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VCFPhaseResolver: DNA phase from VCF GT + PS (#269) (#352)

Second phase resolver in the #269 staging. Reads the phase data that
varcode's VCF loader already parses into Genotype via #267 (shipped
in 2.3.0): GT delimiter (|/) and PS phase-set identifier. No loader
plumbing needed — alt_allele_index is already preserved on
per-variant metadata.

Contract:

- in_cis(v1, v2) -> True if both variants sit in the same phase set
  on the same haplotype slot, False if same phase set on different
  slots, None otherwise.
- Homozygous-alt short-circuit: every called haplotype carries the
  alt, so phase is deterministic — cis with any called variant on
  either haplotype regardless of GT delimiter.
- Multi-allelic aware: a VCF row split into multiple Variants uses
  alt_allele_index to map each Variant to its GT-encoded slot, so
  GT=1|2 correctly reports the first alt on slot 0 and the second
  alt on slot 1.
- Single-sample by construction. Multi-sample VCFs use one resolver
  per sample (phase is per-sample).

Compatible with any tool that writes standard-shaped VCF: WhatsHap,
HapCUT2, DeepVariant, GATK HaplotypeCaller, long-read callers,
population phasers. varcode only reads GT + PS, doesn't care who
wrote them.

Matches IsovarPhaseResolver's interface (in_cis / phased_partners /
source) so downstream code can swap resolvers without branching.
Does NOT attach a mutant_transcript — DNA phasing alone doesn't
produce assembled contigs. A follow-up PR will ship HaplotypeEffect
+ apply_variants_to_transcript to build joint MutantTranscripts
when multiple cis variants hit the same transcript; VCFPhaseResolver
already has the in_cis query that grouping needs.

Tests cover: phased cis, phased trans, cross-block (None), unphased
(None), homozygous-alt short-circuit, multi-allelic slot mapping,
phased_partners walk, interface symmetry with IsovarPhaseResolver.
Source Files on build 24755087014
Detailed source file information is not available for this build.