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Fix the unplaced-reads regression #236 introduced on main #237

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Merged
hyperpolymath merged 1 commit into from
Oct 23, 2026
Merged

Fix the unplaced-reads regression #236 introduced on main #237

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9 changes: 8 additions & 1 deletion src/server/routes/clade_cumulus.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -310,8 +310,15 @@ function _clade_cumulus_post_impl(req::HTTP.Request, study::String, run::String)
for (ri, w) in taxa_rows
row_weight[ri] = get(row_weight, ri, 0.0) + w
end
# `unplaced_reads` reports how much of each row's abundance never
# reached the tree, so its floor is floating-point noise, not the
# *validity* tolerance. `PLACEMENT_WEIGHT_SUM_TOL` (0.05) exists so
# that a candidate list truncated by the placement tool stays
# `:valid`; reusing it here reported 0 unplaced reads for a
# placement at LWR 0.99 whose remaining 1% really is off the tree.
noise_floor = MetaManifold.CladeCumulus.PLACEMENT_WEIGHT_OVER_TOL
short_rows = [(ri, 1.0 - wsum) for (ri, wsum) in row_weight
if wsum < 1.0 - MetaManifold.CladeCumulus.PLACEMENT_WEIGHT_SUM_TOL]
if 1.0 - wsum > noise_floor]
unplaced_reads = OrderedDict{String,Float64}()
for sc in scols
col_vals = df[!, sc]
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