From 988c417b06d0ce1ebf34d3f05d0a30d6af819cf0 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Fri, 24 May 2024 16:38:09 +0000 Subject: [PATCH 01/42] style: replace deprecated delim_whitespace with sep * Previously a FutureWarning was coming up in pytest that 'delim_whitespace' keyword in pd.read_table is deprecated, need to use sep='\s+' instead. * Deprecated in v2.2.0, see https://github.com/pandas-dev/pandas/issues/55569 and https://pandas.pydata.org/docs/whatsnew/v2.2.0.html#other-deprecations for more info --- src/threads_arg/utils.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/src/threads_arg/utils.py b/src/threads_arg/utils.py index 311f5c5..e1cc24b 100644 --- a/src/threads_arg/utils.py +++ b/src/threads_arg/utils.py @@ -54,9 +54,9 @@ def interpolate_map(map_gz, pgen): Reading in map file (format has columns [chrom, SNP, cM-pos, bp]) """ if (map_gz[:-3] == ".gz") : - maps = pd.read_table(map_gz, header=None, compression='gzip', delim_whitespace=True) + maps = pd.read_table(map_gz, header=None, compression='gzip', sep="\\s+") else: - maps = pd.read_table(map_gz, header=None, delim_whitespace=True) + maps = pd.read_table(map_gz, header=None, sep="\\s+") cm_pos_map = maps[2].values.astype(np.float64) phys_pos_map = maps[3].values.astype(np.float64) pvar = pgen.replace("pgen", "pvar") @@ -64,9 +64,9 @@ def interpolate_map(map_gz, pgen): physical_positions = None if os.path.isfile(bim): - physical_positions = np.array(pd.read_table(bim, delim_whitespace=True, header=None, comment='#')[3]).astype(np.float64) + physical_positions = np.array(pd.read_table(bim, sep="\\s+", header=None, comment='#')[3]).astype(np.float64) elif os.path.isfile(pvar): - physical_positions = np.array(pd.read_table(pvar, delim_whitespace=True, header=None, comment='#')[1]).astype(np.float64) + physical_positions = np.array(pd.read_table(pvar, sep="\\s+", header=None, comment='#')[1]).astype(np.float64) else: raise RuntimeError(f"Can't find {bim} or {pvar}") @@ -87,10 +87,10 @@ def get_map_from_bim(pgen, rho): cm_out = None physical_positions = None if os.path.isfile(bim): - physical_positions = np.array(pd.read_table(bim, delim_whitespace=True, header=None, comment='#')[3]).astype(int) + physical_positions = np.array(pd.read_table(bim, sep="\\s+", header=None, comment='#')[3]).astype(int) cm_out = rho * 100 * physical_positions elif os.path.isfile(pvar): - physical_positions = np.array(pd.read_table(pvar, delim_whitespace=True, header=None, comment='#')[1]).astype(int) + physical_positions = np.array(pd.read_table(pvar, sep="\\s+", header=None, comment='#')[1]).astype(int) cm_out = rho * 100 * physical_positions else: raise RuntimeError(f"Can't find {bim} or {pvar}") @@ -101,5 +101,5 @@ def get_map_from_bim(pgen, rho): return cm_out, physical_positions def parse_demography(demography): - d = pd.read_table(demography, delim_whitespace=True, header=None) + d = pd.read_table(demography, sep="\\s+", header=None) return list(d[0]), list(d[1]) From 7534ddc737dbf1b589532367da3a49f0d12d094c Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Tue, 28 May 2024 14:56:15 +0000 Subject: [PATCH 02/42] style: rename operator& to calc_intersection_with (#22) * Purely stylistic as it was noticed that set-like `&` operation was computationally quite expensive. Also aids code navigation. --- src/TGEN.cpp | 6 +++--- src/TgenSegment.hpp | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/TGEN.cpp b/src/TGEN.cpp index f5f6d08..6134f72 100644 --- a/src/TGEN.cpp +++ b/src/TGEN.cpp @@ -148,7 +148,7 @@ class TGENImpl { // std::queue seg_queue; // auto eqr = segments.equal_range(range); // for (SegmentSet::const_iterator iter = eqr.first; iter != eqr.second; iter++) { -// seg_queue.push(*iter & range); +// seg_queue.push(iter->calc_intersection_with(range)); // } // // Process everything in the queue @@ -225,7 +225,7 @@ class TGENImpl { std::queue seg_queue; auto eqr = segments.equal_range(range); for (SegmentSet::const_iterator iter = eqr.first; iter != eqr.second; iter++) { - seg_queue.push(*iter & range); + seg_queue.push(iter->calc_intersection_with(range)); } // Process everything in the queue @@ -259,7 +259,7 @@ class TGENImpl { // We've not yet reached somewhere to copy from, so we keep traversing auto new_eqr = interval_sets[segment.target].equal_range(segment); for (SegmentSet::const_iterator iter = new_eqr.first; iter != new_eqr.second; iter++) { - seg_queue.push(*iter & segment); + seg_queue.push(iter->calc_intersection_with(segment)); } } seg_queue.pop(); diff --git a/src/TgenSegment.hpp b/src/TgenSegment.hpp index 8c18d20..4046237 100644 --- a/src/TgenSegment.hpp +++ b/src/TgenSegment.hpp @@ -40,7 +40,7 @@ class TgenSegment { return os; } - TgenSegment operator&(const TgenSegment& other) const { + TgenSegment calc_intersection_with(const TgenSegment& other) const { int new_first = std::max(lower(), other.lower()); int new_past = std::min(upper(), other.upper()); From 27d341dac95c7e84cc324e26f9a376ce9a89e15c Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Tue, 28 May 2024 15:17:05 +0000 Subject: [PATCH 03/42] refactor: fix Demography warnings (#22) * Reorder class to methods-first * Doxygen-friendly header comments * Use size_t as appropriate --- src/Demography.cpp | 32 ++++++++++++++++---------------- src/Demography.hpp | 26 ++++++++++++-------------- 2 files changed, 28 insertions(+), 30 deletions(-) diff --git a/src/Demography.cpp b/src/Demography.cpp index c6ca316..b8b2f7e 100644 --- a/src/Demography.cpp +++ b/src/Demography.cpp @@ -1,20 +1,20 @@ #include "Demography.hpp" -#include // for std::sort + +#include #include #include #include -#include // to throw errors +#include #include - Demography::Demography(std::vector _sizes, std::vector _times) : times(_times), sizes(_sizes), std_times(std::vector()) { if (times.size() != sizes.size()) { throw std::runtime_error("Demography times and sizes must have equal length"); } - for (int i = 0; i < times.size(); i++) { - if (times[i] < 0 || sizes[i] <= 0) { + for (std::size_t i = 0; i < times.size(); i++) { + if ((times[i] < 0.0) || (sizes[i] <= 0.0)) { throw std::runtime_error("Demography expects non-negative times and strictly positive sizes"); } @@ -33,9 +33,9 @@ Demography::Demography(std::vector _sizes, std::vector _times) } // Compute times in standard coalescent space - int K = times.size(); + std::size_t K = times.size(); std_times.push_back(0.0); - for (int i = 1; i < K; i++) { + for (std::size_t i = 1; i < K; i++) { double d = (times[i] - times[i - 1]) / sizes[i - 1]; std_times.push_back(std_times[i - 1] + d); } @@ -48,24 +48,24 @@ double Demography::std_to_gen(const double t) { if (t < 0) { throw std::runtime_error("Demography can only convert non-negative times to std"); } + // Find the highest i s.t. std_times[i] <= t. - int i = - std::distance(std_times.begin(), std::upper_bound(std_times.begin(), std_times.end(), t)) - 1; + const auto it = std::upper_bound(std_times.begin(), std_times.end(), t); + if (it == std_times.begin()) { + throw std::runtime_error("Cannot work on first element"); + } + + // Static cast is safe as above check ensures it > std_times.begin() + std::size_t i = static_cast(it - std_times.begin() - 1); return times[i] + (t - std_times[i]) * sizes[i]; } -/** - * @brief Compute the expected length of the N-th branch - * - * @param N - * @return double - */ double Demography::expected_branch_length(const int N) { return std_to_gen(2. / N); } std::ostream& operator<<(std::ostream& os, const Demography& d) { - for (int i = 0; i < d.sizes.size(); i++) { + for (std::size_t i = 0; i < d.sizes.size(); i++) { std::cout << d.times[i] << " " << d.sizes[i] << " " << d.std_times[i] << std::endl; } return os; diff --git a/src/Demography.hpp b/src/Demography.hpp index 06efa23..3539104 100644 --- a/src/Demography.hpp +++ b/src/Demography.hpp @@ -1,30 +1,28 @@ #ifndef THREADS_ARG_DEMOGRAPHY_HPP #define THREADS_ARG_DEMOGRAPHY_HPP -#include #include +#include -// This class is a wrapper for simple coalescence time queries under a piecewise-constant demography +/// This class is a wrapper for simple coalescence time queries under a piecewise-constant demography class Demography { public: - // These are in generations - std::vector times; - // These are *haploid* - std::vector sizes; - // Normalised coalescence times - std::vector std_times; - // Expected pairwise coalescent time - double expected_time = 0.0; - Demography(std::vector _times, std::vector _sizes); - // Map a time in the standard coalescent to generations under this demography + /// Map a time in the standard coalescent to generations under this demography double std_to_gen(const double t); - // The expected branch length of a new branch in a tree with N leaves + + /// The expected branch length of a new branch in a tree with N leaves double expected_branch_length(const int N); - // Output + /// Stream output friend std::ostream& operator<<(std::ostream& os, const Demography& demography); + +public: + std::vector times; ///< These are in generations + std::vector sizes; ///< These are *haploid* + std::vector std_times; ///< Normalised coalescence times + double expected_time = 0.0; ///< Expected pairwise coalescent time }; #endif // THREADS_ARG_DEMOGRAPHY_HPP From b8629a80120b162dec25b4e5cf4b68f3897009bd Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Tue, 28 May 2024 16:35:38 +0000 Subject: [PATCH 04/42] fix: more robust validation for std_to_gen (#22) * Following discussion with Arni, safer to check first value rather than t < 0, especially if we start to work with demographies with K > 0 --- src/Demography.cpp | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/Demography.cpp b/src/Demography.cpp index b8b2f7e..db98107 100644 --- a/src/Demography.cpp +++ b/src/Demography.cpp @@ -45,17 +45,18 @@ Demography::Demography(std::vector _sizes, std::vector _times) } double Demography::std_to_gen(const double t) { - if (t < 0) { - throw std::runtime_error("Demography can only convert non-negative times to std"); + if (t < std_times.front()) { + throw std::runtime_error("Demography can only convert times greater than the first entry"); } // Find the highest i s.t. std_times[i] <= t. const auto it = std::upper_bound(std_times.begin(), std_times.end(), t); + + // Defensive check as the t < std_times.front check above should mean `it` is never first if (it == std_times.begin()) { - throw std::runtime_error("Cannot work on first element"); + throw std::runtime_error("Unexpected std_to_gen upper bound finding first element"); } - // Static cast is safe as above check ensures it > std_times.begin() std::size_t i = static_cast(it - std_times.begin() - 1); return times[i] + (t - std_times[i]) * sizes[i]; } From e6016bc03c6e86140580d46a9a3ad495580af6f1 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Tue, 28 May 2024 16:45:43 +0000 Subject: [PATCH 05/42] refactor: fix ImputationMatcher warnings (#22) * NOTE: -Wsign-conversion warning disabled (see below) * Reorder class to methods-first. * Doxygen-friendly header comments. * Use const ref on getters to avoid copying data. * Replace commented-out diagnostic code with #def. See FIXME in CompilerWarnings.cmake about disabling -Wsign-conversion warning. This generates a lot of noise due as many counts in classes are stored as int rather than size_t. Need to review with Arni as some should remain int. --- cmake/CompilerWarnings.cmake | 3 ++- src/ImputationMatcher.cpp | 29 ++++++++++++++-------------- src/ImputationMatcher.hpp | 37 ++++++++++++++++++------------------ 3 files changed, 35 insertions(+), 34 deletions(-) diff --git a/cmake/CompilerWarnings.cmake b/cmake/CompilerWarnings.cmake index c2965c8..eec3ad3 100644 --- a/cmake/CompilerWarnings.cmake +++ b/cmake/CompilerWarnings.cmake @@ -44,7 +44,8 @@ function(set_project_warnings project_name) -Woverloaded-virtual # warn if you overload (not override) a virtual function -Wpedantic # warn if non-standard C++ is used -Wconversion # warn on type conversions that may lose data - -Wsign-conversion # warn on sign conversions + # FIXME for review with Arni, lots of errors due to int <-> size_t conversion. Determine correct types + #-Wsign-conversion # warn on sign conversions -Wnull-dereference # warn if a null dereference is detected -Wdouble-promotion # warn if float is implicit promoted to double -Wformat=2 # warn on security issues around functions that format output (ie printf) diff --git a/src/ImputationMatcher.cpp b/src/ImputationMatcher.cpp index 90cefd4..29a37aa 100644 --- a/src/ImputationMatcher.cpp +++ b/src/ImputationMatcher.cpp @@ -8,12 +8,11 @@ #include #include - ImputationMatcher::ImputationMatcher(int _n_ref, int _n_target, const std::vector& _genetic_positions, double _query_interval_size, int _neighborhood_size) - : num_reference(_n_ref), num_target(_n_target), genetic_positions(_genetic_positions), - query_interval_size(_query_interval_size), neighborhood_size(_neighborhood_size) { + : neighborhood_size(_neighborhood_size), num_reference(_n_ref), num_target(_n_target), + query_interval_size(_query_interval_size), genetic_positions(_genetic_positions) { if (genetic_positions.size() <= 2) { throw std::runtime_error("Need at least 3 sites, found " + std::to_string(genetic_positions.size())); @@ -22,15 +21,17 @@ ImputationMatcher::ImputationMatcher(int _n_ref, int _n_target, num_samples = num_reference + num_target; sites_processed = 0; - // Check maps are strictly increasing - // for (int i = 0; i < num_sites - 1; i++) { - // if (genetic_positions.at(i + 1) <= genetic_positions.at(i)) { - // std::string prompt = "Genetic coordinates must be strictly increasing, found "; - // prompt += std::to_string(genetic_positions[i + 1]) + " after " + - // std::to_string(genetic_positions[i]); - // throw std::runtime_error(prompt); - // } - // } + // Set to 1 for runtime check that maps are strictly increasing +#if 0 + for (int i = 0; i < num_sites - 1; i++) { + if (genetic_positions.at(i + 1) <= genetic_positions.at(i)) { + std::string prompt = "Genetic coordinates must be strictly increasing, found "; + prompt += std::to_string(genetic_positions[i + 1]) + " after " + + std::to_string(genetic_positions[i]); + throw std::runtime_error(prompt); + } + } +#endif int query_site_idx = 1; double gen_pos_offset = genetic_positions[0]; @@ -175,10 +176,10 @@ void ImputationMatcher::process_site(const std::vector& genotype) { sites_processed++; } -std::unordered_map> ImputationMatcher::get_matches() { +const std::unordered_map>& ImputationMatcher::get_matches() const { return match_sets; } -std::vector ImputationMatcher::get_sorting() { +const std::vector& ImputationMatcher::get_sorting() const { return sorting; } diff --git a/src/ImputationMatcher.hpp b/src/ImputationMatcher.hpp index d2202f7..2ac00d3 100644 --- a/src/ImputationMatcher.hpp +++ b/src/ImputationMatcher.hpp @@ -5,23 +5,19 @@ #include #include -// NB this recycles a lot of code from Matcher.hpp +/// This is a version of the Threads haplotype matching algorithm +/// adapted to be used for imputation. +/// NB this recycles a lot of code from Matcher.hpp class ImputationMatcher { +public: + ImputationMatcher(int _n_ref, int _n_target, const std::vector& _genetic_positions, + double _query_interval_size, int _neighborhood_size); -private: - int sites_processed = 0; - int next_query_site_idx = 0; - - // pbwt quantities - std::vector sorting; - std::vector next_sorting; - - // querying quantities - std::vector ref_sorting; + void process_site(const std::vector& genotype); + const std::unordered_map>& get_matches() const; + const std::vector& get_sorting() const; public: - // This is a version of the Threads haplotype matching algorithm - // adapted to be used for imputation. // TODO: include a second pass through data here to get divergence values and not do that using // Threads-fastLS int neighborhood_size = 0; @@ -33,14 +29,17 @@ class ImputationMatcher { double query_interval_size = 0.0; std::unordered_map> match_sets; std::vector genetic_positions; - ImputationMatcher(int _n_ref, int _n_target, const std::vector& _genetic_positions, - double _query_interval_size, int _neighborhood_size); - // Do all the work - void process_site(const std::vector& genotype); - std::unordered_map> get_matches(); +private: + int sites_processed = 0; + int next_query_site_idx = 0; - std::vector get_sorting(); + // pbwt quantities + std::vector sorting; + std::vector next_sorting; + + // querying quantities + std::vector ref_sorting; }; #endif // THREADS_ARG_IMPUTATION_MATCHER_HPP From cdb6359cb012f23550454a4f17ceb0c7a52947b9 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Tue, 28 May 2024 16:47:31 +0000 Subject: [PATCH 06/42] build: update settings.json defaults (#22) * Turn on ENABLE_TESTING and WARNINGS_AS_ERRORS for developers by default (does not affect CI). * Add file associations automatically added during build process --- .vscode/settings.json | 80 +++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 78 insertions(+), 2 deletions(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index 6e42dfb..92dee53 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -7,7 +7,83 @@ "cmake.generator": "Ninja", "cmake.configureOnOpen": false, "cmake.configureSettings": { - //"ENABLE_TESTING": "ON", - //"WARNINGS_AS_ERRORS": "TRUE", + "ENABLE_TESTING": "ON", + "WARNINGS_AS_ERRORS": "TRUE" + }, + "files.associations": { + "iosfwd": "cpp", + "cctype": "cpp", + "clocale": "cpp", + "cmath": "cpp", + "csignal": "cpp", + "cstdarg": "cpp", + "cstddef": "cpp", + "cstdio": "cpp", + "cstdlib": "cpp", + "cstring": "cpp", + "ctime": "cpp", + "cwchar": "cpp", + "cwctype": "cpp", + "array": "cpp", + "atomic": "cpp", + "strstream": "cpp", + "bit": "cpp", + "*.tcc": "cpp", + "bitset": "cpp", + "chrono": "cpp", + "codecvt": "cpp", + "compare": "cpp", + "complex": "cpp", + "concepts": "cpp", + "condition_variable": "cpp", + "cstdint": "cpp", + "deque": "cpp", + "forward_list": "cpp", + "list": "cpp", + "map": "cpp", + "set": "cpp", + "string": "cpp", + "unordered_map": "cpp", + "unordered_set": "cpp", + "vector": "cpp", + "exception": "cpp", + "algorithm": "cpp", + "functional": "cpp", + "iterator": "cpp", + "memory": "cpp", + "memory_resource": "cpp", + "numeric": "cpp", + "optional": "cpp", + "random": "cpp", + "ratio": "cpp", + "regex": "cpp", + "string_view": "cpp", + "system_error": "cpp", + "tuple": "cpp", + "type_traits": "cpp", + "utility": "cpp", + "fstream": "cpp", + "future": "cpp", + "initializer_list": "cpp", + "iomanip": "cpp", + "iostream": "cpp", + "istream": "cpp", + "limits": "cpp", + "mutex": "cpp", + "new": "cpp", + "numbers": "cpp", + "ostream": "cpp", + "semaphore": "cpp", + "sstream": "cpp", + "stdexcept": "cpp", + "stop_token": "cpp", + "streambuf": "cpp", + "thread": "cpp", + "cfenv": "cpp", + "cinttypes": "cpp", + "typeindex": "cpp", + "typeinfo": "cpp", + "valarray": "cpp", + "variant": "cpp" } } From a5f9a7a16eca0cd034adceec9b9be775d303469c Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 12:51:16 +0000 Subject: [PATCH 07/42] style: clang format Demography.hpp (#22) --- src/Demography.hpp | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/src/Demography.hpp b/src/Demography.hpp index 3539104..51317af 100644 --- a/src/Demography.hpp +++ b/src/Demography.hpp @@ -4,7 +4,8 @@ #include #include -/// This class is a wrapper for simple coalescence time queries under a piecewise-constant demography +/// This class is a wrapper for simple coalescence time queries under a piecewise-constant +/// demography class Demography { public: Demography(std::vector _times, std::vector _sizes); @@ -19,10 +20,10 @@ class Demography { friend std::ostream& operator<<(std::ostream& os, const Demography& demography); public: - std::vector times; ///< These are in generations - std::vector sizes; ///< These are *haploid* - std::vector std_times; ///< Normalised coalescence times - double expected_time = 0.0; ///< Expected pairwise coalescent time + std::vector times; ///< These are in generations + std::vector sizes; ///< These are *haploid* + std::vector std_times; ///< Normalised coalescence times + double expected_time = 0.0; ///< Expected pairwise coalescent time }; #endif // THREADS_ARG_DEMOGRAPHY_HPP From ae19ee36ac2e32b612982648c2aae3d064e5dc31 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 12:56:11 +0000 Subject: [PATCH 08/42] refactor: fix HMM.hpp/cpp warnings (#22) * Reorder class to methods-first. * Doxygen-friendly header comments. * Clang format * Warnings picked up shadowed variable in compute_expected_times * Resolve size_t/int with easiest fix where possible * Warnings picked up unused variables (e.g. `trans` line 61) * Added exception for possible data conversion loss in `breakpoints` --- src/HMM.cpp | 33 +++++++++++++++++++-------------- src/HMM.hpp | 31 +++++++++++++++---------------- 2 files changed, 34 insertions(+), 30 deletions(-) diff --git a/src/HMM.cpp b/src/HMM.cpp index bbea44a..d708ce0 100644 --- a/src/HMM.cpp +++ b/src/HMM.cpp @@ -1,9 +1,9 @@ #include "HMM.hpp" + #include #include #include - HMM::HMM(Demography demography, std::vector bp_sizes, std::vector cm_sizes, double mutation_rate, int K) : num_states(K) { @@ -12,7 +12,8 @@ HMM::HMM(Demography demography, std::vector bp_sizes, std::vector trellis_row(num_states, 0.0); std::vector pointer_row(num_states, 0); trellis.push_back(trellis_row); @@ -21,19 +22,19 @@ HMM::HMM(Demography demography, std::vector bp_sizes, std::vector HMM::compute_expected_times(Demography demography, const int K) { - std::vector expected_times; + std::vector result; double k = static_cast(num_states); boost::math::exponential e; for (int i = 1; i <= K; i++) { double t = demography.std_to_gen(quantile(e, (i - 0.5) / k)); - expected_times.push_back(t); + result.push_back(t); } - return expected_times; + return result; } void HMM::compute_recombination_scores(std::vector cm_sizes) { - for (int i = 0; i < cm_sizes.size(); i++) { + for (std::size_t i = 0; i < cm_sizes.size(); i++) { non_transition_score.push_back(std::vector()); transition_score.push_back(std::vector()); for (int k = 0; k < num_states; k++) { @@ -51,14 +52,14 @@ void HMM::compute_recombination_scores(std::vector cm_sizes) { } void HMM::compute_mutation_scores(std::vector bp_sizes, double mutation_rate) { - for (int i = 0; i < bp_sizes.size(); i++) { + for (std::size_t i = 0; i < bp_sizes.size(); i++) { hom_score.push_back(std::vector()); het_score.push_back(std::vector()); for (int k = 0; k < num_states; k++) { double t = expected_times[k]; + // TODO: use mean-bp sizes here as in the main algorithm const double l = 2. * mutation_rate * bp_sizes[i] * t; - const double trans = std::log1p(-std::exp(-l)); // log-prob of mutating het_score[i].push_back(std::log1p(-std::exp(-l))); @@ -75,17 +76,21 @@ void HMM::compute_mutation_scores(std::vector bp_sizes, double mutation_ std::vector HMM::breakpoints(std::vector observations, int start) { // Viterbi // Initialize - int neighborhood_size = observations.size(); + int neighborhood_size = static_cast(observations.size()); std::vector z(neighborhood_size); - int end = start + neighborhood_size; for (int i = 0; i < num_states; i++) { double score = observations[0] ? het_score[start][i] : hom_score[start][i]; trellis[start][i] = score; } + // FIXME review with Arni, defensive check for assignment to 'k' below + if (num_states > std::numeric_limits::max()) { + throw std::runtime_error("Unable to store breakpoints for more than 2^16 states"); + } + // Main routine - double score; - unsigned short running_argmax; + double score = 0.0; + unsigned short running_argmax = 0; for (int j = 1; j < neighborhood_size; j++) { for (int i = 0; i < num_states; i++) { double running_max = 0; @@ -98,7 +103,7 @@ std::vector HMM::breakpoints(std::vector observations, int start) { if (score > running_max || k == 0) { running_max = score; - running_argmax = k; + running_argmax = static_cast(k); } } trellis[j + start][i] = running_max; @@ -113,7 +118,7 @@ std::vector HMM::breakpoints(std::vector observations, int start) { double s = trellis[start + neighborhood_size - 1][k]; if (s > running_max) { running_max = s; - argmax = k; + argmax = static_cast(k); } } diff --git a/src/HMM.hpp b/src/HMM.hpp index 379ecba..c72dbe2 100644 --- a/src/HMM.hpp +++ b/src/HMM.hpp @@ -1,32 +1,31 @@ -#ifndef DEMOGRAPHY -#define DEMOGRAPHY #include "Demography.hpp" -#endif // DEMOGRAPHY -#include #include +#include - -// This class contains the PSMC-like algorithm used to break up segments for small-N inference +/// This class contains the PSMC-like algorithm used to break up segments for small-N inference class HMM { public: - // HMM data - int num_states = 0; - std::vector expected_times; + HMM(Demography demography, std::vector bp_sizes, std::vector cm_sizes, + double mutation_rate, int K); + HMM() = default; - std::vector> non_transition_score; - std::vector> transition_score; - std::vector> hom_score; - std::vector> het_score; void compute_recombination_scores(std::vector cm_sizes); void compute_mutation_scores(std::vector bp_sizes, double mutation_rate); std::vector compute_expected_times(Demography demography, int K); + std::vector breakpoints(std::vector observations, int start); + +public: + // HMM data + int num_states = 0; + std::vector expected_times; // HMM working quantities std::vector> trellis; std::vector> pointers; - HMM(Demography demography, std::vector bp_sizes, std::vector cm_sizes, double mutation_rate, int K); - HMM() {}; - std::vector breakpoints(std::vector observations, int start); + std::vector> non_transition_score; + std::vector> transition_score; + std::vector> hom_score; + std::vector> het_score; }; From 087617a2f55c4d8b3692dec856a4e12c68601974 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 12:59:02 +0000 Subject: [PATCH 09/42] refactor: resolve ImpuationMatcher warnings (#22) * Resolve size_t/int with easiest fix where possible * Comments to pick up in review whether runtime check genetic_positions is needed --- src/ImputationMatcher.cpp | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/ImputationMatcher.cpp b/src/ImputationMatcher.cpp index 29a37aa..77c1659 100644 --- a/src/ImputationMatcher.cpp +++ b/src/ImputationMatcher.cpp @@ -17,10 +17,11 @@ ImputationMatcher::ImputationMatcher(int _n_ref, int _n_target, throw std::runtime_error("Need at least 3 sites, found " + std::to_string(genetic_positions.size())); } - num_sites = genetic_positions.size(); + num_sites = static_cast(genetic_positions.size()); num_samples = num_reference + num_target; sites_processed = 0; + // FIXME Arni/Alex review. OK to remove or instead add an explicit macro? // Set to 1 for runtime check that maps are strictly increasing #if 0 for (int i = 0; i < num_sites - 1; i++) { @@ -35,7 +36,7 @@ ImputationMatcher::ImputationMatcher(int _n_ref, int _n_target, int query_site_idx = 1; double gen_pos_offset = genetic_positions[0]; - for (int i = 0; i < genetic_positions.size(); i++) { + for (int i = 0; i < static_cast(genetic_positions.size()); i++) { double cm = genetic_positions.at(i); if (cm > gen_pos_offset + query_interval_size * query_site_idx) { query_sites.push_back(i); @@ -83,11 +84,11 @@ void ImputationMatcher::process_site(const std::vector& genotype) { } } - if (genotype.size() != num_samples) { + if (static_cast(genotype.size()) != num_samples) { throw std::runtime_error("invalid genotype vector size"); } - if (next_query_site_idx < query_sites.size() && + if (next_query_site_idx < static_cast(query_sites.size()) && sites_processed == query_sites.at(next_query_site_idx)) { next_query_site_idx++; int ref_allele_count = 0; From 3024e4f48be3481a4a9c14323dc7ba3f746f6fde Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 13:02:03 +0000 Subject: [PATCH 10/42] refactor: resolve Matcher warnings (#22) * Reorder header to methods-first * Ensure all member variables initialised * Doxygen-friendly header comments * Clang format * Resolve size_t/int with easiest fix where possible * Remove C-style cast * Parenthesis to clarify conditional precedence --- src/Matcher.cpp | 32 +++++++++++++-------------- src/Matcher.hpp | 58 ++++++++++++++++++++++++++----------------------- 2 files changed, 47 insertions(+), 43 deletions(-) diff --git a/src/Matcher.cpp b/src/Matcher.cpp index 733118e..69c1d86 100644 --- a/src/Matcher.cpp +++ b/src/Matcher.cpp @@ -8,7 +8,6 @@ #include #include - // For a given interval, this contains all the matches for all the samples MatchGroup::MatchGroup(int _num_samples, double _cm_position) : num_samples(_num_samples), cm_position(_cm_position) { @@ -24,7 +23,7 @@ MatchGroup::MatchGroup(const std::vector& target_ids, if (target_ids.size() != matches.size()) { throw std::runtime_error("Inconsistent target/matches sizes"); } - for (int i = 0; i < target_ids.size(); i++) { + for (int i = 0; i < static_cast(target_ids.size()); i++) { match_candidates[target_ids[i]] = matches[i]; } } @@ -78,7 +77,7 @@ void MatchGroup::filter_matches(int min_matches) { // Then determine top 4 candidates for neighboring groups top_four_maps.reserve(num_samples); for (int i = 0; i < num_samples; i++) { - top_four_maps.emplace_back(std::min(4, (int) match_candidates.at(i).size())); + top_four_maps.emplace_back(std::min(4, static_cast(match_candidates.at(i).size()))); std::partial_sort_copy(match_candidates_counts.at(i).begin(), match_candidates_counts.at(i).end(), top_four_maps.at(i).begin(), top_four_maps.at(i).end(), @@ -107,12 +106,13 @@ Matcher::Matcher(int _n, const std::vector& _genetic_positions, double _ double _match_group_interval_size, int _neighborhood_size, int _min_matches) : num_samples(_n), genetic_positions(_genetic_positions), query_interval_size(_query_interval_size), - match_group_interval_size(_match_group_interval_size), neighborhood_size(_neighborhood_size), min_matches(_min_matches) { + match_group_interval_size(_match_group_interval_size), neighborhood_size(_neighborhood_size), + min_matches(_min_matches) { if (genetic_positions.size() <= 2) { throw std::runtime_error("Need at least 3 sites, found " + std::to_string(genetic_positions.size())); } - num_sites = genetic_positions.size(); + num_sites = static_cast(genetic_positions.size()); sites_processed = 0; // Check maps are strictly increasing @@ -130,7 +130,7 @@ Matcher::Matcher(int _n, const std::vector& _genetic_positions, double _ int match_group_site_idx = 1; double gen_pos_offset = genetic_positions[0]; match_group_sites = {0}; - for (int i = 0; i < genetic_positions.size(); i++) { + for (int i = 0; i < static_cast(genetic_positions.size()); i++) { double cm = genetic_positions.at(i); if (cm > gen_pos_offset + query_interval_size * query_site_idx) { query_sites.push_back(i); @@ -162,7 +162,7 @@ Matcher::Matcher(int _n, const std::vector& _genetic_positions, double _ } match_group_idx = 0; std::cout << "Will use " << query_sites.size() << " query sites and " << match_group_sites.size() - << " match_group_sites" << std::endl; + << " match_group_sites" << std::endl; match_groups.reserve(match_group_sites.size()); for (int match_group_site : match_group_sites) { @@ -195,7 +195,7 @@ void Matcher::process_site(const std::vector& genotype) { } int counter0 = 0; int counter1 = 0; - if (genotype.size() != num_samples) { + if (static_cast(genotype.size()) != num_samples) { throw std::runtime_error("invalid genotype vector size"); } @@ -217,14 +217,14 @@ void Matcher::process_site(const std::vector& genotype) { sorting = next_sorting; // Threading-neighbor queries - if (match_group_idx < match_group_sites.size() - 1 && - sites_processed >= match_group_sites.at(match_group_idx + 1)) { + if (match_group_idx < (static_cast(match_group_sites.size()) - 1) && + (sites_processed >= match_group_sites.at(match_group_idx + 1))) { match_group_idx++; match_groups.at(match_group_idx - 1).filter_matches(min_matches); } // If we've reached a query site, query - if (next_query_site_idx < query_sites.size() && + if (next_query_site_idx < static_cast(query_sites.size()) && sites_processed == query_sites.at(next_query_site_idx)) { // Get the arg-sort of the sorting for (int i = 0; i < num_samples; i++) { @@ -238,18 +238,18 @@ void Matcher::process_site(const std::vector& genotype) { // Insert sequences and query in order for (int i = 1; i < num_samples; i++) { std::vector matches; - int allele = genotype.at(i); matches.reserve(neighborhood_size); auto iter = threaded.insert(permutation.at(i)); auto iter_up = iter.first; auto iter_down = iter.first; // Check if genotypes are identical, just to be sure - while (matches.size() < neighborhood_size && (iter_down != threaded.begin() || iter_up != threaded.end())) { + while ((static_cast(matches.size()) < neighborhood_size) && + (iter_down != threaded.begin() || iter_up != threaded.end())) { if (iter_down != threaded.begin()) { iter_down--; matches.push_back(sorting.at(*iter_down)); } - if (matches.size() < neighborhood_size && iter_up != threaded.end()) { + if (static_cast(matches.size()) < neighborhood_size && iter_up != threaded.end()) { iter_up++; if (iter_up != threaded.end()) { matches.push_back(sorting.at(*iter_up)); @@ -273,7 +273,7 @@ void Matcher::process_site(const std::vector& genotype) { } // Special case for last query - if (next_query_site_idx == query_sites.size()) { + if (next_query_site_idx == static_cast(query_sites.size())) { match_groups.at(match_group_sites.size() - 1).filter_matches(min_matches); } } @@ -282,7 +282,7 @@ void Matcher::process_site(const std::vector& genotype) { // Propagate top 4 matches from left and right match groups void Matcher::propagate_adjacent_matches() { - for (int i = 1; i < match_groups.size(); i++) { + for (int i = 1; i < static_cast(match_groups.size()); i++) { MatchGroup& group = match_groups.at(i); MatchGroup& prev = match_groups.at(i - 1); group.insert_tops_from(prev); diff --git a/src/Matcher.hpp b/src/Matcher.hpp index ff468dd..23ded26 100644 --- a/src/Matcher.hpp +++ b/src/Matcher.hpp @@ -5,45 +5,26 @@ #include #include -// for a certain interval, store the matches for all samples +/// for a certain interval, store the matches for all samples class MatchGroup { public: - int num_samples; - std::unordered_map> match_candidates; - std::vector> match_candidates_counts; - std::vector>> top_four_maps; - double cm_position; MatchGroup(int _num_samples, double cm_position); MatchGroup(const std::vector& target_ids, const std::vector>& matches, const double _cm_position); void filter_matches(int min_matches); void insert_tops_from(MatchGroup& other); void clear(); + +public: + int num_samples = 0; + std::unordered_map> match_candidates; + std::vector> match_candidates_counts; + std::vector>> top_four_maps; + double cm_position = 0.0; }; class Matcher { - -private: - int min_matches = 0; - int sites_processed = 0; - int next_query_site_idx = 0; - int match_group_idx = 0; - int min_match_length = 1; - std::vector match_groups; - std::vector sorting; - std::vector next_sorting; - std::vector permutation; - public: - int neighborhood_size = 0; - std::vector query_sites; - std::vector match_group_sites; - int num_samples = 0; - int num_sites = 0; - double query_interval_size = 0.0; - // matches in these groups are considered together in the hmm - double match_group_interval_size = 0.0; - std::vector genetic_positions; Matcher(int _n, const std::vector& _genetic_positions, double _query_interval_size, double _match_group_interval_size, int _neighborhood_size, int _min_matches); @@ -51,6 +32,7 @@ class Matcher { void process_site(const std::vector& genotype); void propagate_adjacent_matches(); void clear(); + std::vector get_matches(); std::vector>> serializable_matches(std::vector& target_ids); @@ -58,6 +40,28 @@ class Matcher { std::vector get_sorting(); std::vector get_permutation(); + +public: + int num_samples = 0; + std::vector genetic_positions; + double query_interval_size = 0.0; + double match_group_interval_size = 0.0; + int neighborhood_size = 0; + std::vector query_sites; + std::vector match_group_sites; + int num_sites = 0; + // matches in these groups are considered together in the hmm + +private: + int min_matches = 0; + int sites_processed = 0; + int next_query_site_idx = 0; + int match_group_idx = 0; + int min_match_length = 1; + std::vector match_groups; + std::vector sorting; + std::vector next_sorting; + std::vector permutation; }; #endif // THREADS_ARG_MATCHER_HPP From 48a6afb5a41d5097d0a3bd6c3e247dfc02f26ad9 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 13:02:56 +0000 Subject: [PATCH 11/42] style: tidy Node cpp/hpp (#22) * Reorder header to methods-first * Clang format --- src/Node.cpp | 1 - src/Node.hpp | 20 ++++++++++---------- 2 files changed, 10 insertions(+), 11 deletions(-) diff --git a/src/Node.cpp b/src/Node.cpp index 4eb6faa..896d59d 100644 --- a/src/Node.cpp +++ b/src/Node.cpp @@ -2,7 +2,6 @@ #include - Node::Node(int _sample_ID, int _divergence, bool _genotype) : sample_ID(_sample_ID), divergence(_divergence), genotype(_genotype) { } diff --git a/src/Node.hpp b/src/Node.hpp index 1b228ef..cdd3481 100644 --- a/src/Node.hpp +++ b/src/Node.hpp @@ -4,8 +4,17 @@ #include #include - class Node { +public: + // Constructors + Node(int sample_ID, int divergence, bool genotype); + + // Node movers-arounders + void insert_above(Node* node); + + // Output + friend std::ostream& operator<<(std::ostream& os, const Node& node); + public: // Node data int sample_ID = 0; @@ -18,15 +27,6 @@ class Node { // "Next below to the right" for 0 and 1 std::array w = {nullptr, nullptr}; - - // Constructors - Node(int sample_ID, int divergence, bool genotype); - - // Node movers-arounders - void insert_above(Node* node); - - // Output - friend std::ostream& operator<<(std::ostream& os, const Node& node); }; #endif // THREADS_ARG_NODE_HPP \ No newline at end of file From 58ce5efc50036fdfb4741226aeec9c7f4a1fa7a5 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 13:06:31 +0000 Subject: [PATCH 12/42] refactor: resolve State cpp/hpp warnings (#22) * Reorder header to methods-first * Class member order initialisation corrected * Const correct `genotype` and `dump` * Doxygen-friendly header comments * Clang format * Review point whether numeric_limits infinity or max --- src/State.cpp | 8 ++++---- src/State.hpp | 56 +++++++++++++++++++++++++-------------------------- 2 files changed, 32 insertions(+), 32 deletions(-) diff --git a/src/State.cpp b/src/State.cpp index 6c8125d..f5bd061 100644 --- a/src/State.cpp +++ b/src/State.cpp @@ -5,7 +5,6 @@ #include #include - TracebackState::TracebackState(int _site, Node* _best_prev_node, TracebackState* _prev) : site(_site), best_prev_node(_best_prev_node), prev(_prev) { } @@ -14,7 +13,7 @@ State::State(Node* _below, double _score, TracebackState* _traceback) : below(_below), score(_score), traceback(_traceback) { } -bool State::genotype() { +bool State::genotype() const { return this->below->above->genotype; } @@ -55,7 +54,8 @@ void StateBranch::prune() { }); std::vector new_states; - double running_min_score = std::numeric_limits::infinity(); + double running_min_score = + std::numeric_limits::infinity(); // FIXME review with Arni - infinity or max? for (const State& s : states) { if (s.score < running_min_score) { new_states.push_back(s); @@ -81,7 +81,7 @@ void StateTree::prune() { } } -std::vector StateTree::dump() { +std::vector StateTree::dump() const { std::vector states; for (auto pair : branches) { for (auto s : pair.second.states) { diff --git a/src/State.hpp b/src/State.hpp index 9ad796b..f509032 100644 --- a/src/State.hpp +++ b/src/State.hpp @@ -3,67 +3,67 @@ #include "Node.hpp" -#include #include +#include class TracebackState { +public: + TracebackState(int _site, Node* _best_prev_node, TracebackState* _prev); + public: int site = 0; - // ID to trace back through to last traceback state - Node* best_prev_node = nullptr; + Node* best_prev_node = nullptr; ///< ID to trace back through to last traceback state TracebackState* prev = nullptr; - - TracebackState(int _site, Node* _best_prev_node, TracebackState* _prev); }; class State { public: - // Nothing here can be const because we want to use std::sort later on - // Panel entry directly below - Node* below = nullptr; - // Score of the current state - double score = 0.0; - // Pointer to last recombinant state - TracebackState* traceback = nullptr; - // Shorthand for this.below->site - bool genotype(); - State(Node* _below, double _score, TracebackState* _traceback); + /// Shorthand for this.below->site + bool genotype() const; + friend std::ostream& operator<<(std::ostream& os, State& state); + +public: + // Nothing here can be const because we want to use std::sort later on + Node* below = nullptr; ///< Panel entry directly below + double score = 0.0; ///< Score of the current state + TracebackState* traceback = nullptr; }; class StatePair { public: - // Panel entry directly below - Node* below_a = nullptr; - Node* below_b = nullptr; - // Score of the current state - double score = 0.0; - // Pointer to last recombinant state - TracebackState* traceback_a = nullptr; - TracebackState* traceback_b = nullptr; - StatePair(Node* _below_a, Node* _below_b, double _score, TracebackState* _traceback_a, TracebackState* _traceback_b); friend std::ostream& operator<<(std::ostream& os, StatePair& state_pair); + +public: + Node* below_a = nullptr; ///< Panel entry directly below + Node* below_b = nullptr; + double score = 0.0; ///< Score of the current state + TracebackState* traceback_a = nullptr; ///< Pointer to last recombinant state + TracebackState* traceback_b = nullptr; }; class StateBranch { public: - std::vector states; void insert(const State& state); void prune(); + +public: + std::vector states; }; class StateTree { public: - std::unordered_map branches; - StateTree(std::vector& states); void prune(); - std::vector dump(); + std::vector dump() const; + +public: + std::unordered_map branches; }; #endif // THREADS_ARG_STATE_HPP From 71e184328b8df79e3d06f6d284e9b2db74c41fc7 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 13:09:10 +0000 Subject: [PATCH 13/42] refactor: resolve TGEN hpp/cpp warnings (#22) * Reorder class to methods-first * Resolve size_t/int with easiest fix where possible * Remove commented-out Eigen-based code; may revisit later * Doxygen-friendly header comments * Clang format --- src/TGEN.cpp | 105 ++++++++------------------------------------------- src/TGEN.hpp | 21 ++++------- 2 files changed, 23 insertions(+), 103 deletions(-) diff --git a/src/TGEN.cpp b/src/TGEN.cpp index 6134f72..9f775dd 100644 --- a/src/TGEN.cpp +++ b/src/TGEN.cpp @@ -10,7 +10,6 @@ #include #include - namespace boost::icl { // See // https://www.boost.org/doc/libs/1_81_0/libs/icl/doc/html/boost_icl/examples/custom_interval.html @@ -70,10 +69,11 @@ class TGENImpl { het_sites(std::move(_het_sites)), positions(std::move(_positions)) { positions.push_back(std::numeric_limits::max()); // position-to-site map - for (int i = 0; i < positions.size(); i++) { + for (int i = 0; i < static_cast(positions.size()); i++) { pos_idx_map[positions[i]] = i; } + // FIXME Arni/Alex review remove eigen for now (note int/size_t indexing)? // set reference genome here reference_genome = Eigen::VectorXi::Zero(positions.size()); reference_genome_vec = std::vector(positions.size(), false); @@ -84,13 +84,12 @@ class TGENImpl { interval_sets.reserve(bp_starts.size()); // Initialize interval maps for each sample. This can get too slow - for (int i = 0; i < bp_starts.size(); i++) { + for (std::size_t i = 0; i < bp_starts.size(); i++) { SegmentSet iset; - int n_segs = bp_starts[i].size(); + int n_segs = static_cast(bp_starts[i].size()); std::vector& sample_hets = het_sites[i]; - int n_hets = sample_hets.size(); + int n_hets = static_cast(sample_hets.size()); int het_site_idx = 0; - int pos_idx = 0; std::vector seg_hets; for (int j = 0; j < n_segs; j++) { int seg_start = bp_starts[i][j]; @@ -116,84 +115,7 @@ class TGENImpl { cached_genotypes_map[0] = -1; } - // Eigen-based query -// Eigen::MatrixXi& query(const int bp_from, const int bp_to, const std::vector& samples) { -// clear_cache(); - -// Deprecated eigen-based query -// Eigen::MatrixXi& TGEN::query(const int bp_from, const int bp_to, const std::vector& samples) { -// clear_cache(); - -// // Find number of expected sites -// int start_pos = *std::lower_bound(positions.begin(), positions.end(), bp_from); -// int end_pos = *std::upper_bound(positions.begin(), positions.end(), bp_to); -// int idx_offset = pos_idx_map[start_pos]; -// genotype_cache.resize(samples.size(), pos_idx_map[end_pos] - idx_offset); - -// TgenSegment range(start_pos, end_pos); - -// for (int i = 0; i < samples.size(); i++) { -// cached_genotypes_map[samples[i]] = i; -// if (samples[i] == 0) { -// auto insert_range = -// Eigen::seq(0, pos_idx_map[end_pos] - idx_offset - 1); // eigen seq is inclusive -// auto copy_range = Eigen::seq(idx_offset, pos_idx_map[end_pos] - 1); -// genotype_cache(i, insert_range) = reference_genome( -// copy_range); //.eval(); //WARNING need .eval() here (or do we? I don't think we do) -// } -// else { -// SegmentSet& segments(interval_sets[samples[i]]); - -// // Initialize the queue -// std::queue seg_queue; -// auto eqr = segments.equal_range(range); -// for (SegmentSet::const_iterator iter = eqr.first; iter != eqr.second; iter++) { -// seg_queue.push(iter->calc_intersection_with(range)); -// } - -// // Process everything in the queue -// while (!seg_queue.empty()) { -// TgenSegment& segment = seg_queue.front(); -// if (cached_genotypes_map.find(segment.target) != cached_genotypes_map.end()) { -// // We've reached somewhere along the tree where we can copy from -// int seg_start_idx = pos_idx_map[segment.lower()]; -// int seg_end_idx = pos_idx_map[segment.upper()]; -// auto insert_range = Eigen::seq( -// seg_start_idx - idx_offset, seg_end_idx - idx_offset - 1); // eigen seq is inclusive -// if (segment.target == 0) { -// auto copy_range = Eigen::seq(seg_start_idx, seg_end_idx - 1); -// // We've reached the root of the tree and copy from the "reference" genome -// genotype_cache(i, insert_range) = reference_genome(copy_range); -// } -// else { -// // We've found a cached genotype to copy from - -// genotype_cache(i, insert_range) = -// genotype_cache(cached_genotypes_map[segment.target], insert_range); -// } - -// // We then flip all the het sites -// for (int h : segment.het_sites) { -// genotype_cache(i, pos_idx_map[h] - idx_offset) = -// 1 - genotype_cache(i, pos_idx_map[h] - idx_offset); -// } -// } -// else { -// // We've not yet reached somewhere to copy from, so we keep traversing -// auto new_eqr = interval_sets[segment.target].equal_range(segment); -// for (SegmentSet::const_iterator iter = new_eqr.first; iter != new_eqr.second; iter++) { -// seg_queue.push(*iter & segment); -// } -// } -// seg_queue.pop(); -// } -// } -// } -// return genotype_cache; -// } - -// std::vector-based query -// Warning: This makes a copy when returned through the python interface + // Warning: This makes a copy when returned through the python interface std::vector>& query(const int bp_from, const int bp_to, const std::vector& samples) { genotypes.clear(); @@ -203,15 +125,14 @@ class TGENImpl { int end_pos = *std::upper_bound(positions.begin(), positions.end(), bp_to); int idx_offset = pos_idx_map[start_pos]; - int n_samples = samples.size(); int n_sites = pos_idx_map[end_pos] - idx_offset; genotypes.reserve(samples.size()); - for (int i = 0; i < samples.size(); i++) { + for (std::size_t i = 0; i < samples.size(); i++) { genotypes.push_back(std::vector(n_sites)); } TgenSegment range(start_pos, end_pos); - for (int i = 0; i < samples.size(); i++) { + for (int i = 0; i < static_cast(samples.size()); i++) { std::vector& current_gt = genotypes.at(i); cached_genotypes_map[samples[i]] = i; if (samples[i] == 0) { @@ -279,11 +200,15 @@ class TGENImpl { TGEN::TGEN(std::vector _positions, std::vector> _bp_starts, std::vector> _target_IDs, std::vector> _het_sites) : pimpl(std::make_unique(std::move(_positions), std::move(_bp_starts), - std::move(_target_IDs), std::move(_het_sites))) {} + std::move(_target_IDs), std::move(_het_sites))) { +} -TGEN::~TGEN() = default; +TGEN::~TGEN() { + // Empty destructor is declared in source rather than header so pimpl destructor is accessible +} -std::vector>& TGEN::query(int start_pos, int end_pos, const std::vector& samples) { +std::vector>& TGEN::query(int start_pos, int end_pos, + const std::vector& samples) { // Forward the call to pimpl return pimpl->query(start_pos, end_pos, samples); } diff --git a/src/TGEN.hpp b/src/TGEN.hpp index 1a886d1..28fd33f 100644 --- a/src/TGEN.hpp +++ b/src/TGEN.hpp @@ -6,27 +6,22 @@ #include #include - -class TGENImpl; // Forward declaration of the implementation class +// Forward declaration of the implementation class // Using PIMPL idiom to prevent libraries that #include "TGEN.hpp" needing to see boost/icl headers +class TGENImpl; class TGEN { - -private: - std::unique_ptr pimpl; // Pointer to implementation - public: - // Constructors TGEN(std::vector _positions, std::vector> _bp_starts, std::vector> _target_IDs, std::vector> _het_sites); + ~TGEN(); - ~TGEN(); // Define the destructor for proper deletion of pimpl - - std::vector>& query(int start_pos, int end_pos, const std::vector& samples); - - // Deprecated Eigen version: - // Eigen::MatrixXi& query(const int start_pos, const int end_pos, const std::vector& samples); + std::vector>& query(int start_pos, int end_pos, + const std::vector& samples); void clear_cache(); + +private: + std::unique_ptr pimpl; ///< Pointer to implementation }; #endif // THREADS_ARG_TGEN_HPP From 6971f573064d9dd51901338aae07bf78299949c9 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 13:11:28 +0000 Subject: [PATCH 14/42] refactor: resolve TgenSegment.hpp warnings (#22) * Ensure member variables initialised in order * remove `_` prefix on members (technically _ as first char is bad practice) * Separate class methods from variables * Clang format --- src/TgenSegment.hpp | 27 ++++++++++++++++----------- 1 file changed, 16 insertions(+), 11 deletions(-) diff --git a/src/TgenSegment.hpp b/src/TgenSegment.hpp index 4046237..1439a53 100644 --- a/src/TgenSegment.hpp +++ b/src/TgenSegment.hpp @@ -9,25 +9,26 @@ // Here is a typical class that may model intervals in your application. class TgenSegment { public: - TgenSegment() : _first(), _past(), target(std::numeric_limits::max()) { + TgenSegment() : target(std::numeric_limits::max()), first(), past() { } + TgenSegment(const TgenSegment& other) - : _first(other._first), _past(other._past), het_sites(other.het_sites), target(other.target) { + : het_sites(other.het_sites), target(other.target), first(other.first), past(other.past) { } - TgenSegment(int lo, int up) : _first(lo), _past(up), target(std::numeric_limits::max()) { + + TgenSegment(int lo, int up) : target(std::numeric_limits::max()), first(lo), past(up) { } + TgenSegment(int lo, int up, std::vector _hets, int _target) - : _first(lo), _past(up), het_sites(_hets), target(_target) { + : het_sites(_hets), target(_target), first(lo), past(up) { } - std::vector het_sites; - int target = std::numeric_limits::max(); - [[nodiscard]] int lower() const { - return _first; + return first; } + [[nodiscard]] int upper() const { - return _past; + return past; } friend std::ostream& operator<<(std::ostream& os, const TgenSegment& seg) { @@ -53,9 +54,13 @@ class TgenSegment { return {new_first, new_past, merged_sites, std::min(target, other.target)}; } +public: + std::vector het_sites; + int target = std::numeric_limits::max(); + private: - int _first = 0; - int _past = 0; + int first = 0; + int past = 0; }; #endif // THREADS_ARG_TGEN_SEGMENT_HPP From ccd49bd5f7fdd15f33c455b0c826bd713ac627c1 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 13:12:40 +0000 Subject: [PATCH 15/42] style: clang format threads_arg_pybind.cpp (#22) --- src/threads_arg_pybind.cpp | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/threads_arg_pybind.cpp b/src/threads_arg_pybind.cpp index 9ac0c77..9b17ed9 100644 --- a/src/threads_arg_pybind.cpp +++ b/src/threads_arg_pybind.cpp @@ -1,5 +1,5 @@ -#include "TGEN.hpp" #include "ImputationMatcher.hpp" +#include "TGEN.hpp" #include "ThreadsLowMem.hpp" #include @@ -63,7 +63,8 @@ PYBIND11_MODULE(threads_arg_python_bindings, m) { py::class_(m, "Matcher") .def(py::init, double, double, int, int>(), "Initialize", py::arg("num_samples"), py::arg("genetic_positions"), py::arg("query_interval_size"), - py::arg("match_group_interval_size"), py::arg("neighborhood_size") = 4, py::arg("min_matches") = 4) + py::arg("match_group_interval_size"), py::arg("neighborhood_size") = 4, + py::arg("min_matches") = 4) .def_readonly("query_sites", &Matcher::query_sites) .def_readonly("genetic_positions", &Matcher::genetic_positions) .def_readonly("query_interval_size", &Matcher::query_interval_size) From 540117b374624a98bae4e185d38dbb517de9195a Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 13:15:35 +0000 Subject: [PATCH 16/42] refactor: resolve ViterbiLowMem hpp/cpp warnings (#22) * Reorder class to methods-first and separate variables from methods * Const correct direct getter methods * Moved coord_id_key out into cpp as it's general to all classes * Resolve size_t/int warnings * Parenthesis to confirm operator precedence in conditional * Clang format --- src/ViterbiLowMem.cpp | 21 ++++++++++++------ src/ViterbiLowMem.hpp | 51 +++++++++++++++++++------------------------ 2 files changed, 37 insertions(+), 35 deletions(-) diff --git a/src/ViterbiLowMem.cpp b/src/ViterbiLowMem.cpp index 4c8106a..51ab460 100644 --- a/src/ViterbiLowMem.cpp +++ b/src/ViterbiLowMem.cpp @@ -7,6 +7,13 @@ #include #include +namespace { + +inline size_t coord_id_key(int i, int j) { + return (static_cast(i) << 32) | static_cast(j); +} + +} // namespace TracebackNode::TracebackNode(int _sample_id, int _site, TracebackNode* _previous, double _score) : sample_id(_sample_id), site(_site), previous(_previous), score(_score) { @@ -31,8 +38,8 @@ void ViterbiPath::reverse() { std::reverse(sample_ids.begin(), sample_ids.end()); } -int ViterbiPath::size() { - return segment_starts.size(); +int ViterbiPath::size() const { + return static_cast(segment_starts.size()); } void ViterbiPath::append(int segment_start, int sample_id) { @@ -68,7 +75,7 @@ void ViterbiPath::map_positions(std::vector& positions) { std::tuple, std::vector, std::vector> ViterbiPath::dump_data_in_range(int start, int end) { int n_segs = size(); - if (start == -1 && end == -1 || n_segs == 0) { + if (((start == -1) && (end == -1)) || (n_segs == 0)) { return std::tuple, std::vector, std::vector>( bp_starts, sample_ids, heights); } @@ -82,8 +89,8 @@ ViterbiPath::dump_data_in_range(int start, int end) { for (int i = 0; i < n_segs; i++) { int seg_start = bp_starts.at(i); int seg_end = i < n_segs - 1 ? bp_starts.at(i + 1) : tmp_end; - if (seg_start <= tmp_start && tmp_start < seg_end || - tmp_start <= seg_start && seg_start < tmp_end) { + if (((seg_start <= tmp_start) && (tmp_start < seg_end)) || + ((tmp_start <= seg_start) && (seg_start < tmp_end))) { out_starts.push_back(std::max(tmp_start, seg_start)); out_ids.push_back(sample_ids.at(i)); out_heights.push_back(heights.at(i)); @@ -211,8 +218,8 @@ TracebackNode* ViterbiState::recursive_insert(std::unordered_map(traceback_states.size()); } ViterbiPath ViterbiState::traceback() { diff --git a/src/ViterbiLowMem.hpp b/src/ViterbiLowMem.hpp index a3352be..16f5254 100644 --- a/src/ViterbiLowMem.hpp +++ b/src/ViterbiLowMem.hpp @@ -7,30 +7,19 @@ #include class TracebackNode { -private: - inline size_t coord_id_key(int i, int j) { - return (size_t) i << 32 | (unsigned int) j; - } +public: + TracebackNode(int _sample_id, int _site, TracebackNode* _previous, double _score); + size_t key(); public: int sample_id = 0; int site = 0; - double score = 0.0; TracebackNode* previous = nullptr; - TracebackNode(int _sample_id, int _site, TracebackNode* _previous, double _score); - size_t key(); + double score = 0.0; }; class ViterbiPath { -private: public: - double score = 0.0; - int target_id = 0; - std::vector bp_starts; - std::vector segment_starts; - std::vector sample_ids; - std::vector heights; - std::vector het_sites; ViterbiPath(int _target_id); ViterbiPath(int _target_id, std::vector _segment_starts, std::vector _sample_ids, std::vector _heights, std::vector _het_sites); @@ -39,16 +28,31 @@ class ViterbiPath { std::tuple, std::vector, std::vector> dump_data_in_range(int start_idx, int end_idx); void reverse(); - int size(); + int size() const; void map_positions(std::vector& positions); + +public: + double score = 0.0; + int target_id = 0; + std::vector bp_starts; + std::vector segment_starts; + std::vector sample_ids; + std::vector heights; + std::vector het_sites; }; class ViterbiState { +public: + ViterbiState(int _target_id, std::vector _sample_ids); + + void process_site(const std::vector& genotype, double rho, double rho_c, double _mu, + double _mu_c); + void set_samples(std::unordered_set new_sample_ids); + int count_branches() const; + void prune(); + ViterbiPath traceback(); private: - inline size_t coord_id_key(int i, int j) { - return (size_t) i << 32 | (unsigned int) j; - } std::unordered_map traceback_states; TracebackNode* recursive_insert(std::unordered_map& state_map, TracebackNode* state); @@ -62,15 +66,6 @@ class ViterbiState { std::vector sample_ids; std::vector sample_scores; std::unordered_map current_tracebacks; - - ViterbiState(int _target_id, std::vector _sample_ids); - - void process_site(const std::vector& genotype, double rho, double rho_c, double _mu, - double _mu_c); - void set_samples(std::unordered_set new_sample_ids); - int count_branches(); - void prune(); - ViterbiPath traceback(); }; #endif // THREADS_ARG_VITERBI_LOW_MEM_HPP From 9d950470407f41dae3d1fa11022f51febaf7fd4c Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 13:19:57 +0000 Subject: [PATCH 17/42] refactor: resolve ThreadsLowMem hpp/cpp warnings (#22) * Reorder class to methods-first and separate variables from methods * Ensure all member variables initialised * Remove commented out member variables * Ensure member variables initialised in correct order * Resolve size_t/int warnings * Replace C-ctyle casts * Parenthesis to confirm operator precedence * Clang format * Some review comments to pick up with regard to parenthesis and commented out code --- src/ThreadsLowMem.cpp | 62 ++++++++++++++++++-------------------- src/ThreadsLowMem.hpp | 70 +++++++++++++++++++++---------------------- 2 files changed, 63 insertions(+), 69 deletions(-) diff --git a/src/ThreadsLowMem.cpp b/src/ThreadsLowMem.cpp index f40bbf8..245622d 100644 --- a/src/ThreadsLowMem.cpp +++ b/src/ThreadsLowMem.cpp @@ -8,15 +8,14 @@ #include #include - ThreadsLowMem::ThreadsLowMem(const std::vector _target_ids, const std::vector& _physical_positions, const std::vector& _genetic_positions, std::vector ne, std::vector ne_times, double _mutation_rate, bool _sparse) - : target_ids(_target_ids), physical_positions(_physical_positions), - genetic_positions(_genetic_positions), demography(Demography(ne, ne_times)), - mutation_rate(_mutation_rate), sparse(_sparse) { - num_samples = target_ids.size(); + : target_ids(_target_ids), mutation_rate(_mutation_rate), + physical_positions(_physical_positions), genetic_positions(_genetic_positions), + sparse(_sparse), demography(Demography(ne, ne_times)) { + num_samples = static_cast(target_ids.size()); if (physical_positions.size() != genetic_positions.size()) { throw std::runtime_error("Map lengths don't match."); } @@ -24,7 +23,7 @@ ThreadsLowMem::ThreadsLowMem(const std::vector _target_ids, throw std::runtime_error("Need at least 3 sites, found " + std::to_string(physical_positions.size())); } - num_sites = physical_positions.size(); + num_sites = static_cast(physical_positions.size()); // Check maps are strictly increasing for (int i = 0; i < num_sites - 1; i++) { @@ -49,7 +48,8 @@ ThreadsLowMem::ThreadsLowMem(const std::vector _target_ids, } // Mean interval size in base-pairs - mean_bp_size = (double) (physical_positions.back() - physical_positions[0]) / (num_sites - 1); + mean_bp_size = + (physical_positions.back() - physical_positions[0]) / static_cast(num_sites - 1); for (int target_id : target_ids) { segment_indices[target_id] = 0; expected_branch_lengths[target_id] = demography.expected_branch_length(target_id + 1); @@ -60,7 +60,7 @@ ThreadsLowMem::ThreadsLowMem(const std::vector _target_ids, het_sites_processed = 0; std::tie(bp_boundaries, bp_sizes) = ThreadsFastLS::site_sizes(physical_positions); - for (int i = 0; i < genetic_positions.size(); i++) { + for (std::size_t i = 0; i < genetic_positions.size(); i++) { if (i == genetic_positions.size() - 1) { // TO allow for closely spaced markers cm_sizes.push_back(0.0000001); @@ -87,7 +87,7 @@ void ThreadsLowMem::initialize_viterbi(std::vector& genotype) { bool group_change = false; - if (match_group_idx < match_groups.size() - 1 && - genetic_positions.at(hmm_sites_processed) >= - match_groups.at(match_group_idx + 1).cm_position) { + if (match_group_idx < (static_cast(match_groups.size()) - 1) && + (genetic_positions.at(hmm_sites_processed) >= + match_groups.at(match_group_idx + 1).cm_position)) { match_group_idx++; group_change = true; } @@ -150,7 +150,6 @@ void ThreadsLowMem::traceback() { } void ThreadsLowMem::process_site_hets(const std::vector& genotype) { - for (int target_id : target_ids) { if (target_id == 0) { if (genotype.at(0) == 1) { @@ -160,8 +159,8 @@ void ThreadsLowMem::process_site_hets(const std::vector& genotype) { else { ViterbiPath& path = paths.at(target_id); int current_seg_idx = segment_indices.at(target_id); - while (current_seg_idx < path.segment_starts.size() - 1 && - het_sites_processed >= path.segment_starts.at(current_seg_idx + 1)) { + while (current_seg_idx < (static_cast(path.segment_starts.size()) - 1) && + (het_sites_processed >= path.segment_starts.at(current_seg_idx + 1))) { current_seg_idx++; } segment_indices.at(target_id) = current_seg_idx; @@ -200,6 +199,7 @@ void ThreadsLowMem::date_segments() { // I get segfault on this? + // FIXME Alex/Arni - in progress, but #def couts for now? // for (int i = 1; i < num_samples; i++) { for (int target_id : target_ids) { if (target_id == 0) { @@ -209,8 +209,8 @@ void ThreadsLowMem::date_segments() { // compute length in bp/cM and num_hets for each segment ViterbiPath& path = paths.at(target_id); ViterbiPath new_path(target_id); - int n_segs = path.segment_starts.size(); - for (int k = 0; k < n_segs; k++) { + std::size_t n_segs = path.segment_starts.size(); + for (std::size_t k = 0; k < n_segs; k++) { int sample_id = path.sample_ids.at(k); int segment_start = path.segment_starts.at(k); int segment_end = k < n_segs - 1 ? path.segment_starts.at(k + 1) : num_sites - 1; @@ -219,33 +219,29 @@ void ThreadsLowMem::date_segments() { if (segment_end == segment_start) { continue; } - double bp_size = physical_positions.at(segment_end) - physical_positions.at(segment_start); - double cm_size = genetic_positions.at(segment_end) - genetic_positions.at(segment_start); // This is inefficient but probably not that bad std::vector segment_hets; for (int h : path.het_sites) { - if (segment_start <= h && h < segment_end || - h == num_sites - 1 && segment_end == num_sites - 1) { + // FIXME Alex/Arnie review parenthesis + if (((segment_start <= h) && (h < segment_end)) || + ((h == num_sites - 1) && (segment_end == num_sites - 1))) { segment_hets.push_back(h); } else if (h >= segment_end) { break; } } - // cout << "found bpsize: " << bp_size << " cmsize " << cm_size << " nhets " << - // segment_hets.size() << " sample " << sample_id << endl; disabling hmm for now - if (target_id < n_hmm_samples && segment_hets.size() > hmm_min_sites) { - // cout << "running hmm on segment [" << segment_start << ", " << segment_end << ")... "; + + if ((target_id < n_hmm_samples) && (static_cast(segment_hets.size()) > hmm_min_sites)) { std::vector het_hom_sites(segment_end - segment_start, false); for (int h : segment_hets) { - // cout << h << endl; het_hom_sites[h - segment_start] = true; } // Here we use the hmm to break the big segment up into smaller segments std::vector breakpoints = psmc.breakpoints(het_hom_sites, segment_start); // cout << "found " << breakpoints.size() << " breakpoints" << endl; - for (int j = 0; j < breakpoints.size(); j++) { + for (std::size_t j = 0; j < breakpoints.size(); j++) { int breakpoint_start = breakpoints[j]; int breakpoint_end = (j == breakpoints.size() - 1) ? segment_end : breakpoints[j + 1]; // there may be off-by-one errors here on the last segment (but who cares?) @@ -257,16 +253,16 @@ void ThreadsLowMem::date_segments() { // Same as above std::vector breakpoint_hets; for (int h : segment_hets) { - if (breakpoint_start <= h && h < breakpoint_end || - h == num_sites - 1 && breakpoint_end == num_sites - 1) { + if (((breakpoint_start <= h) && (h < breakpoint_end)) || + ((h == num_sites - 1) && (breakpoint_end == num_sites - 1))) { breakpoint_hets.push_back(h); } else if (h >= breakpoint_end) { break; } } - double height = ThreadsFastLS::date_segment( - breakpoint_hets.size(), cm_size, bp_size, mutation_rate, demography); + double height = ThreadsFastLS::date_segment(static_cast(breakpoint_hets.size()), + cm_size, bp_size, mutation_rate, demography); new_path.append(breakpoint_start, sample_id, height, breakpoint_hets); } } @@ -274,8 +270,8 @@ void ThreadsLowMem::date_segments() { // there are off-by-one errors here on the last segment (but who cares?) double bp_size = physical_positions.at(segment_end) - physical_positions.at(segment_start); double cm_size = genetic_positions.at(segment_end) - genetic_positions.at(segment_start); - double height = - ThreadsFastLS::date_segment(segment_hets.size(), cm_size, bp_size, mutation_rate, demography); + double height = ThreadsFastLS::date_segment( + static_cast(segment_hets.size()), cm_size, bp_size, mutation_rate, demography); new_path.append(segment_start, sample_id, height, segment_hets); } } diff --git a/src/ThreadsLowMem.hpp b/src/ThreadsLowMem.hpp index 222fa7c..c92b8f0 100644 --- a/src/ThreadsLowMem.hpp +++ b/src/ThreadsLowMem.hpp @@ -1,52 +1,17 @@ #ifndef THREADS_ARG_THREADS_LOW_MEM_HPP #define THREADS_ARG_THREADS_LOW_MEM_HPP +#include "Demography.hpp" #include "Matcher.hpp" #include "ThreadsFastLS.hpp" #include "ViterbiLowMem.hpp" -#include "Demography.hpp" #include #include #include #include class ThreadsLowMem { - -private: - Demography demography; - - // 2. HMM quantites - int hmm_sites_processed; - std::unordered_map hmms; - int match_group_idx; - std::vector match_groups; - - // 3. Path segment and path dating quantites - HMM psmc; - // std::vector cm_sizes; - // std::vector bp_sizes; - int het_sites_processed; - int n_hmm_samples = 100; - int hmm_min_sites = 10; - public: - // This object will only run the HMM for these ids - std::vector target_ids; - std::unordered_map expected_branch_lengths; - double mean_bp_size; - std::unordered_map segment_indices; - std::unordered_map paths; - int num_samples; - int num_sites; - double mutation_rate; - std::vector physical_positions; - std::vector genetic_positions; - std::vector bp_sizes; - std::vector cm_sizes; - std::vector bp_boundaries; - std::vector cm_boundaries; - bool sparse; - ThreadsLowMem(const std::vector _target_ids, const std::vector& _physical_positions, const std::vector& _genetic_positions, std::vector ne, std::vector ne_times, double _mutation_rate, bool _sparse); @@ -78,6 +43,39 @@ class ThreadsLowMem { std::tuple>, std::vector>, std::vector>, std::vector>> serialize_paths(); + +public: + // This object will only run the HMM for these ids + std::vector target_ids; + std::unordered_map expected_branch_lengths; + double mean_bp_size = 0.0; + std::unordered_map segment_indices; + std::unordered_map paths; + int num_samples = 0; + int num_sites = 0; + double mutation_rate = 0.0; + std::vector physical_positions; + std::vector genetic_positions; + std::vector bp_sizes; + std::vector cm_sizes; + std::vector bp_boundaries; + std::vector cm_boundaries; + bool sparse = false; + +private: + Demography demography; + + // 2. HMM quantites + int hmm_sites_processed = 0; + std::unordered_map hmms; + int match_group_idx = 0; + std::vector match_groups; + + // 3. Path segment and path dating quantites + HMM psmc; + int het_sites_processed = 0; + int n_hmm_samples = 100; + int hmm_min_sites = 10; }; #endif // THREADS_ARG_THREADS_LOW_MEM_HPP From c50d8a25f35e4b4de31173ac23c35fc9566c9f02 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 13:27:46 +0000 Subject: [PATCH 18/42] refactor: resolve ThreadsFastLS hpp/cpp warnings (#22) * Reorder class to methods-first and separate variables from methods * Doxygen friendly comments * Moved doxygen comments from cpp to hpp as it's common to have in latter * Ensure all member variables initialised * Ensure all member variables constructed in order * Replaced commented out debug code with #def (for review) * Replace size_t with std::size_t (not sure which headers bring in the former) * Removed unused/shado variables a_next and b_next * Resolve size_t/int warnings * Note around line 1328 - `i` variable duplicated, change to `j` (for review) * Some points for review on double to int conversion (use floor/ceil?) * Parenthesis to confirm operator precedence * Const correct where possible * Clang format --- src/ThreadsFastLS.cpp | 350 +++++++++++++++++------------------------- src/ThreadsFastLS.hpp | 196 +++++++++++++++-------- 2 files changed, 275 insertions(+), 271 deletions(-) diff --git a/src/ThreadsFastLS.cpp b/src/ThreadsFastLS.cpp index c9a1016..1c181c7 100644 --- a/src/ThreadsFastLS.cpp +++ b/src/ThreadsFastLS.cpp @@ -1,4 +1,5 @@ #include "ThreadsFastLS.hpp" + #include #include #include @@ -13,18 +14,26 @@ #include #include +namespace { + +const int END_ALLELE = 0; -int END_ALLELE = 0; +inline size_t pair_key(int i, int j) { + return (static_cast(i) << 32) | static_cast(j); +} -ThreadsFastLS::ThreadsFastLS(std::vector _physical_positions, std::vector _genetic_positions, - double _mutation_rate, std::vector ne, std::vector ne_times, - bool _sparse_sites, - int _n_prune, // Threshold for pruning states in the tdpbwt algorithm - bool _use_hmm, int _burn_in_left, int _burn_in_right) - : physical_positions(_physical_positions), genetic_positions(_genetic_positions), - mutation_rate(_mutation_rate), demography(Demography(ne, ne_times)), - sparse_sites(_sparse_sites), n_prune(_n_prune), use_hmm(_use_hmm), - burn_in_left(_burn_in_left), burn_in_right(_burn_in_right) { +} // namespace + +ThreadsFastLS::ThreadsFastLS(std::vector _physical_positions, + std::vector _genetic_positions, double _mutation_rate, + std::vector ne, std::vector ne_times, + bool _sparse_sites, + int _n_prune, // Threshold for pruning states in the tdpbwt algorithm + bool _use_hmm, int _burn_in_left, int _burn_in_right) + : n_prune(_n_prune), mutation_rate(_mutation_rate), burn_in_left(_burn_in_left), + burn_in_right(_burn_in_right), sparse_sites(_sparse_sites), use_hmm(_use_hmm), + physical_positions(_physical_positions), genetic_positions(_genetic_positions), + demography(Demography(ne, ne_times)) { if (physical_positions.size() != genetic_positions.size()) { std::cerr << "Map lengths don't match.\n"; exit(1); @@ -37,26 +46,28 @@ ThreadsFastLS::ThreadsFastLS(std::vector _physical_positions, std::vecto std::cerr << "Need a strictly positive mutation rate.\n"; exit(1); } - num_sites = physical_positions.size(); + num_sites = static_cast(physical_positions.size()); num_samples = 0; - // Check maps are strictly increasing - // for (int i = 0; i < num_sites - 1; i++) { - // if (physical_positions[i + 1] <= physical_positions[i]) { - // cerr << "Physical positions must be strictly increasing, found "; - // cerr << physical_positions[i + 1] << " after " << physical_positions[i] << endl; - // exit(1); - // } - // if (genetic_positions[i + 1] <= genetic_positions[i]) { - // cerr << "Genetic coordinates must be strictly increasing, found "; - // cerr << genetic_positions[i + 1] << " after " << genetic_positions[i] << endl; - // exit(1); - // } - // } + // FIXME Arni/Alex review. OK to remove or instead add an explicit macro? + // Set to 1 for runtime check that maps are strictly increasing +#if 0 + for (int i = 0; i < num_sites - 1; i++) { + if (physical_positions[i + 1] <= physical_positions[i]) { + cerr << "Physical positions must be strictly increasing, found "; + cerr << physical_positions[i + 1] << " after " << physical_positions[i] << endl; + exit(1); + } + if (genetic_positions[i + 1] <= genetic_positions[i]) { + cerr << "Genetic coordinates must be strictly increasing, found "; + cerr << genetic_positions[i + 1] << " after " << genetic_positions[i] << endl; + exit(1); + } + } +#endif // Initialize map burn-in threading_start = physical_positions.front() + burn_in_left; - // threading_end = physical_positions.back() - burn_in_right + 1; threading_end = physical_positions.back() - burn_in_right; trim_pos_start_idx = 0; for (int i = 0; i < num_sites; i++) { @@ -78,7 +89,8 @@ ThreadsFastLS::ThreadsFastLS(std::vector _physical_positions, std::vecto } } if (trim_pos_start_idx >= trim_pos_end_idx - 3) { - std::cerr << "Too few positions left after applying burn-in, need at least 3. Aborting." << std::endl; + std::cerr << "Too few positions left after applying burn-in, need at least 3. Aborting." + << std::endl; exit(1); } @@ -114,7 +126,7 @@ ThreadsFastLS::ThreadsFastLS(std::vector _physical_positions, std::vecto std::tuple, std::vector> ThreadsFastLS::site_sizes(std::vector positions) { // Find mid-points between sites - int M = positions.size(); + int M = static_cast(positions.size()); std::vector pos_means(M - 1); for (int i = 0; i < M - 1; i++) { pos_means[i] = (positions[i] + positions[i + 1]) / 2.; @@ -143,10 +155,7 @@ ThreadsFastLS::site_sizes(std::vector positions) { return std::tuple(boundaries, site_sizes); } -/** - * - */ -std::vector ThreadsFastLS::trimmed_positions() { +std::vector ThreadsFastLS::trimmed_positions() const { std::vector trim_pos = {physical_positions.cbegin() + trim_pos_start_idx, physical_positions.cbegin() + trim_pos_end_idx}; return trim_pos; @@ -159,14 +168,6 @@ void ThreadsFastLS::delete_hmm() { } } -/** - * @brief Find the next insert position - * - * @param t Pointer to node below the sequence being inserted at site i - * @param g Allele at site i+1 - * @param i The site - * @return Node* Pointer to node below the sequence being inserted at site i+1 - */ Node* ThreadsFastLS::extend_node(Node* t, bool g, int i) { Node* t_next; if (!g && t->w[g]->sample_ID == -1) { @@ -183,18 +184,13 @@ Node* ThreadsFastLS::extend_node(Node* t, bool g, int i) { void ThreadsFastLS::insert(const std::vector& genotype) { insert(num_samples, genotype); } -/** - * @brief Insert a new sequence into the dynamic panel - * - * @param genotype - */ void ThreadsFastLS::insert(const int ID, const std::vector& genotype) { if (ID_map.find(ID) != ID_map.end()) { std::cerr << "ID " << ID << " is already in the panel.\n"; exit(1); } - if (genotype.size() != num_sites) { + if (static_cast(genotype.size()) != num_sites) { std::cerr << "Number of input markers does not match map.\n"; exit(1); } @@ -272,12 +268,6 @@ void ThreadsFastLS::insert(const int ID, const std::vector& genotype) { } } -/** - * @brief Deletes sequence ID from the dynamic panel. This moves the last sequence in the panel - * to the position ID held. See alg 5 from d-PBWT paper. - * - * @param ID - */ void ThreadsFastLS::remove(int ID) { Node* s = panel[ID_map.at(ID)][0].get(); // The last sequence in the panel @@ -322,11 +312,7 @@ void ThreadsFastLS::remove(int ID) { num_samples--; } -/** - * @brief For debugging: print the sample-IDs of the arrayified panel. - * - */ -void ThreadsFastLS::print_sorting() { +void ThreadsFastLS::print_sorting() const { for (int j = 0; j < num_sites + 1; ++j) { Node* node = tops[j].get(); while (node != nullptr) { @@ -339,13 +325,8 @@ void ThreadsFastLS::print_sorting() { } } -/** - * Run Li-Stephens on input haplotype *without* inserting into the dynamic panel. - * See also Algorithm 4 of Lunter (2018), Bioinformatics. - * For imputation we use the IMPUTE/Beagle mutation penalties - */ std::pair ThreadsFastLS::fastLS(const std::vector& genotype, - bool imputation) { + bool imputation) { // Get mutation/recombination penalties; std::vector mu; std::vector mu_c; @@ -373,12 +354,11 @@ std::pair ThreadsFastLS::fastLS(const std::vector& // z holds the best current score double z; int max_states = 0; - bool allele; State best_extension = current_states.back(); for (int i = 0; i < num_sites; i++) { bool allele = genotype[i]; - int n_states = current_states.size(); + int n_states = static_cast(current_states.size()); max_states = std::max(n_states, max_states); if (n_states == 0) { std::cerr << "No states left on stack, something is messed up in the algorithm.\n"; @@ -449,8 +429,7 @@ std::pair ThreadsFastLS::fastLS(const std::vector& } // Pruning is turned off by default - if (n_prune >= 0 && i % 100 == 0 && new_states.size() >= n_prune) { - int old_size = new_states.size(); + if ((n_prune >= 0) && (i % 100 == 0) && (static_cast(new_states.size()) >= n_prune)) { StateTree tree = StateTree(new_states); tree.prune(); current_states = tree.dump(); @@ -467,18 +446,14 @@ std::pair ThreadsFastLS::fastLS(const std::vector& [](const auto& s1, const auto& s2) { return s1.score < s2.score; })); if ((num_samples + 1) % 100 == 0) { - std::cout << "Found best path with score " << min_state.score << " for sequence " << num_samples + 1; + std::cout << "Found best path with score " << min_state.score << " for sequence " + << num_samples + 1; std::cout << ", using a maximum of " << max_states << " states.\n"; } return std::pair(min_state.traceback, min_state.below->above); } -/** - * Run Li-Stephens on input diplotype *without* inserting into the dynamic panel. - * See also Algorithm 4 of Lunter (2018), Bioinformatics. - * Warning: The code here is more verbose than it has to be - **/ std::array, 2> ThreadsFastLS::fastLS_diploid(const std::vector& genotype) { // Get mutation/recombination penalties; @@ -506,7 +481,6 @@ ThreadsFastLS::fastLS_diploid(const std::vector& genotype) { // z holds the best current score for pairs and individual sequences double z; int max_state_pairs = 0; - bool allele; StatePair best_pair = current_pairs.back(); bool extensible_a0; bool extensible_a1; @@ -516,7 +490,7 @@ ThreadsFastLS::fastLS_diploid(const std::vector& genotype) { // Just like haploid, we iterate through sites for (int i = 0; i < num_sites; i++) { int allele = genotype[i]; - int n_state_pairs = current_pairs.size(); + int n_state_pairs = static_cast(current_pairs.size()); std::vector new_pairs; max_state_pairs = std::max(n_state_pairs, max_state_pairs); if (n_state_pairs == 0) { @@ -571,13 +545,13 @@ ThreadsFastLS::fastLS_diploid(const std::vector& genotype) { } // Set local minima, this maps (anchor, traceback) to a score - std::unordered_map local_min; - std::unordered_map extmap_0; - std::unordered_map extmap_1; + std::unordered_map local_min; + std::unordered_map extmap_0; + std::unordered_map extmap_1; for (StatePair& p : current_pairs) { - size_t key_a = pair_key(p.below_a->above->sample_ID, p.traceback_a->site); - size_t key_b = pair_key(p.below_b->above->sample_ID, p.traceback_b->site); + std::size_t key_a = pair_key(p.below_a->above->sample_ID, p.traceback_a->site); + std::size_t key_b = pair_key(p.below_b->above->sample_ID, p.traceback_b->site); double z_pair; // Set/get extensibility @@ -665,16 +639,14 @@ ThreadsFastLS::fastLS_diploid(const std::vector& genotype) { } // START OF MAIN EXTENSION LOOP - std::unordered_map new_local_min; + std::unordered_map new_local_min; for (StatePair& p : current_pairs) { bool extended = false; - size_t key_a = pair_key(p.below_a->above->sample_ID, p.traceback_a->site); - size_t key_b = pair_key(p.below_b->above->sample_ID, p.traceback_b->site); + std::size_t key_a = pair_key(p.below_a->above->sample_ID, p.traceback_a->site); + std::size_t key_b = pair_key(p.below_b->above->sample_ID, p.traceback_b->site); double z_a = local_min.at(key_a); double z_b = local_min.at(key_b); - Node* a_next; - Node* b_next; extensible_a0 = extmap_0.at(key_a); extensible_a1 = extmap_1.at(key_a); extensible_b0 = extmap_0.at(key_b); @@ -687,8 +659,8 @@ ThreadsFastLS::fastLS_diploid(const std::vector& genotype) { if (case1_cost <= std::min({z_a + rho_delta, z_b + rho_delta, z + 2 * rho_delta})) { if (allele == 0) { if (extensible_a0 && extensible_b0) { - a_next = extend_node(p.below_a, 0, i); - b_next = extend_node(p.below_b, 0, i); + Node* a_next = extend_node(p.below_a, 0, i); + Node* b_next = extend_node(p.below_b, 0, i); new_pairs.emplace_back(a_next, b_next, case1_cost, p.traceback_a, p.traceback_b); added_1a.push_back(a_next); added_1b.push_back(b_next); @@ -697,16 +669,16 @@ ThreadsFastLS::fastLS_diploid(const std::vector& genotype) { } else if (allele == 1) { if (extensible_a0 && extensible_b1) { - a_next = extend_node(p.below_a, 0, i); - b_next = extend_node(p.below_b, 1, i); + Node* a_next = extend_node(p.below_a, 0, i); + Node* b_next = extend_node(p.below_b, 1, i); new_pairs.emplace_back(a_next, b_next, case1_cost, p.traceback_a, p.traceback_b); added_1a.push_back(a_next); added_1b.push_back(b_next); extended = true; } if (extensible_a1 && extensible_b0) { - a_next = extend_node(p.below_a, 1, i); - b_next = extend_node(p.below_b, 0, i); + Node* a_next = extend_node(p.below_a, 1, i); + Node* b_next = extend_node(p.below_b, 0, i); new_pairs.emplace_back(a_next, b_next, case1_cost, p.traceback_a, p.traceback_b); added_1a.push_back(a_next); added_1b.push_back(b_next); @@ -715,8 +687,8 @@ ThreadsFastLS::fastLS_diploid(const std::vector& genotype) { } else { if (extensible_a1 && extensible_b1) { - a_next = extend_node(p.below_a, 1, i); - b_next = extend_node(p.below_b, 1, i); + Node* a_next = extend_node(p.below_a, 1, i); + Node* b_next = extend_node(p.below_b, 1, i); new_pairs.emplace_back(a_next, b_next, case1_cost, p.traceback_a, p.traceback_b); added_1a.push_back(a_next); added_1b.push_back(b_next); @@ -729,7 +701,7 @@ ThreadsFastLS::fastLS_diploid(const std::vector& genotype) { local_min[key_a] = std::min(z_a, case1_cost); local_min[key_b] = std::min(z_b, case1_cost); for (auto a1 : added_1a) { - size_t new_key_a = pair_key(a1->above->sample_ID, p.traceback_a->site); + std::size_t new_key_a = pair_key(a1->above->sample_ID, p.traceback_a->site); if (new_local_min.count(new_key_a)) { new_local_min[new_key_a] = std::min(new_local_min.at(new_key_a), case1_cost); } @@ -738,7 +710,7 @@ ThreadsFastLS::fastLS_diploid(const std::vector& genotype) { } } for (auto b1 : added_1b) { - size_t new_key_b = pair_key(b1->above->sample_ID, p.traceback_b->site); + std::size_t new_key_b = pair_key(b1->above->sample_ID, p.traceback_b->site); if (new_local_min.count(new_key_b)) { new_local_min[new_key_b] = std::min(new_local_min.at(new_key_b), case1_cost); } @@ -797,7 +769,7 @@ ThreadsFastLS::fastLS_diploid(const std::vector& genotype) { local_min[key_a] = std::min(local_min.at(key_a), case2_cost); local_min[key_b] = std::min(local_min.at(key_b), case2_cost); for (auto a2 : added_2a) { - size_t new_key_a = pair_key(a2->above->sample_ID, p.traceback_a->site); + std::size_t new_key_a = pair_key(a2->above->sample_ID, p.traceback_a->site); if (new_local_min.count(new_key_a)) { new_local_min[new_key_a] = std::min(new_local_min.at(new_key_a), case2_cost); } @@ -806,7 +778,7 @@ ThreadsFastLS::fastLS_diploid(const std::vector& genotype) { } } for (auto b2 : added_2b) { - size_t new_key_b = pair_key(b2->above->sample_ID, p.traceback_b->site); + std::size_t new_key_b = pair_key(b2->above->sample_ID, p.traceback_b->site); if (new_local_min.count(new_key_b)) { new_local_min[new_key_b] = std::min(new_local_min.at(new_key_b), case2_cost); } @@ -867,7 +839,7 @@ ThreadsFastLS::fastLS_diploid(const std::vector& genotype) { local_min[key_a] = std::min(local_min.at(key_a), case3_cost); local_min[key_b] = std::min(local_min.at(key_b), case3_cost); for (auto a3 : added_3a) { - size_t new_key_a = pair_key(a3->above->sample_ID, p.traceback_a->site); + std::size_t new_key_a = pair_key(a3->above->sample_ID, p.traceback_a->site); if (new_local_min.count(new_key_a)) { new_local_min[new_key_a] = std::min(new_local_min.at(new_key_a), case3_cost); } @@ -876,7 +848,7 @@ ThreadsFastLS::fastLS_diploid(const std::vector& genotype) { } } for (auto b3 : added_3b) { - size_t new_key_b = pair_key(b3->above->sample_ID, p.traceback_b->site); + std::size_t new_key_b = pair_key(b3->above->sample_ID, p.traceback_b->site); if (new_local_min.count(new_key_b)) { new_local_min[new_key_b] = std::min(new_local_min.at(new_key_b), case3_cost); } @@ -896,12 +868,12 @@ ThreadsFastLS::fastLS_diploid(const std::vector& genotype) { } // SINGLE RECOMBINATION EVENTS - std::unordered_set already_recombined; + std::unordered_set already_recombined; std::vector rec_pairs; for (StatePair& p : new_pairs) { - size_t key_a = pair_key(p.below_a->above->sample_ID, p.traceback_a->site); - size_t key_b = pair_key(p.below_b->above->sample_ID, p.traceback_b->site); + std::size_t key_a = pair_key(p.below_a->above->sample_ID, p.traceback_a->site); + std::size_t key_b = pair_key(p.below_b->above->sample_ID, p.traceback_b->site); double recombinant_score = p.score - rho_c[i] + rho[i]; if (!already_recombined.count(key_a) && std::abs(new_local_min.at(key_a) - p.score) < 0.0001) { @@ -967,12 +939,8 @@ ThreadsFastLS::fastLS_diploid(const std::vector& genotype) { std::pair(min_pair.traceback_b, min_pair.below_b->above)}; } -/** - * This is a basic traceback that samples a random haplotype per from all matches per segment and - * also stores the lowest-numbered match (for compression) - */ -std::vector>> ThreadsFastLS::traceback(TracebackState* tb, Node* match, - bool return_all) { +std::vector>> +ThreadsFastLS::traceback(TracebackState* tb, Node* match, bool return_all) { std::vector>> best_path; while (tb != nullptr) { int n_matches = 1; @@ -1000,7 +968,7 @@ std::vector>> ThreadsFastLS::traceback(Tracebac sampled_states = std::vector(div_states.begin(), div_states.end()); } else { - std::uniform_int_distribution<> distrib(0, div_states.size() - 1); + std::uniform_int_distribution<> distrib(0, static_cast(div_states.size()) - 1); sampled_states.reserve(2); std::sample(div_states.begin(), div_states.end(), std::back_inserter(sampled_states), 1, rng); // Add the min-state as well @@ -1016,13 +984,9 @@ std::vector>> ThreadsFastLS::traceback(Tracebac return best_path; } -/** - * Similar to normal traceback, but picks the up-to neighborhood_size best matches and stores their overlap with the - * input sequence returns a list of a tuple of lists :-P I.e., a list of segments, and each segment - * is a tuple (sample_IDs, starts, ends) all of equal length <= neighborhood_size - */ std::vector, std::vector, std::vector>> -ThreadsFastLS::traceback_impute(std::vector& genotypes, TracebackState* tb, Node* match, int neighborhood_size) { +ThreadsFastLS::traceback_impute(std::vector& genotypes, TracebackState* tb, Node* match, + int neighborhood_size) { std::vector, std::vector, std::vector>> imputation_path; int prev_end = num_sites; while (tb != nullptr) { @@ -1070,21 +1034,22 @@ ThreadsFastLS::traceback_impute(std::vector& genotypes, TracebackState* tb } // initialize original index locations - std::vector idx(overlaps.size()); + std::vector idx(overlaps.size()); std::iota(idx.begin(), idx.end(), 0); // sort indexes based on comparing values in v // using std::stable_sort instead of std::sort // to avoid unnecessary index re-orderings // when v contains elements of equal values - std::stable_sort(idx.begin(), idx.end(), [&overlaps](size_t i1, size_t i2) { + std::stable_sort(idx.begin(), idx.end(), [&overlaps](std::size_t i1, std::size_t i2) { return overlaps[i1].second - overlaps[i1].first < overlaps[i2].second - overlaps[i2].first; }); std::vector segment_starts; std::vector sample_ids; std::vector segment_ends; - for (int j = idx.size() - 1; j >= std::max(0, (int) (idx.size() - neighborhood_size)); j--) { + for (int j = static_cast(idx.size()) - 1; + j >= std::max(0, static_cast(idx.size()) - neighborhood_size); j--) { segment_starts.push_back(segment_start); segment_ends.push_back(segment_end); sample_ids.push_back(div_states[idx[j]]); @@ -1098,16 +1063,6 @@ ThreadsFastLS::traceback_impute(std::vector& genotypes, TracebackState* tb return imputation_path; } -/** - * @brief Determine whether state can be extended through panel by appending g. - * May alter - * @param s State at site i - * @param t_next Node at site i+1 - * @param g Candidate genotype for s at i+1 - * @param i The site index - * @return true - * @return false - */ bool ThreadsFastLS::extensible_by(State& s, const Node* t_next, const bool g, const int i) { int next_above_candidate = t_next->above->sample_ID; @@ -1141,7 +1096,7 @@ std::tuple, std::vector> ThreadsFastLS::mutation_pen std::vector mu_c(num_sites); double mean_bp_size = - (double) (physical_positions.back() - physical_positions[0]) / (double) num_sites; + (physical_positions.back() - physical_positions[0]) / static_cast(num_sites); // The expected branch length const double t = demography.expected_branch_length(num_samples + 1); @@ -1155,11 +1110,6 @@ std::tuple, std::vector> ThreadsFastLS::mutation_pen return std::tuple(mu, mu_c); } -/** - * @brief This gives the IMPUTE5 (and Beagle) recombination penalties - * - * @return tuple of penalty vectors - */ std::tuple, std::vector> ThreadsFastLS::mutation_penalties_impute5() { std::vector mu(num_sites); std::vector mu_c(num_sites); @@ -1173,11 +1123,6 @@ std::tuple, std::vector> ThreadsFastLS::mutation_pen return std::tuple(mu, mu_c); } -/** - * @brief This gives the *sparse* recombination penalties - * - * @return tuple of penalty vectors - */ std::tuple, std::vector> ThreadsFastLS::recombination_penalties() { // Recall: 1cM means the expected average number of intervening // chromosomal crossovers in a single generation is 0.01 @@ -1199,12 +1144,8 @@ std::tuple, std::vector> ThreadsFastLS::recombinatio return std::tuple(rho, rho_c); } -/** - * @brief This gives the correct, dense, recombination penalties - * - * @return tuple of penalty vectors - */ -std::tuple, std::vector> ThreadsFastLS::recombination_penalties_correct() { +std::tuple, std::vector> +ThreadsFastLS::recombination_penalties_correct() { // Recall: 1cM means the expected average number of intervening // chromosomal crossovers in a single generation is 0.01 std::vector rho(num_sites); @@ -1225,51 +1166,41 @@ std::tuple, std::vector> ThreadsFastLS::recombinatio return std::tuple(rho, rho_c); } -/** - * @brief Date the segment based on length and n_mismatches using maximum likelihood. (No - * demography) - * - * @param id1 - * @param id2 - * @param start inclusive - * @param end exclusive - * @return double - */ double ThreadsFastLS::date_segment(const int num_het_sites, const int start, const int end) { if (start > end) { std::cerr << "Can't date a segment with length <= 0\n"; exit(1); } - double m = (double) num_het_sites; double bp_size = 0; double cm_size = 0; for (int i = start; i < end; i++) { bp_size += bp_sizes[i]; cm_size += cm_sizes[i]; } - double mu = 2. * mutation_rate * bp_size; - double rho = 2. * 0.01 * cm_size; if (sparse_sites) { return ThreadsFastLS::date_segment_sparse(num_het_sites, cm_size, demography); } else { - return ThreadsFastLS::date_segment(m, cm_size, bp_size, mutation_rate, demography); + // FIXME Alex/Arni review - removed old 'm' variable here, confirm double not needed + return ThreadsFastLS::date_segment(num_het_sites, cm_size, bp_size, mutation_rate, demography); } } double ThreadsFastLS::date_segment(int num_het_sites, double cm_size, double bp_size, - double mutation_rate, Demography& demography) { + double mutation_rate, Demography& demography) { int m = num_het_sites; double mu = 2. * mutation_rate * bp_size; double rho = 2. * 0.01 * cm_size; if (m > 15) { - // cout << "Warning: very many heterozygous sites, defaulting to const-demography method.\n"; + // FIXME Alex/Arni - I have removed many couts but were they still needed for debug? If so I can + // put a #def in cout << "Warning: very many heterozygous sites, defaulting to const-demography + // method.\n"; double gamma = 1. / demography.expected_time; return (m + 2) / (gamma + rho + mu); } double numerator = 0; double denominator = 0; - int K = demography.times.size(); + int K = static_cast(demography.times.size()); for (int k = 0; k < K; k++) { double T1 = demography.times[k]; double gamma_k = 1. / demography.sizes[k]; @@ -1296,12 +1227,16 @@ double ThreadsFastLS::date_segment(int num_het_sites, double cm_size, double bp_ return numerator / denominator; } -double ThreadsFastLS::date_segment_sparse(int num_het_sites, double cm_size, Demography& demography) { - int m = num_het_sites; +double ThreadsFastLS::date_segment_sparse(int num_het_sites, double cm_size, + Demography& demography) { + + // FIXME Arni/Alex review num_het_sites is not used. Remove from args? + (void) num_het_sites; + double rho = 2. * 0.01 * cm_size; double numerator = 0; double denominator = 0; - int K = demography.times.size(); + int K = static_cast(demography.times.size()); for (int k = 0; k < K; k++) { double T1 = demography.times[k]; double gamma_k = 1. / demography.sizes[k]; @@ -1366,9 +1301,10 @@ ThreadsFastLS::thread(const int new_sample_ID, const std::vector& genotype std::vector segment_ages; int total_num_het_sites = 0; // Date segments - for (int i = 0; i < best_path.size(); i++) { + for (int i = 0; i < static_cast(best_path.size()); i++) { int segment_start = std::get<0>(best_path[i]); - int segment_end = (i == best_path.size() - 1) ? num_sites : std::get<0>(best_path[i + 1]); + int segment_end = + (i == (static_cast(best_path.size()) - 1)) ? num_sites : std::get<0>(best_path[i + 1]); std::vector target_ID_L = std::get<1>(best_path[i]); std::vector het_hom_sites = @@ -1381,17 +1317,23 @@ ThreadsFastLS::thread(const int new_sample_ID, const std::vector& genotype } } total_num_het_sites += num_het_sites; - // is it ok to have 100 here? + + // FIXME Alex/Arni review - work in progress, but just checking if these numbers should be + // consts declared above is it ok to have 100 here? if (use_hmm && num_samples < 1000) { // is it ok to have 10 here? if (num_het_sites > 5) { std::vector breakpoints = hmm->breakpoints(het_hom_sites, segment_start); - for (int i = 0; i < breakpoints.size(); i++) { - int breakpoint_start = breakpoints[i]; - int breakpoint_end = (i == breakpoints.size() - 1) ? segment_end : breakpoints[i + 1]; + // FIXME Alex/Arni review - was 'i' but dangerous as shadowing out loop, changed to 'j', + // confirm ok. + for (int j = 0; j < static_cast(breakpoints.size()); j++) { + int breakpoint_start = breakpoints[j]; + int breakpoint_end = + (j == (static_cast(breakpoints.size()) - 1)) ? segment_end : breakpoints[j + 1]; target_IDs.push_back(target_ID_L); bp_starts.push_back(static_cast(ceil(bp_boundaries[breakpoint_start]))); + // FIXME Alex/Arni review - just spotted, checking on context for comment // This is wrong!!! need to actually re-do num het_sites!!!! segment_ages.push_back(date_segment(num_het_sites, breakpoint_start, breakpoint_end)); } @@ -1414,7 +1356,8 @@ ThreadsFastLS::thread(const int new_sample_ID, const std::vector& genotype return remove_burn_in(bp_starts, target_IDs, segment_ages, het_sites); } -std::vector ThreadsFastLS::impute(std::vector& genotype, int neighborhood_size) { +std::vector ThreadsFastLS::impute(std::vector& genotype, + int neighborhood_size) { // vector of sample_ids, seg_starts, seg_ends (buffered) std::vector, std::vector, std::vector>> best_path; Node* match; @@ -1434,7 +1377,7 @@ std::vector ThreadsFastLS::impute(std::vector& genotype seg_ages.push_back(date_segment(0, seg_start, seg_end)); } - int num_segs = best_path.size(); + int num_segs = static_cast(best_path.size()); std::vector imputation_segments; // Special case for the first segment @@ -1443,13 +1386,17 @@ std::vector ThreadsFastLS::impute(std::vector& genotype const std::tuple, std::vector, std::vector>& segment = best_path[i]; const std::vector& samples = std::get<0>(segment); ImputationSegment imp_seg; - imp_seg.seg_start = physical_positions[std::get<1>(segment)[0]]; + // FIXME Alex/Arni review double to int conversion OK? Should it be ceil/floor/round? + imp_seg.seg_start = static_cast(physical_positions[std::get<1>(segment)[0]]); imp_seg.ids = samples; std::vector wts; std::vector ages(samples.size(), seg_ages[i]); imp_seg.ages = ages; for (auto s : samples) { - wts.push_back(1. / samples.size()); + // FIXME Alex/Arni review, s not used, just change to regular for loop for now? + (void) s; + + wts.push_back(1. / static_cast(samples.size())); } imp_seg.weights = wts; imputation_segments.push_back(imp_seg); @@ -1470,9 +1417,10 @@ ThreadsFastLS::diploid_ls(std::vector unphased_genotypes) { } std::tuple, std::vector>, std::vector, std::vector> -ThreadsFastLS::remove_burn_in(std::vector& bp_starts, std::vector>& target_IDs, - std::vector& segment_ages, std::vector& het_sites) { - int num_segments = bp_starts.size(); +ThreadsFastLS::remove_burn_in(std::vector& bp_starts, + std::vector>& target_IDs, + std::vector& segment_ages, std::vector& het_sites) { + int num_segments = static_cast(bp_starts.size()); std::vector trim_starts; std::vector> trim_IDs; @@ -1482,7 +1430,8 @@ ThreadsFastLS::remove_burn_in(std::vector& bp_starts, std::vector(threading_end) : bp_starts[i + 1]; if (threading_start < seg_end) { break; } @@ -1500,8 +1449,12 @@ ThreadsFastLS::remove_burn_in(std::vector& bp_starts, std::vector(threading_start); trim_IDs = {target_IDs.begin() + seg_start_i, target_IDs.begin() + seg_end_i}; trim_ages = {segment_ages.begin() + seg_start_i, segment_ages.begin() + seg_end_i}; } @@ -1515,16 +1468,8 @@ ThreadsFastLS::remove_burn_in(std::vector& bp_starts, std::vector ThreadsFastLS::overflow_region(const std::vector& genotypes, - const int sample_id, const int segment_start, - const int segment_end) { + const int sample_id, const int segment_start, + const int segment_end) { int overlap_start = segment_start; int overlap_end = segment_end; @@ -1569,11 +1510,8 @@ std::pair ThreadsFastLS::overflow_region(const std::vector& geno return std::pair(overlap_start, overlap_end); } -/** - * Fetch het-hom status for id1 and id2 in the region specified by site indices - */ std::vector ThreadsFastLS::fetch_het_hom_sites(const int id1, const int id2, const int start, - const int end) { + const int end) { if (ID_map.find(id1) == ID_map.end()) { std::cerr << "fetch_het_hom_sites bad id1 " << id1 << std::endl; exit(1); @@ -1593,22 +1531,24 @@ std::vector ThreadsFastLS::fetch_het_hom_sites(const int id1, const int id } // Given threading instructions, find all heterozygous sites -std::vector ThreadsFastLS::het_sites_from_thread(const int focal_ID, - const std::vector bp_starts, - const std::vector> target_IDs) { +std::vector +ThreadsFastLS::het_sites_from_thread(const int focal_ID, const std::vector bp_starts, + const std::vector> target_IDs) { std::vector het_sites; - int num_segments = bp_starts.size(); + int num_segments = static_cast(bp_starts.size()); int site_i = 0; for (int seg_i = 0; seg_i < num_segments; seg_i++) { int segment_start = bp_starts[seg_i]; - int segment_end = - seg_i == num_segments - 1 ? physical_positions.back() + 1 : bp_starts[seg_i + 1]; + // FIXME Arni/Alex review - double to int OK, floor/ceil/round? + int segment_end = seg_i == num_segments - 1 ? (static_cast(physical_positions.back()) + 1) + : bp_starts[seg_i + 1]; int target_ID = target_IDs[seg_i][0]; while (segment_start <= physical_positions[site_i] && physical_positions[site_i] < segment_end && site_i < num_sites) { if (panel[ID_map.at(focal_ID)][site_i]->genotype != panel[ID_map.at(target_ID)][site_i]->genotype) { - het_sites.push_back(physical_positions[site_i]); + // FIXME Arni/Alex review - double to int OK, floor/ceil/round? + het_sites.push_back(static_cast(physical_positions[site_i])); } site_i++; } diff --git a/src/ThreadsFastLS.hpp b/src/ThreadsFastLS.hpp index 0193c30..0400e72 100644 --- a/src/ThreadsFastLS.hpp +++ b/src/ThreadsFastLS.hpp @@ -1,8 +1,8 @@ #ifndef THREADS_ARG_THREADS_HPP #define THREADS_ARG_THREADS_HPP -#include "State.hpp" #include "HMM.hpp" +#include "State.hpp" #include #include @@ -12,90 +12,79 @@ struct ImputationSegment { int seg_start = 0; std::vector ids; + // these are at the *start* of the segment std::vector weights; std::vector ages; }; -// This class contains everything for Threads-fastLS +/// This class contains everything for Threads-fastLS class ThreadsFastLS { - -private: - // To access the linked lists in each column - std::vector> tops; - std::vector> bottoms; // Ha, ha - - std::vector> traceback_states; - - // Burn-in quantities - int trim_pos_start_idx = 0; - int trim_pos_end_idx = 0; - - // TODO set random seed at runtime (ticket #20) - std::mt19937 rng{1234}; - - inline size_t pair_key(int i, int j) { - return (size_t) i << 32 | (unsigned int) j; - } +public: + // Constructors and utils + ThreadsFastLS(std::vector _physical_positions, std::vector _genetic_positions, + double _mutation_rate, double ne, bool _sparse_sites, int _n_prune, bool _use_hmm, + int _burn_in_left, int _burn_in_right) + : ThreadsFastLS(_physical_positions, _genetic_positions, _mutation_rate, + std::vector{ne}, std::vector{0.0}, _sparse_sites, _n_prune, + _use_hmm, _burn_in_left, _burn_in_right){}; + ThreadsFastLS(std::vector _physical_positions, std::vector _genetic_positions, + double _mutation_rate, std::vector ne, std::vector ne_times, + bool _sparse_sites, int _n_prune, bool _use_hmm, int _burn_in_left, + int _burn_in_right); + + /// Find the next insert position + /// @param t Pointer to node below the sequence being inserted at site i + /// @param g Allele at site i+1 + /// @param i The site + /// @return Node* Pointer to node below the sequence being inserted at site i+1 Node* extend_node(Node* node, bool genotype, const int i); + + // FIXME Alex/Arni confirm meaning of "May alter" below, also my change to return comment + /// Determine whether state can be extended through panel by appending g. + /// May alter + /// @param s State at site i + /// @param t_next Node at site i+1 + /// @param g Candidate genotype for s at i+1 + /// @param i The site index + /// @return bool true if extensible bool extensible_by(State& s, const Node* t_next, const bool g, const int i); + std::pair pair_extensible_by(StatePair& p, const bool g, const int i); + + /// @param id1 + /// @param id2 + /// @param start inclusive! + /// @param end exclusive! + /// @return bool whether sequences match on the interval bool genotype_interval_match(const int id1, const int id2, const int start, const int end); + + /// Assuming input genotypes match sample_id on [segment_start, segment_end), how much can we + /// extend the region in either direction with out hitting a mismatch std::pair overflow_region(const std::vector& genotypes, const int sample_id, const int segment_start, const int segment_end); - std::vector fetch_het_hom_sites(const int id1, const int id2, const int start, const int end); - std::vector het_sites_from_thread(const int focal_ID, std::vector bp_starts, - std::vector> target_IDs); - -public: - int n_prune; - int num_sites; - int num_samples; - double mutation_rate; - int burn_in_left; - int burn_in_right; - double threading_start; - double threading_end; - // This determines the segment dating formula - bool sparse_sites; - // Whether to internally break up big segments - bool use_hmm; - std::unordered_map ID_map; - std::vector physical_positions; - std::vector genetic_positions; - std::vector bp_sizes; - std::vector cm_sizes; - std::vector bp_boundaries; - std::vector cm_boundaries; - Demography demography; - HMM* hmm; - // The dynamic reference panel - std::vector>> panel; + /// Fetch het-hom status for id1 and id2 in the region specified by site indices + std::vector fetch_het_hom_sites(const int id1, const int id2, const int start, + const int end); - // Constructors and utils - ThreadsFastLS(std::vector _physical_positions, std::vector _genetic_positions, - double _mutation_rate, double ne, bool _sparse_sites, int _n_prune, bool _use_hmm, - int _burn_in_left, int _burn_in_right) - : ThreadsFastLS(_physical_positions, _genetic_positions, _mutation_rate, std::vector{ne}, - std::vector{0.0}, _sparse_sites, _n_prune, _use_hmm, _burn_in_left, - _burn_in_right){}; - ThreadsFastLS(std::vector _physical_positions, std::vector _genetic_positions, - double _mutation_rate, std::vector ne, std::vector ne_times, - bool _sparse_sites, int _n_prune, bool _use_hmm, int _burn_in_left, int _burn_in_right); + std::vector het_sites_from_thread(const int focal_ID, std::vector bp_starts, + std::vector> target_IDs); static std::tuple, std::vector> site_sizes(std::vector positions); // More attributes - std::vector trimmed_positions(); + std::vector trimmed_positions() const; - // Insertion/deletion - // Insert and assign generic ID + /// Insert and assign generic ID void insert(const std::vector& genotype); - // Insert and assign specific ID + + /// Insert a new sequence into the dynamic panel and assign specific ID void insert(const int ID, const std::vector& genotype); - // Remove sample from panel + + /// Deletes sequence ID from the dynamic panel. This moves the last sequence in the panel + /// to the position ID held. See alg 5 from d-PBWT paper. void remove(int ID); // HMM @@ -112,27 +101,102 @@ class ThreadsFastLS { std::vector>> threads_ls(const std::vector& genotype); std::vector impute(std::vector& genotype, int neighborhood_size); + + /// Run Li-Stephens on input haplotype *without* inserting into the dynamic panel. + /// See also Algorithm 4 of Lunter (2018), Bioinformatics. + /// For imputation we use the IMPUTE/Beagle mutation penalties std::pair fastLS(const std::vector& genotype, bool imputation = false); + + /// This is a basic traceback that samples a random haplotype per from all matches per segment and + /// also stores the lowest-numbered match (for compression) std::vector>> traceback(TracebackState* tb, Node* match, bool return_all = false); + + /// Similar to normal traceback, but picks the up-to neighborhood_size best matches and stores + /// their overlap with the input sequence returns a list of a tuple of lists :-P I.e., a list of + /// segments, and each segment is a tuple (sample_IDs, starts, ends) all of equal length <= + /// neighborhood_size std::vector, std::vector, std::vector>> - traceback_impute(std::vector& genotypes, TracebackState* tb, Node* match, int neighborhood_size); + traceback_impute(std::vector& genotypes, TracebackState* tb, Node* match, + int neighborhood_size); + + /// Run Li-Stephens on input diplotype *without* inserting into the dynamic panel. + /// See also Algorithm 4 of Lunter (2018), Bioinformatics. + /// Warning: The code here is more verbose than it has to be std::array, 2> fastLS_diploid(const std::vector& genotype); + std::array>>, 2> diploid_ls(std::vector unphased_genotypes); + + /// This gives the IMPUTE5 (and Beagle) recombination penalties + /// @return tuple of penalty vectors std::tuple, std::vector> mutation_penalties_impute5(); + + /// This gives the *sparse* recombination penalties + /// @return tuple of penalty vectors std::tuple, std::vector> recombination_penalties(); std::tuple, std::vector> mutation_penalties(); + + /// This gives the correct, dense, recombination penalties + /// @return tuple of penalty vectors std::tuple, std::vector> recombination_penalties_correct(); // TMRCA estimation + /// Date the segment based on length and n_mismatches using maximum likelihood. (No + /// demography) + /// @param id1 + /// @param id2 + /// @param start inclusive + /// @param end exclusive + /// @return double double date_segment(const int num_het_sites, const int start, const int end); + static double date_segment(int num_het_sites, double cm_length, double bp_length, double mutation_rate, Demography& demography); static double date_segment_sparse(int num_het_sites, double cm_length, Demography& demography); - // Debugging - void print_sorting(); + + /// For debugging: print the sample-IDs of the arrayified panel + void print_sorting() const; + +public: + int n_prune = 0; + int num_sites = 0; + int num_samples = 0; + double mutation_rate = 0.0; + int burn_in_left = 0; + int burn_in_right = 0; + double threading_start = 0.0; + double threading_end = 0.0; + + bool sparse_sites = false; ///< This determines the segment dating formula + bool use_hmm = false; ///< Whether to internally break up big segments + + std::unordered_map ID_map; + std::vector physical_positions; + std::vector genetic_positions; + std::vector bp_sizes; + std::vector cm_sizes; + std::vector bp_boundaries; + std::vector cm_boundaries; + Demography demography; + HMM* hmm = nullptr; + + // The dynamic reference panel + std::vector>> panel; + +private: + // To access the linked lists in each column + std::vector> tops; + std::vector> bottoms; + std::vector> traceback_states; + + // Burn-in quantities + int trim_pos_start_idx = 0; + int trim_pos_end_idx = 0; + + // TODO set random seed at runtime (ticket #20) + std::mt19937 rng{1234}; }; #endif // THREADS_ARG_THREADS_HPP From ec30348b050e3ec08665bb5b057ae612ca983464 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 13:29:25 +0000 Subject: [PATCH 19/42] build: enable warnings as errors in build (#22) * Note that `-Wsign-conversion` is disabled to avoid changing too much code; need to review what values should be int --- CMakeLists.txt | 4 +--- setup.py | 2 +- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 60d9b8b..e6083ba 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -16,9 +16,7 @@ include(cmake/ProjectSettings.cmake) # Link this 'library' to use the warnings specified in CompilerWarnings.cmake add_library(project_warnings INTERFACE) include(cmake/CompilerWarnings.cmake) - -# FIXME Uncomment to enable warnings -#set_project_warnings(project_warnings) +set_project_warnings(project_warnings) # Sanitiser options if supported by compiler include(cmake/Sanitisers.cmake) diff --git a/setup.py b/setup.py index 1823220..07dd034 100644 --- a/setup.py +++ b/setup.py @@ -46,7 +46,7 @@ def build_extension(self, ext): f"-DCMAKE_LIBRARY_OUTPUT_DIRECTORY={extdir}", f"-DPYTHON_EXECUTABLE={sys.executable}", f"-DCMAKE_BUILD_TYPE={cfg}", - "-DWARNINGS_AS_ERRORS=OFF", + "-DWARNINGS_AS_ERRORS=ON", "-DENABLE_TESTING=OFF", "-DBoost_NO_BOOST_CMAKE=ON", # from arni: o/w boost 1.74 gets confused re. mtx "-DMAKE_DOCS=OFF" From 7460238266e71647e87d16133411bb1e82685eae Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 13:32:19 +0000 Subject: [PATCH 20/42] docs: add GNU v3 license (#22) --- LICENSE | 674 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 674 insertions(+) create mode 100644 LICENSE diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..f288702 --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. We, the Free Software Foundation, use the +GNU General Public License for most of our software; it applies also to +any other work released this way by its authors. You can apply it to +your programs, too. + + When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + + To protect your rights, we need to prevent others from denying you +these rights or asking you to surrender the rights. Therefore, you have +certain responsibilities if you distribute copies of the software, or if +you modify it: responsibilities to respect the freedom of others. + + For example, if you distribute copies of such a program, whether +gratis or for a fee, you must pass on to the recipients the same +freedoms that you received. You must make sure that they, too, receive +or can get the source code. And you must show them these terms so they +know their rights. + + Developers that use the GNU GPL protect your rights with two steps: +(1) assert copyright on the software, and (2) offer you this License +giving you legal permission to copy, distribute and/or modify it. + + For the developers' and authors' protection, the GPL clearly explains +that there is no warranty for this free software. For both users' and +authors' sake, the GPL requires that modified versions be marked as +changed, so that their problems will not be attributed erroneously to +authors of previous versions. + + Some devices are designed to deny users access to install or run +modified versions of the software inside them, although the manufacturer +can do so. This is fundamentally incompatible with the aim of +protecting users' freedom to change the software. The systematic +pattern of such abuse occurs in the area of products for individuals to +use, which is precisely where it is most unacceptable. Therefore, we +have designed this version of the GPL to prohibit the practice for those +products. If such problems arise substantially in other domains, we +stand ready to extend this provision to those domains in future versions +of the GPL, as needed to protect the freedom of users. + + Finally, every program is threatened constantly by software patents. +States should not allow patents to restrict development and use of +software on general-purpose computers, but in those that do, we wish to +avoid the special danger that patents applied to a free program could +make it effectively proprietary. To prevent this, the GPL assures that +patents cannot be used to render the program non-free. + + The precise terms and conditions for copying, distribution and +modification follow. + + TERMS AND CONDITIONS + + 0. Definitions. + + "This License" refers to version 3 of the GNU General Public License. + + "Copyright" also means copyright-like laws that apply to other kinds of +works, such as semiconductor masks. + + "The Program" refers to any copyrightable work licensed under this +License. Each licensee is addressed as "you". "Licensees" and +"recipients" may be individuals or organizations. + + To "modify" a work means to copy from or adapt all or part of the work +in a fashion requiring copyright permission, other than the making of an +exact copy. The resulting work is called a "modified version" of the +earlier work or a work "based on" the earlier work. + + A "covered work" means either the unmodified Program or a work based +on the Program. + + To "propagate" a work means to do anything with it that, without +permission, would make you directly or secondarily liable for +infringement under applicable copyright law, except executing it on a +computer or modifying a private copy. Propagation includes copying, +distribution (with or without modification), making available to the +public, and in some countries other activities as well. + + To "convey" a work means any kind of propagation that enables other +parties to make or receive copies. Mere interaction with a user through +a computer network, with no transfer of a copy, is not conveying. + + An interactive user interface displays "Appropriate Legal Notices" +to the extent that it includes a convenient and prominently visible +feature that (1) displays an appropriate copyright notice, and (2) +tells the user that there is no warranty for the work (except to the +extent that warranties are provided), that licensees may convey the +work under this License, and how to view a copy of this License. If +the interface presents a list of user commands or options, such as a +menu, a prominent item in the list meets this criterion. + + 1. Source Code. + + The "source code" for a work means the preferred form of the work +for making modifications to it. "Object code" means any non-source +form of a work. + + A "Standard Interface" means an interface that either is an official +standard defined by a recognized standards body, or, in the case of +interfaces specified for a particular programming language, one that +is widely used among developers working in that language. + + The "System Libraries" of an executable work include anything, other +than the work as a whole, that (a) is included in the normal form of +packaging a Major Component, but which is not part of that Major +Component, and (b) serves only to enable use of the work with that +Major Component, or to implement a Standard Interface for which an +implementation is available to the public in source code form. A +"Major Component", in this context, means a major essential component +(kernel, window system, and so on) of the specific operating system +(if any) on which the executable work runs, or a compiler used to +produce the work, or an object code interpreter used to run it. + + The "Corresponding Source" for a work in object code form means all +the source code needed to generate, install, and (for an executable +work) run the object code and to modify the work, including scripts to +control those activities. However, it does not include the work's +System Libraries, or general-purpose tools or generally available free +programs which are used unmodified in performing those activities but +which are not part of the work. For example, Corresponding Source +includes interface definition files associated with source files for +the work, and the source code for shared libraries and dynamically +linked subprograms that the work is specifically designed to require, +such as by intimate data communication or control flow between those +subprograms and other parts of the work. + + The Corresponding Source need not include anything that users +can regenerate automatically from other parts of the Corresponding +Source. + + The Corresponding Source for a work in source code form is that +same work. + + 2. Basic Permissions. + + All rights granted under this License are granted for the term of +copyright on the Program, and are irrevocable provided the stated +conditions are met. This License explicitly affirms your unlimited +permission to run the unmodified Program. The output from running a +covered work is covered by this License only if the output, given its +content, constitutes a covered work. This License acknowledges your +rights of fair use or other equivalent, as provided by copyright law. + + You may make, run and propagate covered works that you do not +convey, without conditions so long as your license otherwise remains +in force. You may convey covered works to others for the sole purpose +of having them make modifications exclusively for you, or provide you +with facilities for running those works, provided that you comply with +the terms of this License in conveying all material for which you do +not control copyright. Those thus making or running the covered works +for you must do so exclusively on your behalf, under your direction +and control, on terms that prohibit them from making any copies of +your copyrighted material outside their relationship with you. + + Conveying under any other circumstances is permitted solely under +the conditions stated below. Sublicensing is not allowed; section 10 +makes it unnecessary. + + 3. Protecting Users' Legal Rights From Anti-Circumvention Law. + + No covered work shall be deemed part of an effective technological +measure under any applicable law fulfilling obligations under article +11 of the WIPO copyright treaty adopted on 20 December 1996, or +similar laws prohibiting or restricting circumvention of such +measures. + + When you convey a covered work, you waive any legal power to forbid +circumvention of technological measures to the extent such circumvention +is effected by exercising rights under this License with respect to +the covered work, and you disclaim any intention to limit operation or +modification of the work as a means of enforcing, against the work's +users, your or third parties' legal rights to forbid circumvention of +technological measures. + + 4. Conveying Verbatim Copies. + + You may convey verbatim copies of the Program's source code as you +receive it, in any medium, provided that you conspicuously and +appropriately publish on each copy an appropriate copyright notice; +keep intact all notices stating that this License and any +non-permissive terms added in accord with section 7 apply to the code; +keep intact all notices of the absence of any warranty; and give all +recipients a copy of this License along with the Program. + + You may charge any price or no price for each copy that you convey, +and you may offer support or warranty protection for a fee. + + 5. Conveying Modified Source Versions. + + You may convey a work based on the Program, or the modifications to +produce it from the Program, in the form of source code under the +terms of section 4, provided that you also meet all of these conditions: + + a) The work must carry prominent notices stating that you modified + it, and giving a relevant date. + + b) The work must carry prominent notices stating that it is + released under this License and any conditions added under section + 7. This requirement modifies the requirement in section 4 to + "keep intact all notices". + + c) You must license the entire work, as a whole, under this + License to anyone who comes into possession of a copy. This + License will therefore apply, along with any applicable section 7 + additional terms, to the whole of the work, and all its parts, + regardless of how they are packaged. This License gives no + permission to license the work in any other way, but it does not + invalidate such permission if you have separately received it. + + d) If the work has interactive user interfaces, each must display + Appropriate Legal Notices; however, if the Program has interactive + interfaces that do not display Appropriate Legal Notices, your + work need not make them do so. + + A compilation of a covered work with other separate and independent +works, which are not by their nature extensions of the covered work, +and which are not combined with it such as to form a larger program, +in or on a volume of a storage or distribution medium, is called an +"aggregate" if the compilation and its resulting copyright are not +used to limit the access or legal rights of the compilation's users +beyond what the individual works permit. Inclusion of a covered work +in an aggregate does not cause this License to apply to the other +parts of the aggregate. + + 6. Conveying Non-Source Forms. + + You may convey a covered work in object code form under the terms +of sections 4 and 5, provided that you also convey the +machine-readable Corresponding Source under the terms of this License, +in one of these ways: + + a) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by the + Corresponding Source fixed on a durable physical medium + customarily used for software interchange. + + b) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by a + written offer, valid for at least three years and valid for as + long as you offer spare parts or customer support for that product + model, to give anyone who possesses the object code either (1) a + copy of the Corresponding Source for all the software in the + product that is covered by this License, on a durable physical + medium customarily used for software interchange, for a price no + more than your reasonable cost of physically performing this + conveying of source, or (2) access to copy the + Corresponding Source from a network server at no charge. + + c) Convey individual copies of the object code with a copy of the + written offer to provide the Corresponding Source. This + alternative is allowed only occasionally and noncommercially, and + only if you received the object code with such an offer, in accord + with subsection 6b. + + d) Convey the object code by offering access from a designated + place (gratis or for a charge), and offer equivalent access to the + Corresponding Source in the same way through the same place at no + further charge. You need not require recipients to copy the + Corresponding Source along with the object code. If the place to + copy the object code is a network server, the Corresponding Source + may be on a different server (operated by you or a third party) + that supports equivalent copying facilities, provided you maintain + clear directions next to the object code saying where to find the + Corresponding Source. Regardless of what server hosts the + Corresponding Source, you remain obligated to ensure that it is + available for as long as needed to satisfy these requirements. + + e) Convey the object code using peer-to-peer transmission, provided + you inform other peers where the object code and Corresponding + Source of the work are being offered to the general public at no + charge under subsection 6d. + + A separable portion of the object code, whose source code is excluded +from the Corresponding Source as a System Library, need not be +included in conveying the object code work. + + A "User Product" is either (1) a "consumer product", which means any +tangible personal property which is normally used for personal, family, +or household purposes, or (2) anything designed or sold for incorporation +into a dwelling. In determining whether a product is a consumer product, +doubtful cases shall be resolved in favor of coverage. For a particular +product received by a particular user, "normally used" refers to a +typical or common use of that class of product, regardless of the status +of the particular user or of the way in which the particular user +actually uses, or expects or is expected to use, the product. A product +is a consumer product regardless of whether the product has substantial +commercial, industrial or non-consumer uses, unless such uses represent +the only significant mode of use of the product. + + "Installation Information" for a User Product means any methods, +procedures, authorization keys, or other information required to install +and execute modified versions of a covered work in that User Product from +a modified version of its Corresponding Source. The information must +suffice to ensure that the continued functioning of the modified object +code is in no case prevented or interfered with solely because +modification has been made. + + If you convey an object code work under this section in, or with, or +specifically for use in, a User Product, and the conveying occurs as +part of a transaction in which the right of possession and use of the +User Product is transferred to the recipient in perpetuity or for a +fixed term (regardless of how the transaction is characterized), the +Corresponding Source conveyed under this section must be accompanied +by the Installation Information. But this requirement does not apply +if neither you nor any third party retains the ability to install +modified object code on the User Product (for example, the work has +been installed in ROM). + + The requirement to provide Installation Information does not include a +requirement to continue to provide support service, warranty, or updates +for a work that has been modified or installed by the recipient, or for +the User Product in which it has been modified or installed. Access to a +network may be denied when the modification itself materially and +adversely affects the operation of the network or violates the rules and +protocols for communication across the network. + + Corresponding Source conveyed, and Installation Information provided, +in accord with this section must be in a format that is publicly +documented (and with an implementation available to the public in +source code form), and must require no special password or key for +unpacking, reading or copying. + + 7. Additional Terms. + + "Additional permissions" are terms that supplement the terms of this +License by making exceptions from one or more of its conditions. +Additional permissions that are applicable to the entire Program shall +be treated as though they were included in this License, to the extent +that they are valid under applicable law. If additional permissions +apply only to part of the Program, that part may be used separately +under those permissions, but the entire Program remains governed by +this License without regard to the additional permissions. + + When you convey a copy of a covered work, you may at your option +remove any additional permissions from that copy, or from any part of +it. (Additional permissions may be written to require their own +removal in certain cases when you modify the work.) You may place +additional permissions on material, added by you to a covered work, +for which you have or can give appropriate copyright permission. + + Notwithstanding any other provision of this License, for material you +add to a covered work, you may (if authorized by the copyright holders of +that material) supplement the terms of this License with terms: + + a) Disclaiming warranty or limiting liability differently from the + terms of sections 15 and 16 of this License; or + + b) Requiring preservation of specified reasonable legal notices or + author attributions in that material or in the Appropriate Legal + Notices displayed by works containing it; or + + c) Prohibiting misrepresentation of the origin of that material, or + requiring that modified versions of such material be marked in + reasonable ways as different from the original version; or + + d) Limiting the use for publicity purposes of names of licensors or + authors of the material; or + + e) Declining to grant rights under trademark law for use of some + trade names, trademarks, or service marks; or + + f) Requiring indemnification of licensors and authors of that + material by anyone who conveys the material (or modified versions of + it) with contractual assumptions of liability to the recipient, for + any liability that these contractual assumptions directly impose on + those licensors and authors. + + All other non-permissive additional terms are considered "further +restrictions" within the meaning of section 10. If the Program as you +received it, or any part of it, contains a notice stating that it is +governed by this License along with a term that is a further +restriction, you may remove that term. If a license document contains +a further restriction but permits relicensing or conveying under this +License, you may add to a covered work material governed by the terms +of that license document, provided that the further restriction does +not survive such relicensing or conveying. + + If you add terms to a covered work in accord with this section, you +must place, in the relevant source files, a statement of the +additional terms that apply to those files, or a notice indicating +where to find the applicable terms. + + Additional terms, permissive or non-permissive, may be stated in the +form of a separately written license, or stated as exceptions; +the above requirements apply either way. + + 8. Termination. + + You may not propagate or modify a covered work except as expressly +provided under this License. Any attempt otherwise to propagate or +modify it is void, and will automatically terminate your rights under +this License (including any patent licenses granted under the third +paragraph of section 11). + + However, if you cease all violation of this License, then your +license from a particular copyright holder is reinstated (a) +provisionally, unless and until the copyright holder explicitly and +finally terminates your license, and (b) permanently, if the copyright +holder fails to notify you of the violation by some reasonable means +prior to 60 days after the cessation. + + Moreover, your license from a particular copyright holder is +reinstated permanently if the copyright holder notifies you of the +violation by some reasonable means, this is the first time you have +received notice of violation of this License (for any work) from that +copyright holder, and you cure the violation prior to 30 days after +your receipt of the notice. + + Termination of your rights under this section does not terminate the +licenses of parties who have received copies or rights from you under +this License. If your rights have been terminated and not permanently +reinstated, you do not qualify to receive new licenses for the same +material under section 10. + + 9. Acceptance Not Required for Having Copies. + + You are not required to accept this License in order to receive or +run a copy of the Program. Ancillary propagation of a covered work +occurring solely as a consequence of using peer-to-peer transmission +to receive a copy likewise does not require acceptance. However, +nothing other than this License grants you permission to propagate or +modify any covered work. These actions infringe copyright if you do +not accept this License. Therefore, by modifying or propagating a +covered work, you indicate your acceptance of this License to do so. + + 10. Automatic Licensing of Downstream Recipients. + + Each time you convey a covered work, the recipient automatically +receives a license from the original licensors, to run, modify and +propagate that work, subject to this License. You are not responsible +for enforcing compliance by third parties with this License. + + An "entity transaction" is a transaction transferring control of an +organization, or substantially all assets of one, or subdividing an +organization, or merging organizations. If propagation of a covered +work results from an entity transaction, each party to that +transaction who receives a copy of the work also receives whatever +licenses to the work the party's predecessor in interest had or could +give under the previous paragraph, plus a right to possession of the +Corresponding Source of the work from the predecessor in interest, if +the predecessor has it or can get it with reasonable efforts. + + You may not impose any further restrictions on the exercise of the +rights granted or affirmed under this License. For example, you may +not impose a license fee, royalty, or other charge for exercise of +rights granted under this License, and you may not initiate litigation +(including a cross-claim or counterclaim in a lawsuit) alleging that +any patent claim is infringed by making, using, selling, offering for +sale, or importing the Program or any portion of it. + + 11. Patents. + + A "contributor" is a copyright holder who authorizes use under this +License of the Program or a work on which the Program is based. The +work thus licensed is called the contributor's "contributor version". + + A contributor's "essential patent claims" are all patent claims +owned or controlled by the contributor, whether already acquired or +hereafter acquired, that would be infringed by some manner, permitted +by this License, of making, using, or selling its contributor version, +but do not include claims that would be infringed only as a +consequence of further modification of the contributor version. For +purposes of this definition, "control" includes the right to grant +patent sublicenses in a manner consistent with the requirements of +this License. + + Each contributor grants you a non-exclusive, worldwide, royalty-free +patent license under the contributor's essential patent claims, to +make, use, sell, offer for sale, import and otherwise run, modify and +propagate the contents of its contributor version. + + In the following three paragraphs, a "patent license" is any express +agreement or commitment, however denominated, not to enforce a patent +(such as an express permission to practice a patent or covenant not to +sue for patent infringement). To "grant" such a patent license to a +party means to make such an agreement or commitment not to enforce a +patent against the party. + + If you convey a covered work, knowingly relying on a patent license, +and the Corresponding Source of the work is not available for anyone +to copy, free of charge and under the terms of this License, through a +publicly available network server or other readily accessible means, +then you must either (1) cause the Corresponding Source to be so +available, or (2) arrange to deprive yourself of the benefit of the +patent license for this particular work, or (3) arrange, in a manner +consistent with the requirements of this License, to extend the patent +license to downstream recipients. "Knowingly relying" means you have +actual knowledge that, but for the patent license, your conveying the +covered work in a country, or your recipient's use of the covered work +in a country, would infringe one or more identifiable patents in that +country that you have reason to believe are valid. + + If, pursuant to or in connection with a single transaction or +arrangement, you convey, or propagate by procuring conveyance of, a +covered work, and grant a patent license to some of the parties +receiving the covered work authorizing them to use, propagate, modify +or convey a specific copy of the covered work, then the patent license +you grant is automatically extended to all recipients of the covered +work and works based on it. + + A patent license is "discriminatory" if it does not include within +the scope of its coverage, prohibits the exercise of, or is +conditioned on the non-exercise of one or more of the rights that are +specifically granted under this License. You may not convey a covered +work if you are a party to an arrangement with a third party that is +in the business of distributing software, under which you make payment +to the third party based on the extent of your activity of conveying +the work, and under which the third party grants, to any of the +parties who would receive the covered work from you, a discriminatory +patent license (a) in connection with copies of the covered work +conveyed by you (or copies made from those copies), or (b) primarily +for and in connection with specific products or compilations that +contain the covered work, unless you entered into that arrangement, +or that patent license was granted, prior to 28 March 2007. + + Nothing in this License shall be construed as excluding or limiting +any implied license or other defenses to infringement that may +otherwise be available to you under applicable patent law. + + 12. No Surrender of Others' Freedom. + + If conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot convey a +covered work so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you may +not convey it at all. For example, if you agree to terms that obligate you +to collect a royalty for further conveying from those to whom you convey +the Program, the only way you could satisfy both those terms and this +License would be to refrain entirely from conveying the Program. + + 13. Use with the GNU Affero General Public License. + + Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU Affero General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the special requirements of the GNU Affero General Public License, +section 13, concerning interaction through a network will apply to the +combination as such. + + 14. Revised Versions of this License. + + The Free Software Foundation may publish revised and/or new versions of +the GNU General Public License from time to time. Such new versions will +be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + + Each version is given a distinguishing version number. If the +Program specifies that a certain numbered version of the GNU General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU General Public License, you may choose any version ever published +by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future +versions of the GNU General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + + Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + + 15. Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. From cdf897ad9b154fed29aebf16bf3e9da3c2a747c8 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 13:37:53 +0000 Subject: [PATCH 21/42] style: change -7 and -9 references with named const vars (#22) * -9 is now ALLELE_MISSING * -7 is now ALLELE_UNPHASED_HET --- src/ViterbiLowMem.cpp | 7 ++++--- src/threads_arg/__main__.py | 6 +++--- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/src/ViterbiLowMem.cpp b/src/ViterbiLowMem.cpp index 51ab460..2c8ce80 100644 --- a/src/ViterbiLowMem.cpp +++ b/src/ViterbiLowMem.cpp @@ -9,6 +9,9 @@ namespace { +const int ALLELE_MISSING = -9; +const int ALLELE_UNPHASED_HET = -7; + inline size_t coord_id_key(int i, int j) { return (static_cast(i) << 32) | static_cast(j); } @@ -119,7 +122,6 @@ ViterbiState::ViterbiState(int _target_id, std::vector _sample_ids) best_match = sample_ids.at(0); } -// -9 is "missing" (not implemented yet) and -7 is "unphased" void ViterbiState::process_site(const std::vector& genotype, double rho, double rho_c, double mu, double mu_c) { int current_site = sites_processed; @@ -131,8 +133,7 @@ void ViterbiState::process_site(const std::vector& genotype, double rho, do for (int sample_id : sample_ids) { int allele = genotype.at(sample_id); double copy_penalty; - // "-7" encodes unphased heterozygotes, because why not - if (allele == -7 || observed_allele == -7) { + if ((allele == ALLELE_UNPHASED_HET) || (observed_allele == ALLELE_UNPHASED_HET)) { copy_penalty = (mu_c + mu) / 2.; } else { diff --git a/src/threads_arg/__main__.py b/src/threads_arg/__main__.py index 380a079..d510c3c 100644 --- a/src/threads_arg/__main__.py +++ b/src/threads_arg/__main__.py @@ -263,9 +263,9 @@ def partial_viterbi(pgen, mode, num_samples_hap, physical_positions, genetic_pos phased_out = np.empty((g_size, num_samples_hap // 2), dtype=np.uint8) if (phased_out == 0).any(): unphased_sites, unphased_samples = (1 - phased_out).nonzero() - # We encode "unphased het" by "-7" - alleles_out[unphased_sites, 2 * unphased_samples] = -7 - alleles_out[unphased_sites, 2 * unphased_samples + 1] = -7 + ALLELE_UNPHASED_HET = -7 + alleles_out[unphased_sites, 2 * unphased_samples] = ALLELE_UNPHASED_HET + alleles_out[unphased_sites, 2 * unphased_samples + 1] = ALLELE_UNPHASED_HET reader.read_alleles_and_phasepresent_range(b_start, b_end, alleles_out, phased_out) # For each variant in chunk, pass the genotypes through Threads-LS From 1480b18a003f2fc88dd127268df4f07c98076a96 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 17:47:05 +0000 Subject: [PATCH 22/42] style: #define for genetic position runtime check (#22) * After reviewing with Arni, this check may still be useful as currently if genetic positions are out of order then there is a potential segfault. Left enabled whilst investigating --- src/ImputationMatcher.cpp | 10 ++++++---- src/ThreadsFastLS.cpp | 10 ++++++---- 2 files changed, 12 insertions(+), 8 deletions(-) diff --git a/src/ImputationMatcher.cpp b/src/ImputationMatcher.cpp index 77c1659..fe311b0 100644 --- a/src/ImputationMatcher.cpp +++ b/src/ImputationMatcher.cpp @@ -8,6 +8,10 @@ #include #include +// Uncomment this #define to enable a runtime check that genetic position are in order. This +// diagnostic check is left in whilst we may have issues during development. +// #define IMPUTATION_MATCHER_CHECK_IN_ORDER + ImputationMatcher::ImputationMatcher(int _n_ref, int _n_target, const std::vector& _genetic_positions, double _query_interval_size, int _neighborhood_size) @@ -21,9 +25,7 @@ ImputationMatcher::ImputationMatcher(int _n_ref, int _n_target, num_samples = num_reference + num_target; sites_processed = 0; - // FIXME Arni/Alex review. OK to remove or instead add an explicit macro? - // Set to 1 for runtime check that maps are strictly increasing -#if 0 +#ifdef IMPUTATION_MATCHER_CHECK_IN_ORDER for (int i = 0; i < num_sites - 1; i++) { if (genetic_positions.at(i + 1) <= genetic_positions.at(i)) { std::string prompt = "Genetic coordinates must be strictly increasing, found "; @@ -32,7 +34,7 @@ ImputationMatcher::ImputationMatcher(int _n_ref, int _n_target, throw std::runtime_error(prompt); } } -#endif +#endif // IMPUTATION_MATCHER_CHECK_IN_ORDER int query_site_idx = 1; double gen_pos_offset = genetic_positions[0]; diff --git a/src/ThreadsFastLS.cpp b/src/ThreadsFastLS.cpp index 1c181c7..29445ee 100644 --- a/src/ThreadsFastLS.cpp +++ b/src/ThreadsFastLS.cpp @@ -14,6 +14,10 @@ #include #include +// Uncomment this #define to enable a runtime check that genetic position are in order. This +// diagnostic check is left in whilst we may have issues during development. +// #define THREADS_FAST_LS_CHECK_IN_ORDER + namespace { const int END_ALLELE = 0; @@ -49,9 +53,7 @@ ThreadsFastLS::ThreadsFastLS(std::vector _physical_positions, num_sites = static_cast(physical_positions.size()); num_samples = 0; - // FIXME Arni/Alex review. OK to remove or instead add an explicit macro? - // Set to 1 for runtime check that maps are strictly increasing -#if 0 +#ifdef THREADS_FAST_LS_CHECK_IN_ORDER for (int i = 0; i < num_sites - 1; i++) { if (physical_positions[i + 1] <= physical_positions[i]) { cerr << "Physical positions must be strictly increasing, found "; @@ -64,7 +66,7 @@ ThreadsFastLS::ThreadsFastLS(std::vector _physical_positions, exit(1); } } -#endif +#endif // THREADS_FAST_LS_CHECK_IN_ORDER // Initialize map burn-in threading_start = physical_positions.front() + burn_in_left; From 1028384e4109310f4bc57f590a6aa28ebdd6e1f9 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 17:48:44 +0000 Subject: [PATCH 23/42] style: remove review comment for unsigned short (#22) * After review with Arni, the original reason for using unsigned short is not clear. The explicit exception for overflows captures this for now and we will do a check on static_casts in future, may be possible to just save these as ints/size_t values. --- src/HMM.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/src/HMM.cpp b/src/HMM.cpp index d708ce0..5c5386e 100644 --- a/src/HMM.cpp +++ b/src/HMM.cpp @@ -83,7 +83,6 @@ std::vector HMM::breakpoints(std::vector observations, int start) { trellis[start][i] = score; } - // FIXME review with Arni, defensive check for assignment to 'k' below if (num_states > std::numeric_limits::max()) { throw std::runtime_error("Unable to store breakpoints for more than 2^16 states"); } From 00c48f85428ddbe3470c04ef61f690f6d0960762 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 17:52:10 +0000 Subject: [PATCH 24/42] fix: replace use of numeric_limit infinity with max (#22) * Setting to infinity may be mathematically undefined float behaviour, where max is definitely stable. --- src/State.cpp | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/State.cpp b/src/State.cpp index f5bd061..cd742cc 100644 --- a/src/State.cpp +++ b/src/State.cpp @@ -54,8 +54,7 @@ void StateBranch::prune() { }); std::vector new_states; - double running_min_score = - std::numeric_limits::infinity(); // FIXME review with Arni - infinity or max? + double running_min_score = std::numeric_limits::max(); for (const State& s : states) { if (s.score < running_min_score) { new_states.push_back(s); From 68ef0ec7f54535042812c1e50a31c724c43162e6 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 17:53:29 +0000 Subject: [PATCH 25/42] style: change fastls review point to ticket (#22) * Reviewing this code, it looks like the segment is passed the wrong size. Needs more investigation. --- src/ThreadsFastLS.cpp | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/ThreadsFastLS.cpp b/src/ThreadsFastLS.cpp index 29445ee..548aff9 100644 --- a/src/ThreadsFastLS.cpp +++ b/src/ThreadsFastLS.cpp @@ -1335,8 +1335,7 @@ ThreadsFastLS::thread(const int new_sample_ID, const std::vector& genotype (j == (static_cast(breakpoints.size()) - 1)) ? segment_end : breakpoints[j + 1]; target_IDs.push_back(target_ID_L); bp_starts.push_back(static_cast(ceil(bp_boundaries[breakpoint_start]))); - // FIXME Alex/Arni review - just spotted, checking on context for comment - // This is wrong!!! need to actually re-do num het_sites!!!! + // TODO Pass right number of heterozygous sites to date segments when HMM is used (ticket #24) segment_ages.push_back(date_segment(num_het_sites, breakpoint_start, breakpoint_end)); } } From 00afd2d1dbddb104e5f0b63a7d6cad4bba64c033 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 17:54:50 +0000 Subject: [PATCH 26/42] style: give fastls magic value meaningful name (#22) --- src/ThreadsFastLS.cpp | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/ThreadsFastLS.cpp b/src/ThreadsFastLS.cpp index 548aff9..de144d3 100644 --- a/src/ThreadsFastLS.cpp +++ b/src/ThreadsFastLS.cpp @@ -21,6 +21,7 @@ namespace { const int END_ALLELE = 0; +const int HMM_SPLIT_THRESHOLD = 1000; inline size_t pair_key(int i, int j) { return (static_cast(i) << 32) | static_cast(j); @@ -1320,9 +1321,7 @@ ThreadsFastLS::thread(const int new_sample_ID, const std::vector& genotype } total_num_het_sites += num_het_sites; - // FIXME Alex/Arni review - work in progress, but just checking if these numbers should be - // consts declared above is it ok to have 100 here? - if (use_hmm && num_samples < 1000) { + if (use_hmm && num_samples < HMM_SPLIT_THRESHOLD) { // is it ok to have 10 here? if (num_het_sites > 5) { std::vector breakpoints = hmm->breakpoints(het_hom_sites, segment_start); From 0f1048789d4492e1e4b49917211381dcb05b889d Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 17:56:17 +0000 Subject: [PATCH 27/42] style: remove unused fast ls date_segment_sparse arg (#22) * Confirmed in review this will not be needed. --- src/ThreadsFastLS.cpp | 7 ++----- src/ThreadsFastLS.hpp | 2 +- 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/src/ThreadsFastLS.cpp b/src/ThreadsFastLS.cpp index de144d3..e07e792 100644 --- a/src/ThreadsFastLS.cpp +++ b/src/ThreadsFastLS.cpp @@ -1181,7 +1181,7 @@ double ThreadsFastLS::date_segment(const int num_het_sites, const int start, con cm_size += cm_sizes[i]; } if (sparse_sites) { - return ThreadsFastLS::date_segment_sparse(num_het_sites, cm_size, demography); + return ThreadsFastLS::date_segment_sparse(cm_size, demography); } else { // FIXME Alex/Arni review - removed old 'm' variable here, confirm double not needed @@ -1230,12 +1230,9 @@ double ThreadsFastLS::date_segment(int num_het_sites, double cm_size, double bp_ return numerator / denominator; } -double ThreadsFastLS::date_segment_sparse(int num_het_sites, double cm_size, +double ThreadsFastLS::date_segment_sparse(double cm_size, Demography& demography) { - // FIXME Arni/Alex review num_het_sites is not used. Remove from args? - (void) num_het_sites; - double rho = 2. * 0.01 * cm_size; double numerator = 0; double denominator = 0; diff --git a/src/ThreadsFastLS.hpp b/src/ThreadsFastLS.hpp index 0400e72..0e9c604 100644 --- a/src/ThreadsFastLS.hpp +++ b/src/ThreadsFastLS.hpp @@ -154,7 +154,7 @@ class ThreadsFastLS { static double date_segment(int num_het_sites, double cm_length, double bp_length, double mutation_rate, Demography& demography); - static double date_segment_sparse(int num_het_sites, double cm_length, Demography& demography); + static double date_segment_sparse(double cm_length, Demography& demography); /// For debugging: print the sample-IDs of the arrayified panel void print_sorting() const; From db8478bca4c04a64a4054774f8e92a392a71ad86 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 17:59:49 +0000 Subject: [PATCH 28/42] style: remove fastls review comments from review (#22) * The behaviour of the double to int case is still functionally the same so OK. To clarify, this cast will be a _floor_ operation. * the .begin() usage is valid, it's a implicit range constructor. * i to j rename definitely correct; we're not sure why this has not caused problems until now. --- src/ThreadsFastLS.cpp | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/src/ThreadsFastLS.cpp b/src/ThreadsFastLS.cpp index e07e792..158fc95 100644 --- a/src/ThreadsFastLS.cpp +++ b/src/ThreadsFastLS.cpp @@ -1184,7 +1184,6 @@ double ThreadsFastLS::date_segment(const int num_het_sites, const int start, con return ThreadsFastLS::date_segment_sparse(cm_size, demography); } else { - // FIXME Alex/Arni review - removed old 'm' variable here, confirm double not needed return ThreadsFastLS::date_segment(num_het_sites, cm_size, bp_size, mutation_rate, demography); } } @@ -1195,9 +1194,6 @@ double ThreadsFastLS::date_segment(int num_het_sites, double cm_size, double bp_ double mu = 2. * mutation_rate * bp_size; double rho = 2. * 0.01 * cm_size; if (m > 15) { - // FIXME Alex/Arni - I have removed many couts but were they still needed for debug? If so I can - // put a #def in cout << "Warning: very many heterozygous sites, defaulting to const-demography - // method.\n"; double gamma = 1. / demography.expected_time; return (m + 2) / (gamma + rho + mu); } @@ -1323,8 +1319,6 @@ ThreadsFastLS::thread(const int new_sample_ID, const std::vector& genotype if (num_het_sites > 5) { std::vector breakpoints = hmm->breakpoints(het_hom_sites, segment_start); - // FIXME Alex/Arni review - was 'i' but dangerous as shadowing out loop, changed to 'j', - // confirm ok. for (int j = 0; j < static_cast(breakpoints.size()); j++) { int breakpoint_start = breakpoints[j]; int breakpoint_end = @@ -1383,7 +1377,6 @@ std::vector ThreadsFastLS::impute(std::vector& genotype const std::tuple, std::vector, std::vector>& segment = best_path[i]; const std::vector& samples = std::get<0>(segment); ImputationSegment imp_seg; - // FIXME Alex/Arni review double to int conversion OK? Should it be ceil/floor/round? imp_seg.seg_start = static_cast(physical_positions[std::get<1>(segment)[0]]); imp_seg.ids = samples; std::vector wts; @@ -1427,7 +1420,6 @@ ThreadsFastLS::remove_burn_in(std::vector& bp_starts, // Keep segments that start on or before threading_start int seg_start_i = 0; for (int i = 0; i < num_segments; i++) { - // FIXME Alex/Arni review double to int conversion OK? Should it be ceil/floor/round? int seg_end = i == num_segments - 1 ? static_cast(threading_end) : bp_starts[i + 1]; if (threading_start < seg_end) { break; @@ -1447,10 +1439,7 @@ ThreadsFastLS::remove_burn_in(std::vector& bp_starts, } } - // FIXME Alex/Arni - is usage correct? .begin() is an iterator not value, adding a value then - // assigning to an int trim_starts = {bp_starts.begin() + seg_start_i, bp_starts.begin() + seg_end_i}; - // FIXME Alex/Arni - direct cast from double OK? trim_starts[0] = static_cast(threading_start); trim_IDs = {target_IDs.begin() + seg_start_i, target_IDs.begin() + seg_end_i}; trim_ages = {segment_ages.begin() + seg_start_i, segment_ages.begin() + seg_end_i}; @@ -1536,7 +1525,6 @@ ThreadsFastLS::het_sites_from_thread(const int focal_ID, const std::vector int site_i = 0; for (int seg_i = 0; seg_i < num_segments; seg_i++) { int segment_start = bp_starts[seg_i]; - // FIXME Arni/Alex review - double to int OK, floor/ceil/round? int segment_end = seg_i == num_segments - 1 ? (static_cast(physical_positions.back()) + 1) : bp_starts[seg_i + 1]; int target_ID = target_IDs[seg_i][0]; @@ -1544,7 +1532,6 @@ ThreadsFastLS::het_sites_from_thread(const int focal_ID, const std::vector physical_positions[site_i] < segment_end && site_i < num_sites) { if (panel[ID_map.at(focal_ID)][site_i]->genotype != panel[ID_map.at(target_ID)][site_i]->genotype) { - // FIXME Arni/Alex review - double to int OK, floor/ceil/round? het_sites.push_back(static_cast(physical_positions[site_i])); } site_i++; From cf4cff624c2bd0c8bac7d5b930a82df528930c24 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 18:00:27 +0000 Subject: [PATCH 29/42] style: fixup fastls extensible_by doxygen (#22) --- src/ThreadsFastLS.hpp | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/ThreadsFastLS.hpp b/src/ThreadsFastLS.hpp index 0e9c604..5b593e1 100644 --- a/src/ThreadsFastLS.hpp +++ b/src/ThreadsFastLS.hpp @@ -40,9 +40,7 @@ class ThreadsFastLS { /// @return Node* Pointer to node below the sequence being inserted at site i+1 Node* extend_node(Node* node, bool genotype, const int i); - // FIXME Alex/Arni confirm meaning of "May alter" below, also my change to return comment - /// Determine whether state can be extended through panel by appending g. - /// May alter + /// Determine whether state can be extended through panel by appending genotype 'g' /// @param s State at site i /// @param t_next Node at site i+1 /// @param g Candidate genotype for s at i+1 From b262a6146b8f29f2cb74a9e20d003eb259e50aca Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 18:01:37 +0000 Subject: [PATCH 30/42] style: tidier/faster weights initialisation in fastls (#22) * Checked in review, can just be done in constructor as they all have the same weighting value --- src/ThreadsFastLS.cpp | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/src/ThreadsFastLS.cpp b/src/ThreadsFastLS.cpp index 158fc95..518b1a6 100644 --- a/src/ThreadsFastLS.cpp +++ b/src/ThreadsFastLS.cpp @@ -1379,16 +1379,10 @@ std::vector ThreadsFastLS::impute(std::vector& genotype ImputationSegment imp_seg; imp_seg.seg_start = static_cast(physical_positions[std::get<1>(segment)[0]]); imp_seg.ids = samples; - std::vector wts; + std::vector weights(samples.size(), 1. / static_cast(samples.size())); std::vector ages(samples.size(), seg_ages[i]); imp_seg.ages = ages; - for (auto s : samples) { - // FIXME Alex/Arni review, s not used, just change to regular for loop for now? - (void) s; - - wts.push_back(1. / static_cast(samples.size())); - } - imp_seg.weights = wts; + imp_seg.weights = weights; imputation_segments.push_back(imp_seg); } return imputation_segments; From 15f8e60ef33eef5d528b423f503aa75a517f374b Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 18:05:27 +0000 Subject: [PATCH 31/42] style: remove commented out code (#22) * Checked in review, this is no longer needed. * Also made count_branches const. --- src/ThreadsLowMem.cpp | 16 ++-------------- src/ThreadsLowMem.hpp | 2 +- 2 files changed, 3 insertions(+), 15 deletions(-) diff --git a/src/ThreadsLowMem.cpp b/src/ThreadsLowMem.cpp index 245622d..36949c2 100644 --- a/src/ThreadsLowMem.cpp +++ b/src/ThreadsLowMem.cpp @@ -183,7 +183,7 @@ void ThreadsLowMem::date_segments() { throw std::runtime_error( "Can't date segments, not all sites have been parsed for heterozygosity."); } - // for (int i = 1; i < num_samples; i++) { + for (int target_id : target_ids) { if (target_id == 0) { continue; @@ -197,16 +197,10 @@ void ThreadsLowMem::date_segments() { } } - // I get segfault on this? - - // FIXME Alex/Arni - in progress, but #def couts for now? - // for (int i = 1; i < num_samples; i++) { for (int target_id : target_ids) { if (target_id == 0) { continue; } - // cout << "dating sample " << i << endl; - // compute length in bp/cM and num_hets for each segment ViterbiPath& path = paths.at(target_id); ViterbiPath new_path(target_id); std::size_t n_segs = path.segment_starts.size(); @@ -214,8 +208,6 @@ void ThreadsLowMem::date_segments() { int sample_id = path.sample_ids.at(k); int segment_start = path.segment_starts.at(k); int segment_end = k < n_segs - 1 ? path.segment_starts.at(k + 1) : num_sites - 1; - // cout << "dating segment [" << segment_start << ", " << segment_end << ") no. " << k << " - // out of " << n_segs - 1 << endl; if (segment_end == segment_start) { continue; } @@ -223,7 +215,6 @@ void ThreadsLowMem::date_segments() { // This is inefficient but probably not that bad std::vector segment_hets; for (int h : path.het_sites) { - // FIXME Alex/Arnie review parenthesis if (((segment_start <= h) && (h < segment_end)) || ((h == num_sites - 1) && (segment_end == num_sites - 1))) { segment_hets.push_back(h); @@ -240,7 +231,6 @@ void ThreadsLowMem::date_segments() { } // Here we use the hmm to break the big segment up into smaller segments std::vector breakpoints = psmc.breakpoints(het_hom_sites, segment_start); - // cout << "found " << breakpoints.size() << " breakpoints" << endl; for (std::size_t j = 0; j < breakpoints.size(); j++) { int breakpoint_start = breakpoints[j]; int breakpoint_end = (j == breakpoints.size() - 1) ? segment_end : breakpoints[j + 1]; @@ -280,9 +270,8 @@ void ThreadsLowMem::date_segments() { return; } -int ThreadsLowMem::count_branches() { +int ThreadsLowMem::count_branches() const { int n_branches = 0; - // for (int i = 1; i < num_samples; i++) { for (int target_id : target_ids) { if (target_id == 0) { continue; @@ -293,7 +282,6 @@ int ThreadsLowMem::count_branches() { } void ThreadsLowMem::prune() { - // for (int i = 1; i < num_samples; i++) { for (int target_id : target_ids) { if (target_id == 0) { continue; diff --git a/src/ThreadsLowMem.hpp b/src/ThreadsLowMem.hpp index c92b8f0..1e2ecda 100644 --- a/src/ThreadsLowMem.hpp +++ b/src/ThreadsLowMem.hpp @@ -37,7 +37,7 @@ class ThreadsLowMem { // 4. save output (done on Python side) - int count_branches(); + int count_branches() const; // Make pickle-able path output std::tuple>, std::vector>, From 8da01a34e76b1b80cce68356907ed5096b861b53 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Thu, 30 May 2024 18:12:21 +0000 Subject: [PATCH 32/42] build: remove eigen (#22) * Apparently there were some performance issues so this was commented out in the code. It turned out the only left over uses of it were not being used, so for now it's OK to move out of the project until we can revist (theoretically it should be a performance boost, not a loss) --- .devcontainer/Dockerfile | 1 - .github/workflows/build-cpp-libs.yml | 8 ++++---- .github/workflows/build-wheels.yml | 4 ++-- .github/workflows/ctest-macos.yml | 2 +- .github/workflows/ctest-ubuntu.yml | 2 +- .github/workflows/pytest-ubuntu.yml | 2 +- README.md | 3 --- src/CMakeLists.txt | 19 ------------------- src/TGEN.cpp | 9 --------- src/TGEN.hpp | 1 - src/threads_arg_pybind.cpp | 1 - 11 files changed, 9 insertions(+), 43 deletions(-) diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index f814bb0..cc1018a 100644 --- a/.devcontainer/Dockerfile +++ b/.devcontainer/Dockerfile @@ -25,5 +25,4 @@ RUN apt-get install -y \ RUN apt-get install -y \ python3-dev \ libboost-dev \ - libeigen3-dev \ pybind11-dev diff --git a/.github/workflows/build-cpp-libs.yml b/.github/workflows/build-cpp-libs.yml index c3b3dfa..05e8cd5 100644 --- a/.github/workflows/build-cpp-libs.yml +++ b/.github/workflows/build-cpp-libs.yml @@ -19,16 +19,16 @@ jobs: include: - os: ubuntu-22.04 build-type: Debug - system-deps: "sudo apt -y install libboost-dev libboost-math-dev libeigen3-dev" + system-deps: "sudo apt -y install libboost-dev libboost-math-dev" - os: ubuntu-22.04 build-type: Release - system-deps: "sudo apt -y install libboost-dev libboost-math-dev libeigen3-dev" + system-deps: "sudo apt -y install libboost-dev libboost-math-dev" - os: macos-14 build-type: Debug - system-deps: "brew install boost eigen" + system-deps: "brew install boost" - os: macos-14 build-type: Release - system-deps: "brew install boost eigen" + system-deps: "brew install boost" steps: diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml index f80bc56..02fc999 100644 --- a/.github/workflows/build-wheels.yml +++ b/.github/workflows/build-wheels.yml @@ -27,12 +27,12 @@ jobs: - os: macos-13 arch: x86_64 py-vers: cp38-* cp39-* cp310-* cp311-* cp312-* - before-all: brew install cmake ninja boost eigen + before-all: brew install cmake ninja boost extra-env: CC="$(brew --prefix llvm@15)/bin/clang" CXX="$(brew --prefix llvm@15)/bin/clang++" HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1 - os: macos-14 arch: arm64 py-vers: cp39-* cp310-* cp311-* cp312-* - before-all: brew install cmake ninja boost eigen + before-all: brew install cmake ninja boost extra-env: CC="$(brew --prefix llvm@15)/bin/clang" CXX="$(brew --prefix llvm@15)/bin/clang++" HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1 env: diff --git a/.github/workflows/ctest-macos.yml b/.github/workflows/ctest-macos.yml index baf3af5..f0a8882 100644 --- a/.github/workflows/ctest-macos.yml +++ b/.github/workflows/ctest-macos.yml @@ -16,7 +16,7 @@ jobs: uses: actions/checkout@v2 - name: install system packages - run: brew install boost eigen + run: brew install boost - name: make build directory run: mkdir build_dir diff --git a/.github/workflows/ctest-ubuntu.yml b/.github/workflows/ctest-ubuntu.yml index e7cc5c0..dcd7e2f 100644 --- a/.github/workflows/ctest-ubuntu.yml +++ b/.github/workflows/ctest-ubuntu.yml @@ -21,7 +21,7 @@ jobs: - name: install system packages run: | sudo apt -y update - sudo apt -y install libboost-dev libeigen3-dev + sudo apt -y install libboost-dev - name: make build directory run: mkdir build_dir diff --git a/.github/workflows/pytest-ubuntu.yml b/.github/workflows/pytest-ubuntu.yml index c809702..7395f96 100644 --- a/.github/workflows/pytest-ubuntu.yml +++ b/.github/workflows/pytest-ubuntu.yml @@ -38,7 +38,7 @@ jobs: - name: install system packages run: | sudo apt -y update - sudo apt -y install libboost-dev libeigen3-dev + sudo apt -y install libboost-dev - name: install python dependencies run: | diff --git a/README.md b/README.md index 7ecd6aa..1abd197 100644 --- a/README.md +++ b/README.md @@ -8,12 +8,9 @@ module load git/2.36.0-GCCcore-11.3.0-nodocs module load Python/3.10.4-GCCcore-11.3.0 module load GSL/2.7-GCC-11.3.0 module load Boost/1.79.0-GCC-11.3.0 -module load Eigen/3.4.0-GCCcore-11.3.0 module load pybind11/2.9.2-GCCcore-11.3.0 ``` -NB: Eigen is only used for functionality in TGEN.cpp. We can consider releasing without TGEN to have fewer dependencies. - Fire up and activate a new venv: ``` python -m venv venv diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 5dd6146..975fddc 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -14,23 +14,6 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU") endif() endif() -# Try to find Eigen3 version 3.4 locally installed -find_package(Eigen3 3.4 QUIET) - -if(NOT Eigen3_FOUND) - include(FetchContent) - message(STATUS "Suitable local version of Eigen3 (>= 3.4) not found, fetching from repository...") - FetchContent_Declare( - Eigen3 - GIT_REPOSITORY https://gitlab.com/libeigen/eigen.git - GIT_TAG 9df21dc8b4b576a7aa5c0094daa8d7e8b8be60f0 # 3.4 branch at 2024-03-15 - GIT_SHALLOW TRUE - ) - FetchContent_MakeAvailable(Eigen3) - set(Eigen3_VERSION "3.4") -endif() -message(STATUS "Found Eigen3 ${Eigen3_VERSION}") - # Threads static library set(threads_arg_src Demography.cpp @@ -77,8 +60,6 @@ target_link_libraries(threads_arg PRIVATE Boost::headers project_warnings - PUBLIC - Eigen3::Eigen ) # Conditionally create python bindings diff --git a/src/TGEN.cpp b/src/TGEN.cpp index 9f775dd..fb57a87 100644 --- a/src/TGEN.cpp +++ b/src/TGEN.cpp @@ -2,7 +2,6 @@ #include "TgenSegment.hpp" -#include #include #include @@ -51,15 +50,12 @@ class TGENImpl { std::vector interval_sets; std::unordered_map pos_idx_map; - Eigen::VectorXi reference_genome; std::vector reference_genome_vec; std::vector> bp_starts; std::vector> target_IDs; std::vector> het_sites; std::vector positions; std::vector> genotypes; - - Eigen::MatrixXi genotype_cache; std::unordered_map cached_genotypes_map; // Constructor @@ -73,12 +69,8 @@ class TGENImpl { pos_idx_map[positions[i]] = i; } - // FIXME Arni/Alex review remove eigen for now (note int/size_t indexing)? - // set reference genome here - reference_genome = Eigen::VectorXi::Zero(positions.size()); reference_genome_vec = std::vector(positions.size(), false); for (int h : het_sites[0]) { - reference_genome[pos_idx_map.at(h)] = 1; reference_genome_vec[pos_idx_map.at(h)] = true; } @@ -192,7 +184,6 @@ class TGENImpl { void clear_cache() { cached_genotypes_map.clear(); - genotype_cache.resize(0, 0); cached_genotypes_map[0] = -1; } }; diff --git a/src/TGEN.hpp b/src/TGEN.hpp index 28fd33f..75379b7 100644 --- a/src/TGEN.hpp +++ b/src/TGEN.hpp @@ -1,7 +1,6 @@ #ifndef THREADS_ARG_TGEN_HPP #define THREADS_ARG_TGEN_HPP -#include #include #include #include diff --git a/src/threads_arg_pybind.cpp b/src/threads_arg_pybind.cpp index 9b17ed9..ca32667 100644 --- a/src/threads_arg_pybind.cpp +++ b/src/threads_arg_pybind.cpp @@ -2,7 +2,6 @@ #include "TGEN.hpp" #include "ThreadsLowMem.hpp" -#include #include #include #include From 58ef72f6907676f0b01cdc8d7b72549bd286e9a8 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Fri, 31 May 2024 11:33:02 +0000 Subject: [PATCH 33/42] docs: add copyright headers (#22) --- CMakeLists.txt | 17 +++++++++++++++-- setup.py | 16 ++++++++++++++++ src/CMakeLists.txt | 17 +++++++++++++++-- src/Demography.cpp | 16 ++++++++++++++++ src/Demography.hpp | 16 ++++++++++++++++ src/HMM.cpp | 16 ++++++++++++++++ src/HMM.hpp | 16 ++++++++++++++++ src/ImputationMatcher.cpp | 16 ++++++++++++++++ src/ImputationMatcher.hpp | 16 ++++++++++++++++ src/Matcher.cpp | 16 ++++++++++++++++ src/Matcher.hpp | 16 ++++++++++++++++ src/Node.cpp | 16 ++++++++++++++++ src/Node.hpp | 16 ++++++++++++++++ src/State.cpp | 16 ++++++++++++++++ src/State.hpp | 16 ++++++++++++++++ src/TGEN.cpp | 16 ++++++++++++++++ src/TGEN.hpp | 16 ++++++++++++++++ src/TgenSegment.hpp | 16 ++++++++++++++++ src/ThreadsFastLS.cpp | 16 ++++++++++++++++ src/ThreadsFastLS.hpp | 16 ++++++++++++++++ src/ThreadsLowMem.cpp | 16 ++++++++++++++++ src/ThreadsLowMem.hpp | 16 ++++++++++++++++ src/ViterbiLowMem.cpp | 16 ++++++++++++++++ src/ViterbiLowMem.hpp | 16 ++++++++++++++++ src/threads_arg/__init__.py | 16 ++++++++++++++++ src/threads_arg/__main__.py | 16 ++++++++++++++++ src/threads_arg/mapping_utils.py | 16 ++++++++++++++++ src/threads_arg/utils.py | 16 ++++++++++++++++ src/threads_arg_pybind.cpp | 16 ++++++++++++++++ test/CMakeLists.txt | 17 +++++++++++++++-- test/test_data_snapshot.py | 16 ++++++++++++++++ test/test_demography.cpp | 16 ++++++++++++++++ test/test_viterbi_state.cpp | 16 ++++++++++++++++ 33 files changed, 525 insertions(+), 6 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index e6083ba..197cef7 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,5 +1,18 @@ -# This file is part of https://github.com/PalamaraLab/threads which is released under the GPL-3.0 license. -# See accompanying LICENSE and COPYING for copyright notice and full details. +# This file is part of the Threads software suite. +# Copyright (C) 2024 Threads Developers. +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . cmake_minimum_required(VERSION 3.16) message(STATUS "Using CMake version ${CMAKE_VERSION}") diff --git a/setup.py b/setup.py index 07dd034..70a9b2e 100644 --- a/setup.py +++ b/setup.py @@ -1,3 +1,19 @@ +# This file is part of the Threads software suite. +# Copyright (C) 2024 Threads Developers. +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + # Based on https://github.com/pybind/cmake_example import os diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 975fddc..451e5c2 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -1,5 +1,18 @@ -# This file is part of https://github.com/PalamaraLab/threads which is released under the GPL-3.0 license. -# See accompanying LICENSE and COPYING for copyright notice and full details. +# This file is part of the Threads software suite. +# Copyright (C) 2024 Threads Developers. +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . # Find Boost find_package(Boost REQUIRED) diff --git a/src/Demography.cpp b/src/Demography.cpp index db98107..6c1c9c4 100644 --- a/src/Demography.cpp +++ b/src/Demography.cpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #include "Demography.hpp" #include diff --git a/src/Demography.hpp b/src/Demography.hpp index 51317af..f6249ee 100644 --- a/src/Demography.hpp +++ b/src/Demography.hpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #ifndef THREADS_ARG_DEMOGRAPHY_HPP #define THREADS_ARG_DEMOGRAPHY_HPP diff --git a/src/HMM.cpp b/src/HMM.cpp index 5c5386e..2f7d6f4 100644 --- a/src/HMM.cpp +++ b/src/HMM.cpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #include "HMM.hpp" #include diff --git a/src/HMM.hpp b/src/HMM.hpp index c72dbe2..0ce0201 100644 --- a/src/HMM.hpp +++ b/src/HMM.hpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #include "Demography.hpp" #include diff --git a/src/ImputationMatcher.cpp b/src/ImputationMatcher.cpp index fe311b0..19e0390 100644 --- a/src/ImputationMatcher.cpp +++ b/src/ImputationMatcher.cpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #include "ImputationMatcher.hpp" #include diff --git a/src/ImputationMatcher.hpp b/src/ImputationMatcher.hpp index 2ac00d3..8479db8 100644 --- a/src/ImputationMatcher.hpp +++ b/src/ImputationMatcher.hpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #ifndef THREADS_ARG_IMPUTATION_MATCHER_HPP #define THREADS_ARG_IMPUTATION_MATCHER_HPP diff --git a/src/Matcher.cpp b/src/Matcher.cpp index 69c1d86..a95ac05 100644 --- a/src/Matcher.cpp +++ b/src/Matcher.cpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #include "Matcher.hpp" #include diff --git a/src/Matcher.hpp b/src/Matcher.hpp index 23ded26..8b408d8 100644 --- a/src/Matcher.hpp +++ b/src/Matcher.hpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #ifndef THREADS_ARG_MATCHER_HPP #define THREADS_ARG_MATCHER_HPP diff --git a/src/Node.cpp b/src/Node.cpp index 896d59d..12bf8a9 100644 --- a/src/Node.cpp +++ b/src/Node.cpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #include "Node.hpp" #include diff --git a/src/Node.hpp b/src/Node.hpp index cdd3481..1c07075 100644 --- a/src/Node.hpp +++ b/src/Node.hpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #ifndef THREADS_ARG_NODE_HPP #define THREADS_ARG_NODE_HPP diff --git a/src/State.cpp b/src/State.cpp index cd742cc..b726adb 100644 --- a/src/State.cpp +++ b/src/State.cpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #include "State.hpp" #include diff --git a/src/State.hpp b/src/State.hpp index f509032..fcc589f 100644 --- a/src/State.hpp +++ b/src/State.hpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #ifndef THREADS_ARG_STATE_HPP #define THREADS_ARG_STATE_HPP diff --git a/src/TGEN.cpp b/src/TGEN.cpp index fb57a87..fdee447 100644 --- a/src/TGEN.cpp +++ b/src/TGEN.cpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #include "TGEN.hpp" #include "TgenSegment.hpp" diff --git a/src/TGEN.hpp b/src/TGEN.hpp index 75379b7..79b9c2a 100644 --- a/src/TGEN.hpp +++ b/src/TGEN.hpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #ifndef THREADS_ARG_TGEN_HPP #define THREADS_ARG_TGEN_HPP diff --git a/src/TgenSegment.hpp b/src/TgenSegment.hpp index 1439a53..169da45 100644 --- a/src/TgenSegment.hpp +++ b/src/TgenSegment.hpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #ifndef THREADS_ARG_TGEN_SEGMENT_HPP #define THREADS_ARG_TGEN_SEGMENT_HPP diff --git a/src/ThreadsFastLS.cpp b/src/ThreadsFastLS.cpp index 518b1a6..abfc330 100644 --- a/src/ThreadsFastLS.cpp +++ b/src/ThreadsFastLS.cpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #include "ThreadsFastLS.hpp" #include diff --git a/src/ThreadsFastLS.hpp b/src/ThreadsFastLS.hpp index 5b593e1..81a7ce5 100644 --- a/src/ThreadsFastLS.hpp +++ b/src/ThreadsFastLS.hpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #ifndef THREADS_ARG_THREADS_HPP #define THREADS_ARG_THREADS_HPP diff --git a/src/ThreadsLowMem.cpp b/src/ThreadsLowMem.cpp index 36949c2..c7f5c67 100644 --- a/src/ThreadsLowMem.cpp +++ b/src/ThreadsLowMem.cpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #include "ThreadsLowMem.hpp" #include diff --git a/src/ThreadsLowMem.hpp b/src/ThreadsLowMem.hpp index 1e2ecda..182d694 100644 --- a/src/ThreadsLowMem.hpp +++ b/src/ThreadsLowMem.hpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #ifndef THREADS_ARG_THREADS_LOW_MEM_HPP #define THREADS_ARG_THREADS_LOW_MEM_HPP diff --git a/src/ViterbiLowMem.cpp b/src/ViterbiLowMem.cpp index 2c8ce80..e0172d7 100644 --- a/src/ViterbiLowMem.cpp +++ b/src/ViterbiLowMem.cpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #include "ViterbiLowMem.hpp" #include #include diff --git a/src/ViterbiLowMem.hpp b/src/ViterbiLowMem.hpp index 16f5254..a889add 100644 --- a/src/ViterbiLowMem.hpp +++ b/src/ViterbiLowMem.hpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #ifndef THREADS_ARG_VITERBI_LOW_MEM_HPP #define THREADS_ARG_VITERBI_LOW_MEM_HPP diff --git a/src/threads_arg/__init__.py b/src/threads_arg/__init__.py index 580401a..6ef93f0 100644 --- a/src/threads_arg/__init__.py +++ b/src/threads_arg/__init__.py @@ -1 +1,17 @@ +# This file is part of the Threads software suite. +# Copyright (C) 2024 Threads Developers. +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + from threads_arg_python_bindings import * diff --git a/src/threads_arg/__main__.py b/src/threads_arg/__main__.py index d510c3c..62a579c 100644 --- a/src/threads_arg/__main__.py +++ b/src/threads_arg/__main__.py @@ -1,3 +1,19 @@ +# This file is part of the Threads software suite. +# Copyright (C) 2024 Threads Developers. +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + import os import gc import sys diff --git a/src/threads_arg/mapping_utils.py b/src/threads_arg/mapping_utils.py index 3dc00e0..9ae4d5a 100644 --- a/src/threads_arg/mapping_utils.py +++ b/src/threads_arg/mapping_utils.py @@ -1,3 +1,19 @@ +# This file is part of the Threads software suite. +# Copyright (C) 2024 Threads Developers. +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + import arg_needle_lib import numpy as np import logging diff --git a/src/threads_arg/utils.py b/src/threads_arg/utils.py index e1cc24b..f355c50 100644 --- a/src/threads_arg/utils.py +++ b/src/threads_arg/utils.py @@ -1,3 +1,19 @@ +# This file is part of the Threads software suite. +# Copyright (C) 2024 Threads Developers. +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + import os import numpy as np import h5py diff --git a/src/threads_arg_pybind.cpp b/src/threads_arg_pybind.cpp index ca32667..4168f65 100644 --- a/src/threads_arg_pybind.cpp +++ b/src/threads_arg_pybind.cpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #include "ImputationMatcher.hpp" #include "TGEN.hpp" #include "ThreadsLowMem.hpp" diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt index 0dddbfc..7614629 100644 --- a/test/CMakeLists.txt +++ b/test/CMakeLists.txt @@ -1,5 +1,18 @@ -# This file is part of https://github.com/PalamaraLab/threads which is released under the GPL-3.0 license. -# See accompanying LICENSE and COPYING for copyright notice and full details. +# This file is part of the Threads software suite. +# Copyright (C) 2024 Threads Developers. +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . # Get Catch2 Include(FetchContent) diff --git a/test/test_data_snapshot.py b/test/test_data_snapshot.py index 9c9cb4f..318b76f 100644 --- a/test/test_data_snapshot.py +++ b/test/test_data_snapshot.py @@ -1,3 +1,19 @@ +# This file is part of the Threads software suite. +# Copyright (C) 2024 Threads Developers. +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + import numpy as np import h5py import tempfile diff --git a/test/test_demography.cpp b/test/test_demography.cpp index fa9b815..51f0809 100644 --- a/test/test_demography.cpp +++ b/test/test_demography.cpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #include "Demography.hpp" #include diff --git a/test/test_viterbi_state.cpp b/test/test_viterbi_state.cpp index e1bdabe..3356a6d 100644 --- a/test/test_viterbi_state.cpp +++ b/test/test_viterbi_state.cpp @@ -1,3 +1,19 @@ +// This file is part of the Threads software suite. +// Copyright (C) 2024 Threads Developers. +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program. If not, see . + #include "HMM.hpp" #include From 0705d9bbaec00a8db810f35f609a9207e14b25d6 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Fri, 31 May 2024 11:53:43 +0000 Subject: [PATCH 34/42] style: replace FIXMEs comments with ticket ids (#22) --- cmake/CompilerWarnings.cmake | 2 +- src/HMM.cpp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cmake/CompilerWarnings.cmake b/cmake/CompilerWarnings.cmake index eec3ad3..f2f5400 100644 --- a/cmake/CompilerWarnings.cmake +++ b/cmake/CompilerWarnings.cmake @@ -44,7 +44,7 @@ function(set_project_warnings project_name) -Woverloaded-virtual # warn if you overload (not override) a virtual function -Wpedantic # warn if non-standard C++ is used -Wconversion # warn on type conversions that may lose data - # FIXME for review with Arni, lots of errors due to int <-> size_t conversion. Determine correct types + # TODO Change int to size_t where appropriate (ticket #26) #-Wsign-conversion # warn on sign conversions -Wnull-dereference # warn if a null dereference is detected -Wdouble-promotion # warn if float is implicit promoted to double diff --git a/src/HMM.cpp b/src/HMM.cpp index 2f7d6f4..dd48636 100644 --- a/src/HMM.cpp +++ b/src/HMM.cpp @@ -28,7 +28,7 @@ HMM::HMM(Demography demography, std::vector bp_sizes, std::vector trellis_row(num_states, 0.0); std::vector pointer_row(num_states, 0); From 2edb77051ec3ba4183f8b3c018110002fd0a0022 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Fri, 31 May 2024 13:25:27 +0000 Subject: [PATCH 35/42] fix: resolve warnings found by clang (#22) * Unlike GCC, clang needs to explicitly be told -Wno-sign-conversion * Removed unused vars * Removed implicit copy constructor TgenSegment * Removed std::move on unique ptr (copy elision warning) --- cmake/CompilerWarnings.cmake | 3 ++- src/Matcher.hpp | 1 - src/TgenSegment.hpp | 4 ---- src/ThreadsFastLS.cpp | 11 ++--------- src/ViterbiLowMem.cpp | 1 - 5 files changed, 4 insertions(+), 16 deletions(-) diff --git a/cmake/CompilerWarnings.cmake b/cmake/CompilerWarnings.cmake index f2f5400..2adab9c 100644 --- a/cmake/CompilerWarnings.cmake +++ b/cmake/CompilerWarnings.cmake @@ -44,7 +44,8 @@ function(set_project_warnings project_name) -Woverloaded-virtual # warn if you overload (not override) a virtual function -Wpedantic # warn if non-standard C++ is used -Wconversion # warn on type conversions that may lose data - # TODO Change int to size_t where appropriate (ticket #26) + # TODO replace -Wno-sign-conversion with -Wsign-conversion (ticket #26) + -Wno-sign-conversion # disabled until int/size_t resolved #-Wsign-conversion # warn on sign conversions -Wnull-dereference # warn if a null dereference is detected -Wdouble-promotion # warn if float is implicit promoted to double diff --git a/src/Matcher.hpp b/src/Matcher.hpp index 8b408d8..fbe5a41 100644 --- a/src/Matcher.hpp +++ b/src/Matcher.hpp @@ -73,7 +73,6 @@ class Matcher { int sites_processed = 0; int next_query_site_idx = 0; int match_group_idx = 0; - int min_match_length = 1; std::vector match_groups; std::vector sorting; std::vector next_sorting; diff --git a/src/TgenSegment.hpp b/src/TgenSegment.hpp index 169da45..1a89c84 100644 --- a/src/TgenSegment.hpp +++ b/src/TgenSegment.hpp @@ -28,10 +28,6 @@ class TgenSegment { TgenSegment() : target(std::numeric_limits::max()), first(), past() { } - TgenSegment(const TgenSegment& other) - : het_sites(other.het_sites), target(other.target), first(other.first), past(other.past) { - } - TgenSegment(int lo, int up) : target(std::numeric_limits::max()), first(lo), past(up) { } diff --git a/src/ThreadsFastLS.cpp b/src/ThreadsFastLS.cpp index abfc330..7d08355 100644 --- a/src/ThreadsFastLS.cpp +++ b/src/ThreadsFastLS.cpp @@ -222,7 +222,7 @@ void ThreadsFastLS::insert(const int ID, const std::vector& genotype) { panel.emplace_back(std::vector>(num_sites + 1)); Node* t0 = bottoms[0].get(); - panel[ID_map.at(ID)][0] = std::move(std::make_unique(ID, 0, genotype[0])); + panel[ID_map.at(ID)][0] = std::make_unique(ID, 0, genotype[0]); Node* z0 = panel[ID_map.at(ID)][0].get(); // Inserts z0 above t0 @@ -238,7 +238,7 @@ void ThreadsFastLS::insert(const int ID, const std::vector& genotype) { bool g_k = genotype[k]; bool next_genotype = (k == num_sites - 1) ? END_ALLELE : genotype[k + 1]; // Add current thingy to panel - panel[ID_map.at(ID)][k + 1] = std::move(std::make_unique(ID, k + 1, next_genotype)); + panel[ID_map.at(ID)][k + 1] = std::make_unique(ID, k + 1, next_genotype); z_next = panel[ID_map.at(ID)][k + 1].get(); tmp = z_k->above; while (tmp->sample_ID != -1 && tmp->genotype != g_k) { @@ -962,7 +962,6 @@ std::vector>> ThreadsFastLS::traceback(TracebackState* tb, Node* match, bool return_all) { std::vector>> best_path; while (tb != nullptr) { - int n_matches = 1; int segment_start = tb->site; int match_id = match->sample_ID; std::vector div_states = {match_id}; @@ -977,7 +976,6 @@ ThreadsFastLS::traceback(TracebackState* tb, Node* match, bool return_all) { break; } div_states.push_back(div_node->sample_ID); - n_matches += 1; if (div_node->sample_ID < min_id) { min_id = div_node->sample_ID; } @@ -1009,7 +1007,6 @@ ThreadsFastLS::traceback_impute(std::vector& genotypes, TracebackState* tb std::vector, std::vector, std::vector>> imputation_path; int prev_end = num_sites; while (tb != nullptr) { - int n_matches = 1; int segment_start = tb->site; int segment_end = prev_end; prev_end = segment_start; @@ -1028,7 +1025,6 @@ ThreadsFastLS::traceback_impute(std::vector& genotypes, TracebackState* tb break; } div_states.push_back(div_node->sample_ID); - n_matches += 1; if (div_node->sample_ID < min_id) { min_id = div_node->sample_ID; } @@ -1037,7 +1033,6 @@ ThreadsFastLS::traceback_impute(std::vector& genotypes, TracebackState* tb div_node = match->below; while (div_node != nullptr && div_node->divergence <= segment_start) { div_states.push_back(div_node->sample_ID); - n_matches += 1; if (div_node->sample_ID < min_id) { min_id = div_node->sample_ID; } @@ -1311,7 +1306,6 @@ ThreadsFastLS::thread(const int new_sample_ID, const std::vector& genotype std::vector bp_starts; std::vector> target_IDs; std::vector segment_ages; - int total_num_het_sites = 0; // Date segments for (int i = 0; i < static_cast(best_path.size()); i++) { int segment_start = std::get<0>(best_path[i]); @@ -1328,7 +1322,6 @@ ThreadsFastLS::thread(const int new_sample_ID, const std::vector& genotype num_het_sites++; } } - total_num_het_sites += num_het_sites; if (use_hmm && num_samples < HMM_SPLIT_THRESHOLD) { // is it ok to have 10 here? diff --git a/src/ViterbiLowMem.cpp b/src/ViterbiLowMem.cpp index e0172d7..499cf47 100644 --- a/src/ViterbiLowMem.cpp +++ b/src/ViterbiLowMem.cpp @@ -25,7 +25,6 @@ namespace { -const int ALLELE_MISSING = -9; const int ALLELE_UNPHASED_HET = -7; inline size_t coord_id_key(int i, int j) { From 56243011c7031193c39a47a2527ce0a9573dae55 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Fri, 31 May 2024 13:26:43 +0000 Subject: [PATCH 36/42] build: update auto-generated file associations (#22) --- .vscode/settings.json | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index 92dee53..a67d847 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -84,6 +84,8 @@ "typeindex": "cpp", "typeinfo": "cpp", "valarray": "cpp", - "variant": "cpp" + "variant": "cpp", + "core": "cpp", + "geometry": "cpp" } } From 6ed287bf304dd6f9f589ef897e92a9dc75548e2d Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Fri, 31 May 2024 13:42:53 +0000 Subject: [PATCH 37/42] fix: GCC found potentially uninitialised variable (#22) --- src/ThreadsFastLS.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ThreadsFastLS.cpp b/src/ThreadsFastLS.cpp index 7d08355..c74f8f5 100644 --- a/src/ThreadsFastLS.cpp +++ b/src/ThreadsFastLS.cpp @@ -571,7 +571,7 @@ ThreadsFastLS::fastLS_diploid(const std::vector& genotype) { for (StatePair& p : current_pairs) { std::size_t key_a = pair_key(p.below_a->above->sample_ID, p.traceback_a->site); std::size_t key_b = pair_key(p.below_b->above->sample_ID, p.traceback_b->site); - double z_pair; + double z_pair = 0.0; // Set/get extensibility if (extmap_0.count(key_a)) { From 8141f0c0e5ae4e2fe68ab043debec0307e66dce4 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Fri, 31 May 2024 14:00:54 +0000 Subject: [PATCH 38/42] fix: update demography exception condition (#22) * The text was adjusted as we tweaked the condition logic on the first arg, after finding potential access to -1th index during tidy. --- test/test_demography.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/test_demography.cpp b/test/test_demography.cpp index 51f0809..c2edca1 100644 --- a/test/test_demography.cpp +++ b/test/test_demography.cpp @@ -46,6 +46,6 @@ TEST_CASE("Demography constructor exceptions") { TEST_CASE("Demography std_to_gen exceptions") { SECTION("std_to_gen value must be non-negative") { Demography d{{1}, {0}}; - CHECK_THROWS_WITH(d.std_to_gen(-1), Catch::Matchers::ContainsSubstring("Demography can only convert non-negative times to std")); + CHECK_THROWS_WITH(d.std_to_gen(-1), Catch::Matchers::ContainsSubstring("Demography can only convert times greater than the first entry")); } } From 5e329a0ee4eaa67a83248150f71b42963ae65fee Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Fri, 31 May 2024 14:27:34 +0000 Subject: [PATCH 39/42] fix: ensure vector has valid size (#22) * The previous use of `int` raised an warning in GCC that the size of boundaries could be invalid and generate a null ptr deref. Changing to `size_t` removes possibility of negative cases. --- src/ThreadsFastLS.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/ThreadsFastLS.cpp b/src/ThreadsFastLS.cpp index c74f8f5..72aeec9 100644 --- a/src/ThreadsFastLS.cpp +++ b/src/ThreadsFastLS.cpp @@ -145,15 +145,15 @@ ThreadsFastLS::ThreadsFastLS(std::vector _physical_positions, std::tuple, std::vector> ThreadsFastLS::site_sizes(std::vector positions) { // Find mid-points between sites - int M = static_cast(positions.size()); + std::size_t M = positions.size(); std::vector pos_means(M - 1); - for (int i = 0; i < M - 1; i++) { + for (std::size_t i = 0; i < M - 1; i++) { pos_means[i] = (positions[i] + positions[i + 1]) / 2.; } // Find the mean size of mid-point differences std::vector site_sizes(M); // Mid-point deltas tell us about the area around each site - for (int i = 1; i < M - 1; i++) { + for (std::size_t i = 1; i < M - 1; i++) { site_sizes[i] = (pos_means[i] - pos_means[i - 1]); } double mean_size = (pos_means[M - 2] - pos_means[0]) / double(M - 2); @@ -168,7 +168,7 @@ ThreadsFastLS::site_sizes(std::vector positions) { std::vector boundaries(M + 1); boundaries[0] = positions[0]; boundaries[M] = positions[M - 1]; - for (int i = 1; i < M; i++) { + for (std::size_t i = 1; i < M; i++) { boundaries[i] = pos_means[i - 1]; } return std::tuple(boundaries, site_sizes); From 8fa0fb2a6b7d7f7c4ea24d241cdb1862925df819 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Fri, 31 May 2024 14:28:24 +0000 Subject: [PATCH 40/42] style: tidy remaining size_t to std::size_t (#22) --- src/ThreadsFastLS.cpp | 14 +++++++------- src/ViterbiLowMem.cpp | 25 +++++++++++++------------ src/ViterbiLowMem.hpp | 12 ++++++------ 3 files changed, 26 insertions(+), 25 deletions(-) diff --git a/src/ThreadsFastLS.cpp b/src/ThreadsFastLS.cpp index 72aeec9..99b26b2 100644 --- a/src/ThreadsFastLS.cpp +++ b/src/ThreadsFastLS.cpp @@ -1,16 +1,16 @@ // This file is part of the Threads software suite. // Copyright (C) 2024 Threads Developers. -// +// // This program is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. -// +// // This program is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. -// +// // You should have received a copy of the GNU General Public License // along with this program. If not, see . @@ -39,7 +39,7 @@ namespace { const int END_ALLELE = 0; const int HMM_SPLIT_THRESHOLD = 1000; -inline size_t pair_key(int i, int j) { +inline std::size_t pair_key(int i, int j) { return (static_cast(i) << 32) | static_cast(j); } @@ -1237,8 +1237,7 @@ double ThreadsFastLS::date_segment(int num_het_sites, double cm_size, double bp_ return numerator / denominator; } -double ThreadsFastLS::date_segment_sparse(double cm_size, - Demography& demography) { +double ThreadsFastLS::date_segment_sparse(double cm_size, Demography& demography) { double rho = 2. * 0.01 * cm_size; double numerator = 0; @@ -1334,7 +1333,8 @@ ThreadsFastLS::thread(const int new_sample_ID, const std::vector& genotype (j == (static_cast(breakpoints.size()) - 1)) ? segment_end : breakpoints[j + 1]; target_IDs.push_back(target_ID_L); bp_starts.push_back(static_cast(ceil(bp_boundaries[breakpoint_start]))); - // TODO Pass right number of heterozygous sites to date segments when HMM is used (ticket #24) + // TODO Pass right number of heterozygous sites to date segments when HMM is used (ticket + // #24) segment_ages.push_back(date_segment(num_het_sites, breakpoint_start, breakpoint_end)); } } diff --git a/src/ViterbiLowMem.cpp b/src/ViterbiLowMem.cpp index 499cf47..27273f5 100644 --- a/src/ViterbiLowMem.cpp +++ b/src/ViterbiLowMem.cpp @@ -1,16 +1,16 @@ // This file is part of the Threads software suite. // Copyright (C) 2024 Threads Developers. -// +// // This program is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. -// +// // This program is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. -// +// // You should have received a copy of the GNU General Public License // along with this program. If not, see . @@ -27,7 +27,7 @@ namespace { const int ALLELE_UNPHASED_HET = -7; -inline size_t coord_id_key(int i, int j) { +inline std::size_t coord_id_key(int i, int j) { return (static_cast(i) << 32) | static_cast(j); } @@ -37,7 +37,7 @@ TracebackNode::TracebackNode(int _sample_id, int _site, TracebackNode* _previous : sample_id(_sample_id), site(_site), previous(_previous), score(_score) { } -size_t TracebackNode::key() { +std::size_t TracebackNode::key() const { return coord_id_key(site, sample_id); } @@ -129,7 +129,7 @@ ViterbiState::ViterbiState(int _target_id, std::vector _sample_ids) std::to_string(target_id)); } for (int sample_id : sample_ids) { - size_t key = coord_id_key(0, sample_id); + std::size_t key = coord_id_key(0, sample_id); traceback_states.emplace(key, TracebackNode(sample_id, 0, nullptr, 0.)); current_tracebacks[sample_id] = &traceback_states.at(key); } @@ -158,7 +158,7 @@ void ViterbiState::process_site(const std::vector& genotype, double rho, do // If we've just added new sites (this will happen vary rarely), // recombine from previous best state new_score = best_score + copy_penalty + rho; - size_t key = coord_id_key(current_site, sample_id); + std::size_t key = coord_id_key(current_site, sample_id); traceback_states.emplace(key, TracebackNode(sample_id, current_site, prev_best, new_score)); current_tracebacks[sample_id] = &traceback_states.at(key); } @@ -173,7 +173,7 @@ void ViterbiState::process_site(const std::vector& genotype, double rho, do else { // If we recombine, add a new branch new_score = best_score + copy_penalty + rho; - size_t key = coord_id_key(current_site, sample_id); + std::size_t key = coord_id_key(current_site, sample_id); traceback_states.emplace(key, TracebackNode(sample_id, current_site, prev_best, new_score)); current_tracebacks.at(sample_id) = &traceback_states.at(key); } @@ -203,7 +203,7 @@ void ViterbiState::set_samples(std::unordered_set new_sample_ids) { } void ViterbiState::prune() { - std::unordered_map tmp_traceback_states; + std::unordered_map tmp_traceback_states; for (int sample_id : sample_ids) { TracebackNode* state = current_tracebacks.at(sample_id); @@ -220,12 +220,13 @@ void ViterbiState::prune() { } // add everything above and return a key to the new address -TracebackNode* ViterbiState::recursive_insert(std::unordered_map& state_map, - TracebackNode* state) { +TracebackNode* +ViterbiState::recursive_insert(std::unordered_map& state_map, + TracebackNode* state) { if (state == nullptr) { return nullptr; } - size_t key = state->key(); + std::size_t key = state->key(); if (!state_map.count(key)) { TracebackNode* parent = state->previous; TracebackNode* new_parent = recursive_insert(state_map, parent); diff --git a/src/ViterbiLowMem.hpp b/src/ViterbiLowMem.hpp index a889add..9a288ea 100644 --- a/src/ViterbiLowMem.hpp +++ b/src/ViterbiLowMem.hpp @@ -1,16 +1,16 @@ // This file is part of the Threads software suite. // Copyright (C) 2024 Threads Developers. -// +// // This program is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. -// +// // This program is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. -// +// // You should have received a copy of the GNU General Public License // along with this program. If not, see . @@ -25,7 +25,7 @@ class TracebackNode { public: TracebackNode(int _sample_id, int _site, TracebackNode* _previous, double _score); - size_t key(); + std::size_t key() const; public: int sample_id = 0; @@ -69,8 +69,8 @@ class ViterbiState { ViterbiPath traceback(); private: - std::unordered_map traceback_states; - TracebackNode* recursive_insert(std::unordered_map& state_map, + std::unordered_map traceback_states; + TracebackNode* recursive_insert(std::unordered_map& state_map, TracebackNode* state); public: From 32e4882d193a000f21493cca4e2818d457acd91f Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Mon, 3 Jun 2024 10:52:50 +0000 Subject: [PATCH 41/42] fix: throw error on invalid allele (#22) * Updating my original fix with feedback from Arni: throw exception on unhandled allele; init `z_pair` penalty/cost value to numeric max. --- src/ThreadsFastLS.cpp | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/ThreadsFastLS.cpp b/src/ThreadsFastLS.cpp index 99b26b2..1f81f5e 100644 --- a/src/ThreadsFastLS.cpp +++ b/src/ThreadsFastLS.cpp @@ -571,7 +571,7 @@ ThreadsFastLS::fastLS_diploid(const std::vector& genotype) { for (StatePair& p : current_pairs) { std::size_t key_a = pair_key(p.below_a->above->sample_ID, p.traceback_a->site); std::size_t key_b = pair_key(p.below_b->above->sample_ID, p.traceback_b->site); - double z_pair = 0.0; + double z_pair = std::numeric_limits::max(); // Set/get extensibility if (extmap_0.count(key_a)) { @@ -642,6 +642,10 @@ ThreadsFastLS::fastLS_diploid(const std::vector& genotype) { z_pair = p.score + 2 * mutation_cost; } } + else { + throw std::runtime_error("Illegal genotype value " + std::to_string(allele)); + } + if (!local_min.count(key_a)) { // Set local minima local_min[key_a] = z_pair; From f8defe708e839d2774f9d73235451f9e2b9e9021 Mon Sep 17 00:00:00 2001 From: Alex Allmont Date: Mon, 3 Jun 2024 10:58:26 +0000 Subject: [PATCH 42/42] build: remove h5py from devcontainer deps (#22) * This dependency comes in automatically with arg-needle-lib and can cause confusion if done beforehand, e.g. running on a platform like macos which does not yet have a pypi build. Also makes image creation faster. --- .devcontainer/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index cc1018a..18f386b 100644 --- a/.devcontainer/Dockerfile +++ b/.devcontainer/Dockerfile @@ -9,7 +9,7 @@ RUN apt-get install -y \ # Packages for local testing RUN pip install --upgrade pip setuptools wheel -RUN pip install pytest h5py numpy +RUN pip install pytest numpy # Packages for local build RUN pip install cmake ninja