BayesTyper (v1.1)

bioinformatics-centre · Aug 16, 2017 · 1e34c12 · 1e34c12
1 parent 3372b1e
commit 1e34c12
Show file tree

Hide file tree

Showing 138 changed files with 1,383 additions and 1,570 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -14,7 +14,7 @@ execute_process(
   OUTPUT_STRIP_TRAILING_WHITESPACE
 )
 
-SET(CMAKE_CXX_FLAGS "--std=c++11 -g -Wall -O3 -DBT_VERSION='\"${GIT_BRANCH} ${GIT_LAST_COMMIT_HASH}\"' -lpthread")
+SET(CMAKE_CXX_FLAGS "--std=c++11 -g -Wall -O3 -DBT_VERSION='\"v1.1 ${GIT_LAST_COMMIT_HASH}\"' -lpthread")
 
 FIND_PACKAGE(Boost COMPONENTS program_options system filesystem iostreams REQUIRED)
 message(STATUS ${Boost_LIBRARIES})

diff --git a/include/bayesTyper/BitsetCompare.hpp b/include/bayesTyper/BitsetCompare.hpp
@@ -1,6 +1,6 @@
 
 /*
-BitsetCompare.hpp - This file is part of BayesTyper (v0.9)
+BitsetCompare.hpp - This file is part of BayesTyper (v1.1)
 
 
 The MIT License (MIT)

diff --git a/include/bayesTyper/ChromosomePloidy.hpp b/include/bayesTyper/ChromosomePloidy.hpp
@@ -1,6 +1,6 @@
 
 /*
-ChromosomePloidy.hpp - This file is part of BayesTyper (v0.9)
+ChromosomePloidy.hpp - This file is part of BayesTyper (v1.1)
 
 
 The MIT License (MIT)

diff --git a/include/bayesTyper/Combinator.hpp b/include/bayesTyper/Combinator.hpp
@@ -1,6 +1,6 @@
 
 /*
-Combinator.hpp - This file is part of BayesTyper (v0.9)
+Combinator.hpp - This file is part of BayesTyper (v1.1)
 
 
 The MIT License (MIT)

diff --git a/include/bayesTyper/CountAllocation.hpp b/include/bayesTyper/CountAllocation.hpp
@@ -1,6 +1,6 @@
 
 /*
-CountAllocation.hpp - This file is part of BayesTyper (v0.9)
+CountAllocation.hpp - This file is part of BayesTyper (v1.1)
 
 
 The MIT License (MIT)

diff --git a/include/bayesTyper/CountDistribution.hpp b/include/bayesTyper/CountDistribution.hpp
@@ -1,6 +1,6 @@
 
 /*
-CountDistribution.hpp - This file is part of BayesTyper (v0.9)
+CountDistribution.hpp - This file is part of BayesTyper (v1.1)
 
 
 The MIT License (MIT)

diff --git a/include/bayesTyper/DiscreteSampler.hpp b/include/bayesTyper/DiscreteSampler.hpp
@@ -1,6 +1,6 @@
 
 /*
-DiscreteSampler.hpp - This file is part of BayesTyper (v0.9)
+DiscreteSampler.hpp - This file is part of BayesTyper (v1.1)
 
 
 The MIT License (MIT)

diff --git a/include/bayesTyper/FrequencyDistribution.hpp b/include/bayesTyper/FrequencyDistribution.hpp
@@ -1,6 +1,6 @@
 
 /*
-FrequencyDistribution.hpp - This file is part of BayesTyper (v0.9)
+FrequencyDistribution.hpp - This file is part of BayesTyper (v1.1)
 
 
 The MIT License (MIT)

diff --git a/include/bayesTyper/GenotypeWriter.hpp b/include/bayesTyper/GenotypeWriter.hpp
@@ -1,6 +1,6 @@
 
 /*
-GenotypeWriter.hpp - This file is part of BayesTyper (v0.9)
+GenotypeWriter.hpp - This file is part of BayesTyper (v1.1)
 
 
 The MIT License (MIT)
@@ -74,7 +74,7 @@ class GenotypeWriter {
 		void writeVariantStats(ofstream *, const Genotypes::VariantStats &, const VariantInfo &);
 		void writeAlleleCover(ofstream *, vector<ushort> *, VariantInfo *);
 		void writeSamples(ofstream *, const vector<Genotypes::SampleStats> &, const VariantInfo &);
-		void writeAlleleKmerStats(ofstream *, const vector<FixedKmerStats> &);
+		void writeAlleleKmerStats(ofstream *, const AlleleKmerStats &);
 
 		void addAlleleKmerEstimates(const vector<Genotypes::SampleStats> &);
 

diff --git a/include/bayesTyper/Genotypes.hpp b/include/bayesTyper/Genotypes.hpp
@@ -1,6 +1,6 @@
 
 /*
-Genotypes.hpp - This file is part of BayesTyper (v0.9)
+Genotypes.hpp - This file is part of BayesTyper (v1.1)
 
 
 The MIT License (MIT)
@@ -57,7 +57,7 @@ class Genotypes {
 		ushort variant_cluster_size;
 		uint variant_cluster_group_size;
 
-		uchar has_complex_region : 1, has_redundant_sequence : 1;
+		bool has_redundant_sequence;
 
 		VariantInfo variant_info;
 		vector<ushort> non_covered_alleles;
@@ -82,7 +82,7 @@ class Genotypes {
 		    vector<float> genotype_posteriors;
 
 		    vector<float> allele_posteriors;
-			vector<FixedKmerStats> allele_kmer_stats;
+			AlleleKmerStats allele_kmer_stats;
 
 			bool is_allele_kmer_estimate_variant;
 
@@ -94,8 +94,6 @@ class Genotypes {
 			SampleStats(const ushort num_alleles, const uint num_genotypes) : genotype_posteriors(num_genotypes, 0), allele_posteriors(num_alleles, 0) {
 
 				genotype_estimate.reserve(2);
-				allele_kmer_stats.reserve(num_alleles);
-
 				is_allele_kmer_estimate_variant = false;
 			}
 		};

diff --git a/include/bayesTyper/HaplotypeFrequencyDistribution.hpp b/include/bayesTyper/HaplotypeFrequencyDistribution.hpp
@@ -1,6 +1,6 @@
 
 /*
-HaplotypeFrequencyDistribution.hpp - This file is part of BayesTyper (v0.9)
+HaplotypeFrequencyDistribution.hpp - This file is part of BayesTyper (v1.1)
 
 
 The MIT License (MIT)

diff --git a/include/bayesTyper/HybridHash.hpp b/include/bayesTyper/HybridHash.hpp
@@ -1,6 +1,6 @@
 
 /*
-HybridHash.hpp - This file is part of BayesTyper (v0.9)
+HybridHash.hpp - This file is part of BayesTyper (v1.1)
 
 
 The MIT License (MIT)

diff --git a/include/bayesTyper/HybridHash.tpp b/include/bayesTyper/HybridHash.tpp
@@ -1,3 +1,32 @@
+
+/*
+HybridHash.tpp - This file is part of BayesTyper (v1.1)
+
+
+The MIT License (MIT)
+
+Copyright (c) 2016 Jonas Andreas Sibbesen and Lasse Maretty
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+*/
+
+
 #include <iostream>
 #include <math.h>
 #include <assert.h>

diff --git a/include/bayesTyper/InferenceEngine.hpp b/include/bayesTyper/InferenceEngine.hpp
@@ -1,6 +1,6 @@
 
 /*
-InferenceEngine.hpp - This file is part of BayesTyper (v0.9)
+InferenceEngine.hpp - This file is part of BayesTyper (v1.1)
 
 
 The MIT License (MIT)
@@ -68,11 +68,12 @@ class InferenceEngine {
 
 		const uint prng_seed;
 		const ushort num_threads;
-		const ushort num_haplotype_candidates_per_sample;
+		const ushort max_sample_haplotype_candidates;
 		const uchar num_genomic_rate_gc_bias_bins;
 		const ushort gibbs_burn;
 		const ushort gibbs_samples;
 		const ushort num_gibbs_chains;
+		const float kmer_subsampling_rate;
 		const uint max_haplotype_variant_kmers;
 		const ushort num_parameter_estimation_samples;
 		const uint num_parameter_estimation_snvs;

diff --git a/include/bayesTyper/Kmer.hpp b/include/bayesTyper/Kmer.hpp
@@ -1,6 +1,6 @@
 
 /*
-Kmer.hpp - This file is part of BayesTyper (v0.9)
+Kmer.hpp - This file is part of BayesTyper (v1.1)
 
 
 The MIT License (MIT)

diff --git a/include/bayesTyper/Kmer.tpp b/include/bayesTyper/Kmer.tpp
@@ -1,4 +1,31 @@
 
+/*
+Kmer.tpp - This file is part of BayesTyper (v1.1)
+
+
+The MIT License (MIT)
+
+Copyright (c) 2016 Jonas Andreas Sibbesen and Lasse Maretty
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+*/
+
 
 template<uchar size>
 const bitset<size*2> & Kmer<size>::getKmer() {

diff --git a/include/bayesTyper/KmerCounter.hpp b/include/bayesTyper/KmerCounter.hpp
@@ -1,6 +1,6 @@
 
 /*
-KmerCounter.hpp - This file is part of BayesTyper (v0.9)
+KmerCounter.hpp - This file is part of BayesTyper (v1.1)
 
 
 The MIT License (MIT)
@@ -53,7 +53,7 @@ class KmerCounter {
 
 		KmerCounter(KmerHash * const, Utils::SmallmerSet * const, const ushort);
 
-		ulong countVariantClusterSmallmers(vector<VariantClusterGroup *> *);
+		ulong countVariantClusterSmallmers(vector<VariantClusterGraph *> *);
 		ulong countInterclusterKmers(const vector<VariantFileParser::InterClusterRegion> &);
 		ulong countSampleKmers(const vector<Sample> &);
 		void countVariantClusterKmers(vector<VariantClusterGroup *> *, const uint, const ushort, const ushort);
@@ -79,7 +79,7 @@ class KmerCounter {
 
 		uchar min_sample_kmer_count;
 
-		void countVariantClusterSmallmersCallback(vector<VariantClusterGroup *> *, const ushort, mutex *, ulong *);
+		void countVariantClusterSmallmersCallback(vector<VariantClusterGraph *> *, const ushort, mutex *, ulong *);
 		void countInterclusterKmersCallback(const vector<VariantFileParser::InterClusterRegion> &, const ushort, mutex *, ulong *);
 		void countSampleKmersCallBack(ProducerConsumerQueue<KmerBatchInfo *> *, ProducerConsumerQueue<KmerBatchInfo *> *, mutex *, ulong *);
 		void countVariantClusterKmersCallback(vector<VariantClusterGroup *> *, const uint, const ushort, const ushort, const ushort);

diff --git a/include/bayesTyper/KmerCounts.hpp b/include/bayesTyper/KmerCounts.hpp
@@ -1,6 +1,6 @@
 
 /*
-KmerCounts.hpp - This file is part of BayesTyper (v0.9)
+KmerCounts.hpp - This file is part of BayesTyper (v1.1)
 
 
 The MIT License (MIT)

diff --git a/include/bayesTyper/KmerFactory.hpp b/include/bayesTyper/KmerFactory.hpp
@@ -1,6 +1,6 @@
 
 /*
-KmerFactory.hpp - This file is part of BayesTyper (v0.9)
+KmerFactory.hpp - This file is part of BayesTyper (v1.1)
 
 
 The MIT License (MIT)
@@ -55,11 +55,12 @@ class KmerFactory {
 		const uint prng_seed;
 		const string vcf_file;
 		const string genome_file;
+		const string output_prefix;
 		const string decoy_file;
 		const ushort num_threads;
 		const uint max_allele_length;
 		const double copy_number_variant_threshold;
-		const ushort num_haplotype_candidates_per_sample;
+		const ushort max_sample_haplotype_candidates;
 		const uchar num_genomic_rate_gc_bias_bins;
 
 		ulong number_of_variants;

diff --git a/include/bayesTyper/KmerHash.hpp b/include/bayesTyper/KmerHash.hpp
@@ -1,6 +1,6 @@
 
 /*
-KmerHash.hpp - This file is part of BayesTyper (v0.9)
+KmerHash.hpp - This file is part of BayesTyper (v1.1)
 
 
 The MIT License (MIT)

diff --git a/include/bayesTyper/KmerStats.hpp b/include/bayesTyper/KmerStats.hpp
@@ -1,6 +1,6 @@
 
 /*
-KmerStats.hpp - This file is part of BayesTyper (v0.9)
+KmerStats.hpp - This file is part of BayesTyper (v1.1)
 
 
 The MIT License (MIT)
@@ -45,86 +45,31 @@ class KmerStats {
 		KmerStats();
 
 		void reset();
-		void addKmer(KmerCounts * const, const ushort, const float);
+		void addValue(const pair<float, bool> &);
 
-		float getCount() const;		
+		uint getCount() const;		
 		pair<float, bool> getFraction() const;
 		pair<float, bool> getMean() const;
 
-	protected:
-
-		float count;
-		float fraction;
-		float mean;
-};
-
-class FixedKmerStats {
-
-	public:
-
-		FixedKmerStats();
-		FixedKmerStats(const float, const float, const float);
-
-		float getCount() const;		
-		float getFraction() const;
-		float getMean() const;
+	private:
 
-		float count;
+		uint count;
 		float fraction;
 		float mean;
 };
 
-class MedianKmerStats {
-
-	public:
-
-		MedianKmerStats();
-
-		void addKmerStats(const KmerStats &);
-
-		pair<float, bool> getMedianCount();		
-		pair<float, bool> getMedianFraction();
-		pair<float, bool> getMedianMean();
-
-	private:
-
-		struct floatLess {
-
-			bool operator() (const float & first, const float & second) const {
-
-				if (Utils::floatCompare(first, second)) {
-
-					return false;
-
-				} else {
-
-					return first < second;
-				}
-			}
-		};
-
-		pair<float, bool> median(SortedLinearMap<float, uint, floatLess> &, const uint);
-
-		SortedLinearMap<float, uint, floatLess> count_values;
-		uint num_count_values;
-
-		SortedLinearMap<float, uint, floatLess> fraction_values;
-		uint num_fraction_values;
-
-		SortedLinearMap<float, uint, floatLess> mean_values;
-		uint num_mean_values;
-};
-
-class VariantKmerStats {
+class AlleleKmerStats {
 
 	public:
 
-		vector<vector<MedianKmerStats> > allele_kmer_stats;
+		vector<KmerStats> count_stats;
+		vector<KmerStats> fraction_stats;
+		vector<KmerStats> mean_stats;
 
-		VariantKmerStats();
-		VariantKmerStats(const ushort, const ushort);
+		AlleleKmerStats() {};
+		AlleleKmerStats(const ushort);
 
-		void addAlleleKmerStats(const KmerStats &, const ushort, const ushort);
+		void addKmerStats(const KmerStats &, const ushort);
 };
 
 #endif