https://github.com/ekg/freebayes
Tip revision: 9755e43db74f9fa8ad2653d6a771d7a8d148ee66 authored by Erik Garrison on 10 December 2013, 00:24:08 UTC
Setting Release-Version v0.9.10
Setting Release-Version v0.9.10
Tip revision: 9755e43
CNV.h
#ifndef __CNV_H
#define __CNV_H
#include <map>
#include <string>
#include <iostream>
#include <fstream>
#include <vector>
#include <utility>
#include <stdlib.h>
#include "split.h"
using namespace std;
typedef map<string, map<string, map<pair<long int, long int>, int> > > SampleSeqCNVMap;
class CNVMap {
public:
CNVMap(void) : defaultPloidy(2) { }
void setDefaultPloidy(int defploidy);
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;
};
#endif