Add extant sequence reconstruction (-esr) and gap-aware ASR/ESR (-gap-asr, -gap-esr) - #223
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trongnhanuit wants to merge 60 commits into
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trongnhanuit wants to merge 60 commits into
trongnhanuit wants to merge 60 commits into
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…eversible implementations of computeLikelihoodBranch
…responding output file
…ase: given a treefile and a single alignment
…equence even if users specify -blfix
…R2 + rate model from the original model
…s don't contain any gap
… while some others are non-gapped
# Conflicts: # alignment/alignment.cpp # alignment/alignment.h # tree/discordance.cpp # tree/phylokernelnew.h # tree/phylokernelnonrev.h # tree/phylosupertree.cpp # tree/phylosupertree.h # tree/phylotreesse.cpp # utils/tools.cpp
The ESR feature's Alignment::convertToBin()/SuperAlignment::convertToBin() compiled and merged cleanly but relied on pre-refactor APIs and an incomplete metadata copy: - addPattern(pat, site) / countConstSite() no longer exist on master; addPattern() now appends to site_pattern internally instead of writing by index, and countConstSites() (plural) replaces countConstSite(). - convertToBin()'s metadata copy was missing char_partition/tree_len and used a manual seq_names loop instead of direct assignment, unlike the established initAlignmentCopy() convention used by convertToCodonOrAA/convertCodonToAA/convertCodonToDNA. - SuperAlignment::convertToBin() crashed (SIGABRT) on any partition model under -gap-asr/-gap-esr: it called the (now pattern-populating) Alignment::convertToBin() on the destination SuperAlignment, then SuperAlignment::buildPattern() (via init()) asserted the pattern list was still empty before building its own unrelated partition-presence pattern. Clear the leftover patterns before init(), matching the never-pre-populate convention used by SuperAlignment::extractSubAlignment(). - runPhyloAnalysisAfterReadingAln() referenced an undeclared model_info; thread it through from the caller as an optional parameter, matching the ModelCheckpoint plumbing already present on runPhyloAnalysis(). Verified with a 9-alignment x 4-feature x 2-binary comparison (DNA/AA/codon, standard/mixture/partition models, -asr/-gap-asr/-esr/-gap-esr) against a nhan_esr baseline build: all 72 cases now pass with matching reconstructed states and log-likelihoods. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
…der on binary data when reconstructing gapped-ASR/ESR
…conducting -gap-asr/esr
…d_seq_reconstruction
…hem after that run is done
…afe numeric scaling (rare cases)
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Summary
-esr / --extant: marginal extant (tip) sequence reconstruction — the leaf-node analogue of -asr. Each tip's own data is masked and its states are predicted from the rest of the tree.
-gap-asr / --gap-ancestral and -gap-esr / --gap-extant: adds a gap/non-gap posterior (p_gap) alongside the character-state reconstruction. The alignment is recoded as binary presence/absence, a second fixed-topology analysis runs on that binary data, and the two posteriors are merged in the output.
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