https://github.com/ekg/freebayes
Tip revision: 60850dc518fc453622cbb40ad6dd9f67644ed859 authored by Pjotr Prins on 16 December 2020, 10:18:06 UTC
Disable cmake, but leave the file with a message
Disable cmake, but leave the file with a message
Tip revision: 60850dc
CNV.h
#ifndef __CNV_H
#define __CNV_H
#include <map>
#include <string>
#include <iostream>
#include <fstream>
#include <vector>
#include <utility>
#include <stdlib.h>
#include <algorithm>
#include <tuple>
#include "split.h"
using namespace std;
typedef map<string, map<string, vector<tuple<long int, long int, int> > > > SampleSeqCNVMap;
class CNVMap {
public:
CNVMap(void) : defaultPloidy(2) { }
void setDefaultPloidy(int defploidy);
void setSamplePloidy(const string& sample, int ploidy);
bool load(string const& filename);
int ploidy(string const& sample, string const& seq, long int position);
void setPloidy(string const& sample, string const& seq, long int start, long int end, int ploidy);
private:
// note: this map is stored as 0-based, end position exclusive
SampleSeqCNVMap sampleSeqCNV;
int defaultPloidy;
map<string, int> samplePloidy;
};
#endif