From c153f2edac461eb455f26e1a8a2e7450c45de9fb Mon Sep 17 00:00:00 2001
From: Mark Chernyshev <mark26111@gmail.com>
Date: Fri, 15 Nov 2024 09:58:31 +0100
Subject: [PATCH] small docs changes

---
 src/CHMMera.jl | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/src/CHMMera.jl b/src/CHMMera.jl
index 2997554..b74f199 100644
--- a/src/CHMMera.jl
+++ b/src/CHMMera.jl
@@ -40,7 +40,7 @@ If the argument `detailed` is false, only `recombinations` is computed.
 - `mutation_probabilities::Vector{Float64} = [0.0047, 0.01, 0.05, 0.1, 0.15, 0.2]`: A vector of mutation probabilities.
 - `base_mutation_probability::Float64 = 0.05`: The base mutation probability. Used as starting point for Baum-Welch.
 - `prior_probability::Float64 = 0.02`: The prior probability of a sequence being chimeric.
-- `detailed::Bool = false`: A boolean indicating whether to calculate `startingpoint`, `pathevaluation`, and `logsiteprobabilities`.
+- `detailed::Bool = false`: A boolean indicating whether to calculate `pathevaluation` and `logsiteprobabilities`.
 """
 get_recombination_events(queries::Vector{String}, references::Vector{String}; bw::Bool = true, mutation_probabilities::Vector{Float64} = [0.0047, 0.01, 0.05, 0.1, 0.15, 0.2], base_mutation_probability::Float64 = 0.05, prior_probability::Float64 = 0.02, detailed::Bool = false) =
     get_recombination_events(as_ints.(queries), as_ints.(references), bw, mutation_probabilities, base_mutation_probability, prior_probability, detailed)
@@ -48,8 +48,8 @@ get_recombination_events(queries::Vector{String}, references::Vector{String}; bw
 function get_chimera_probabilities(queries::Vector{Vector{UInt8}}, references::Vector{Vector{UInt8}}, bw::Bool = true, mutation_probabilities::Vector{Float64} = [0.0047, 0.01, 0.05, 0.1, 0.15, 0.2], base_mutation_probability::Float64 = 0.05, prior_probability::Float64 = 0.02)
     hmm = bw ? ApproximateHMM(vovtomatrix(references), prior_probability) : FullHMM(vovtomatrix(references), mutation_probabilities, prior_probability)
     mutation_probabilities = bw ? [base_mutation_probability for i in 1:length(references)] : mutation_probabilities
-    # split query iteration among threads
     chimera_probabiltiies = zeros(length(queries))
+    # split query iteration among threads
     Threads.@threads for i in eachindex(queries)
         chimera_probabiltiies[i] = chimeraprobability(queries[i], hmm, copy(mutation_probabilities))
     end
@@ -61,18 +61,16 @@ function get_recombination_events(queries::Vector{Vector{UInt8}}, references::Ve
     hmm = bw ? ApproximateHMM(vovtomatrix(references), prior_probability) : FullHMM(vovtomatrix(references), mutation_probabilities, prior_probability)
     mutation_probabilities = bw ? [base_mutation_probability for i in eachindex(references)] : mutation_probabilities
 
-    # split query iteration among threads
     recomb_type = detailed ? DetailedRecombinationEvents : RecombinationEvents
     recombination_events = Vector{recomb_type}(undef, length(queries))
-
+    # split query iteration among threads
     Threads.@threads for i in eachindex(queries)
         recombination_events[i] = get_recombination_events(queries[i], hmm, copy(mutation_probabilities), Val(detailed))
     end
     return recombination_events
 end
 
-# multiple dispatch to figure out if we want starting point or pathevaluation
-# no starting point or path evaluation
+# no path evaluation or logsiteprobabilities
 function get_recombination_events(query::Vector{UInt8}, hmm::HMM, mutation_probabilities::Vector{Float64}, ::Val{false})
     findrecombinations(query, hmm, mutation_probabilities)
 end