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/*
* variant_file.h
*
* Created on: Dec 12, 2012
* Author: amarcketta
*/
#ifndef VARIANT_FILE_H_
#define VARIANT_FILE_H_
#include <algorithm>
#include <bitset>
#include <cstdlib>
#include <cmath>
#include <cstdio>
#include <cstring>
#include <iomanip>
#include <iostream>
#include <fstream>
#include <limits>
#include <set>
#include <sstream>
#include <map>
#include <numeric>
#include <stdint.h>
#include <stdio.h>
#include <string>
#include <sys/stat.h>
#include <vector>
#include <zlib.h>
#include "parameters.h"
#include "entry.h"
#include "gamma.h"
#include "vcf_entry.h"
#include "bcf_entry.h"
#include "header.h"
#ifdef VCFTOOLS_PCA
#include "dgeev.h"
#endif
extern output_log LOG;
using namespace std;
class variant_file
{
public:
string filename;
bool compressed;
istream *file_in;
ifstream file_tmp;
unsigned int gzMAX_LINE_LEN;
gzFile gzfile_in;
header meta_data;
vector<bool> include_indv;
unsigned int N_entries;
unsigned int N_kept_entries;
int N_kept_individuals() const;
int N_kept_sites() const;
int N_total_sites() const;
virtual void open() = 0;
virtual void open_gz() = 0;
virtual void close() = 0;
virtual bool eof() = 0;
virtual void get_entry(vector<char> &out) = 0;
virtual entry* get_entry_object() = 0;
void ByteSwap(unsigned char *b, int n) const;
static inline bool is_big_endian() { long one= 1; return !(*((char *)(&one))); };
void apply_filters(const parameters ¶ms);
void filter_individuals(const set<string> &indv_to_keep, const set<string> &indv_to_exclude, const string &indv_to_keep_filename, const string &indv_to_exclude_filename, bool keep_then_exclude=true);
void filter_individuals_by_keep_list(const set<string> &indv_to_keep, const string &indv_to_keep_filename);
void filter_individuals_by_exclude_list(const set<string> &indv_to_exclude, const string &indv_to_exclude_filename);
void filter_individuals_randomly(int max_N_indv);
void output_frequency(const parameters ¶ms, bool output_counts=false);
void output_individuals_by_mean_depth(const parameters ¶ms);
void output_site_depth(const parameters ¶ms, bool output_mean=true);
void output_genotype_depth(const parameters ¶ms);
void output_het(const parameters ¶ms);
void output_hwe(const parameters ¶ms);
void output_SNP_density(const parameters ¶ms);
void output_indv_missingness(const parameters ¶ms);
void output_site_missingness(const parameters ¶ms);
void output_haplotype_r2(const parameters ¶ms);
void output_genotype_r2(const parameters ¶ms);
void output_genotype_chisq(const parameters ¶ms, double min_pval);
void output_interchromosomal_genotype_r2(const parameters ¶ms);
void output_interchromosomal_haplotype_r2(const parameters & params);
void output_haplotype_r2_of_SNP_list_vs_all_others(const parameters ¶ms);
void output_genotype_r2_of_SNP_list_vs_all_others(const parameters ¶ms);
void output_singletons(const parameters ¶ms);
void output_TsTv(const parameters ¶ms);
void output_TsTv_by_count(const parameters ¶ms);
void output_TsTv_by_quality(const parameters ¶ms);
void output_TsTv_summary(const parameters ¶ms);
void output_per_site_nucleotide_diversity(const parameters ¶ms);
void output_windowed_nucleotide_diversity(const parameters ¶ms);
void output_Tajima_D(const parameters ¶ms);
void output_site_quality(const parameters ¶ms);
void output_FILTER_summary(const parameters ¶ms);
void output_kept_sites(const parameters ¶ms);
void output_removed_sites(const parameters ¶ms);
void output_LROH(const parameters ¶ms);
void output_indv_relatedness_Yang(const parameters ¶ms);
void output_indv_relatedness_Manichaikul(const parameters ¶ms);
void output_PCA(const parameters ¶ms);
void output_PCA_SNP_loadings(const parameters ¶ms);
void output_indel_hist(const parameters ¶ms);
void output_as_012_matrix(const parameters ¶ms);
void output_as_plink(const parameters ¶ms);
void output_as_plink_tped(const parameters ¶ms);
void output_BEAGLE_genotype_likelihoods(const parameters ¶ms, int GL_or_PL=0);
void output_as_IMPUTE(const parameters ¶ms);
void output_as_LDhat_phased(const parameters ¶ms);
void output_as_LDhat_unphased(const parameters ¶ms);
void output_FORMAT_information(const parameters ¶ms);
void output_weir_and_cockerham_fst(const parameters ¶ms);
void output_windowed_weir_and_cockerham_fst(const parameters ¶ms);
void output_sites_in_files(const parameters ¶ms, variant_file &diff_vcf_file);
void output_sites_in_files(const parameters ¶ms, variant_file &diff_vcf_file, map<pair<string, int>, pair<string,string> > &CHROMPOS_to_filename_pair);
void output_indv_in_files(const parameters ¶ms, variant_file &diff_vcf_file);
void output_discordance_by_site(const parameters ¶ms, variant_file &diff_vcf_file);
void output_discordance_matrix(const parameters ¶ms, variant_file &diff_vcf_file);
void output_discordance_by_indv(const parameters ¶ms, variant_file &diff_vcf_file);
void output_switch_error(const parameters ¶ms, variant_file &diff_vcf_file);
void output_INFO_for_each_site(const parameters ¶ms);
void write_stats(const parameters ¶ms);
virtual void print(const parameters ¶ms) = 0;
virtual void print_bcf(const parameters ¶ms) = 0;
void calc_hap_r2(entry *e, entry *e2, double &r2, double &D, double &Dprime, int &chr_count);
void calc_geno_r2(entry *e, entry *e2, double &r2, int &chr_count);
void calc_r2_em(entry *e, entry *e2, double &r2, int &indv_count);
void calc_geno_chisq(entry *e, entry *e2, double &chisq, double &dof, double &pval, int &indv_count);
void return_indv_union(variant_file &file2, map<string, pair< int, int> > &combined_individuals, const string &indv_ID_map_file="");
void return_site_union(variant_file &file2, const parameters ¶ms, map<pair<string, int>, pair<string, string> > &out);
void get_default_contigs(vector<string> &contig_vector);
virtual ~variant_file();
};
#endif /* VARIANT_FILE_H_ */
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