Adaptive Allele-Haplotype Incidence Indexing for Pangenome Queries: Representation, Reconstruction, and Benchmarking
Roberto Garrone
Population-scale analysis of phased genetic variants requires both allele-carrier retrieval and ordered haplotype context. We examine H1, an adaptive allele-haplotype incidence-row index, and H2, a canonical edge-path representation derived from a fixed, nonoverlapping variant catalog. We prove conditional reconstruction of abstract H2 walks and distinguish this property from unrestricted equivalence to genomic variation graphs. A completed local notebook experiment used a chromosome 1 interval (20-22 Mb), 200 diploid individuals, 24,921 SNV/indel records, and 45 SVTYPE-annotated records. For 24,966 extracted nonreference rows across 400 haplotypes, the serialized H1 incidence-row files occupied 0.872 MiB with a simple adaptive layout and 1.126 MiB with a custom Roaring-like layout, versus 1.190 MiB for a bitmap-payload baseline; a whole-file Zstandard archive of the adaptive layout occupied 0.207 MiB. For a separately constructed nonoverlapping SNV projection containing 22,727 sites, indexed H2 edge sequences occupied 75,130,882 bytes in a raw format and 5,156,418 bytes with context-Huffman encoding (14.57-fold reduction). Carrier-equivalence and graph-adjacency assertions passed in the notebook, but full crosscallset phasing, nucleotide-level SV reconstruction, and comparison with production indexes remain unresolved. The measurements establish a restricted implementation feasibility result, not superior end-to-end pangenome compression.
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