Claude/fix twin matrix sizes bn n ve#120
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smasongarrison merged 5 commits intomztwinsfrom Feb 13, 2026
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Two issues caused the sparse matrices from the two mz_method paths to differ structurally: 1. The merging method iterated over mz_pairs (row indices) but treated the values as IDs. Changed to iterate over mz_id_pairs which holds the actual pedigree IDs. Currently masked because test data has sequential IDs matching row positions, but would break with non-sequential IDs. 2. The different computational paths (column-merge-before-tcrossprod vs pedigree-modify-then-post-copy) leave different explicit zeros in the sparse matrix. Added Matrix::drop0() before returning to normalize the sparse representation so both methods produce structurally identical results. https://claude.ai/code/session_01PXbgV7bdA9sg7St6xBbg3T
The merging method's post-copy (r[idx2,] <- r[idx1,]) causes Matrix to coerce from dsCMatrix (symmetric, one triangle) to dgCMatrix (general, both triangles), doubling @i/@x slot lengths. Add forceSymmetric() after the post-copy to restore symmetric storage. Also guard the merging pedigree modification with a component check (additive only) to match the restoration block, and move the verbose message inside the merging if-block so it only prints when merging actually occurs. https://claude.ai/code/session_01PXbgV7bdA9sg7St6xBbg3T
sum(A, B) sums all elements of both matrices, which can never be 0 for non-negative relatedness values. Use sum(A - B) to check that the element-wise differences are zero. https://claude.ai/code/session_01PXbgV7bdA9sg7St6xBbg3T
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