gvl.write documents that variant input must be left-aligned, but performs no check in the write/genotype path. Non-left-aligned indels are silently assumed canonical, which can misplace variants relative to the reference during haplotype reconstruction.
It should raise a clear ValueError (mirroring the multi-allelic guard at python/genvarloader/_dataset/_write.py:389) instructing the user to left-align (bcftools norm -f ref.fa).
Found via property-based testing (Phase 2 test overhaul). A clean-rejection test (tests/integration/dataset/test_haps_property.py) is marked xfail pending this validation.
gvl.writedocuments that variant input must be left-aligned, but performs no check in the write/genotype path. Non-left-aligned indels are silently assumed canonical, which can misplace variants relative to the reference during haplotype reconstruction.It should raise a clear
ValueError(mirroring the multi-allelic guard atpython/genvarloader/_dataset/_write.py:389) instructing the user to left-align (bcftools norm -f ref.fa).Found via property-based testing (Phase 2 test overhaul). A clean-rejection test (
tests/integration/dataset/test_haps_property.py) is markedxfailpending this validation.