Cacao marker harmonization and revision diagnostics

Analysis software for the study Coordinate conventions and marker density shape coverage of cacao aroma loci. This repository release contains two separately versioned components: the original cacao marker harmonization pipeline (3.0.0) and revision diagnostics (1.0.0). The original pipeline analyzes marker identity, reference-derived SNP coordinates, positional representation, matched-background sensitivity and conditional unphased genotype-dosage correlations. The diagnostics add own-filter recovery, identifier-link and coordinate audits, adjusted genotype correlations, per-peak coordinate anchors and gene-background sensitivity analyses. The original pipeline starts from provider workbooks and the pinned Criollo v2 reference. The diagnostics use the complete published Supplementary Data S1 and original provider workbooks; they do not repeat genome alignment. Component instructions, provenance and validation records are included. Third-party source workbooks and reference assets must be obtained separately. Figure-generation code is supplied separately in Online Resource 6. The repository release identifier is r1-2026.10.26. Component versions remain 3.0.0 and 1.0.0.