instantiated from JSON representing a variant. The class currently supports converting the variant to a HTSlib record.
This allows a single variant (input as JSON) to be added to a sample already in the dataset. The current implementation simply generates temporary VCF and TBI files for the variant then ingests them.
This allows a single variant (input as JSON) to be added to a sample already in the dataset.
spencerseale
reviewed
Aug 6, 2025
Holding off for now. We're considering making the implementation/API more transactional to reduce fragmentation. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in 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Outdated suggestions cannot be applied.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.
@simonjwhite Would like the ability to add variants one at a time to support liftover. This PR adds that functionality.
Currently the feature is only available via the
add-variantcommand in the CLI, which accepts a single variant as JSON. For example:tiledbvcf add-variant -u ./1000-genomes-dragen-v3.7.6-dataset --json '{"chrom":"chr1","pos":10,"ref":"A","alt":"T","sample":"HG03914","id":"rs123","qual":30.0,"info":{"DP":45,"AF":0.3},"format":{"GT":"0/1","DP":15,"GQ":25},"filter":["PASS"]}'Notes:
.vcf.gzand.tbifiles and then ingests themadd-variantcommand via pass-through flags/dev/shm/for performance--tmp-dirflagI will add tests and proceed with the Python API after getting feedback on the current implementation.