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/* Copyright (C) 2013 Ion Torrent Systems, Inc. All Rights Reserved */
#ifndef DECISIONTREEDATA_H
#define DECISIONTREEDATA_H
#include "api/BamReader.h"
#include <iostream>
#include <sstream>
#include <string>
#include <algorithm>
#include <iterator>
#include <math.h>
#include <vector>
#include "ClassifyVariant.h"
#include "StackEngine.h"
#include "VcfFormat.h"
class EvaluatedGenotype{
public:
bool genotype_already_set;
float evaluated_genotype_quality;
float evaluated_variant_quality;
vector<int> genotype_component;
EvaluatedGenotype(){
genotype_already_set = false;
evaluated_genotype_quality = 0.0f;
evaluated_variant_quality = 0.0f;
genotype_component.assign(2,0); // 0/0 = reference call
};
string GenotypeAsString();
bool IsReference();
};
// all the data needed to make a decision for filtration
// characterize the variant, and the outcome from whatever evaluator we use
class DecisionTreeData {
public:
vcf::Variant * variant; //!< VCF record of this variant position
vector<AlleleIdentity> allele_identity_vector; //!< Detailed information for each candidate allele
vector<string> info_fields; //!< Additional information to be printed out in vcf FR tag
MultiBook all_summary_stats;
vector<VariantOutputInfo> summary_info_vector;
vector<int> filteredAllelesIndex;
bool best_variant_filtered;
bool best_allele_set;
int best_allele_index;
bool isBestAlleleSNP;
bool reference_genotype;
EvaluatedGenotype eval_genotype;
float tune_xbias; // not tuned, removed from filters
float tune_sbias;
DecisionTreeData(vcf::Variant &candidate_variant) /*: multi_allele(candidate_variant)*/ {
variant = &candidate_variant;
best_allele_set = false;
best_allele_index = 0;
best_variant_filtered=false;
isBestAlleleSNP = false;
reference_genotype = false;
tune_xbias = 0.005f; // tune calculation of chi-square bias = proportioinal variance by frequency
tune_sbias = 0.5f; // safety factor for small allele counts for transformed strand bias
};
void OverrideFilter(string & _filter_reason, int _allele);
void FilterOneAllele(int i_alt,VariantOutputInfo &l_summary_info,
AlleleIdentity &l_variant_identity, const ControlCallAndFilters &my_filters,
const VariantSpecificParams& variant_specific_params);
void FilterAlleles(const ControlCallAndFilters &my_filters, const vector<VariantSpecificParams>& variant_specific_params);
void AccumulateFilteredAlleles();
void BestSNPsSuppressInDels(bool heal_snps);
void FindBestAlleleIdentity();
void FindBestAlleleByScore();
void GenotypeFromBestAlleleIndex(vcf::Variant &candidate_variant, const ExtendParameters ¶meters);
void GenotypeFromEvaluator(vcf::Variant &candidate_variant, const ExtendParameters ¶meters);
void FilterMyCandidate(vcf::Variant &candidate_variant, const ExtendParameters ¶meters);
void BestAlleleFilterMyCandidate(vcf::Variant &candidate_variant, const ExtendParameters ¶meters);
void GenotypeAlleleFilterMyCandidate(vcf::Variant &candidate_variant, const ExtendParameters ¶meters);
void SimplifySNPsIfNeeded(VariantCandidate &candidate_variant, const ExtendParameters ¶meters);
bool SetGenotype(vcf::Variant &candidate_variant, const ExtendParameters ¶meters, float gt_quality);
void DecisionTreeOutputToVariant(VariantCandidate &candidate_variant, const ExtendParameters ¶meters);
void AggregateFilterInformation(vcf::Variant &candidate_variant, const vector<VariantSpecificParams>& variant_specific_params, const ExtendParameters ¶meters);
void FillInFiltersAtEnd(VariantCandidate &candidate_variant,const ExtendParameters ¶meters);
void SetupFromMultiAllele(const EnsembleEval &my_ensemble);
void AddStrandBiasTags(vcf::Variant &candidate_variant);
void AddPositionBiasTags(vcf::Variant &candidate_variant);
void AddCountInformationTags(vcf::Variant &candidate_variant, const string &sampleName);
string GenotypeStringFromAlleles(std::vector<int> &allowedGenotypes, bool refAlleleFound);
bool AllowedGenotypesFromSummary(std::vector<int> &allowedGenotypes);
string GenotypeFromStatus(vcf::Variant &candidate_variant, const ExtendParameters ¶meters);
void SpecializedFilterFromLatentVariables(vcf::Variant &candidate_variant, const float bias_radius, int _allele);
void SpecializedFilterFromHypothesisBias(vcf::Variant &candidate_variant, AlleleIdentity allele_identity, const float deletion_bias, const float insertion_bias, int _allele);
void FilterAlleleHypothesisBias(float ref_bias, float var_bias, float threshold_bias, int _allele);
void FilterOnSpecialTags(vcf::Variant &candidate_variant, const ExtendParameters ¶meters, const vector<VariantSpecificParams>& variant_specific_params);
void FilterOnStringency(vcf::Variant &candidate_variant, const float data_quality_stringency, int _check_allele_index);
void FilterOnPositionBias(int i_alt, MultiBook &m_summary_stats, VariantOutputInfo &l_summary_info, const ControlCallAndFilters &my_filters, const VariantSpecificParams& variant_specific_params);
void FilterBlackList(const vector<VariantSpecificParams>& variant_specific_params);
void FilterSSE(vcf::Variant &candidate_variant, const ClassifyFilters &filter_variant, const vector<VariantSpecificParams>& variant_specific_params);
};
void FilterByBasicThresholds(stringstream &s, int i_alt, MultiBook &m_summary_stats,
VariantOutputInfo &l_summary_info,
const BasicFilters &basic_filter, float tune_xbias, float tune_bias);
void AutoFailTheCandidate(vcf::Variant &candidate_variant, bool use_position_bias);
float FreqThresholdByType(AlleleIdentity &variant_identity, const ControlCallAndFilters &my_controls, const VariantSpecificParams& variant_specific_params);
void DetectSSEForNoCall(AlleleIdentity &var_identity, float sseProbThreshold, float minRatioReadsOnNonErrorStrand, float relative_safety_level, vcf::Variant &candidate_variant, unsigned _altAlleIndex);
void SetQualityByDepth(vcf::Variant &candidate_variant);
#endif // DECISIONTREEDATA_H
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