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
NonCall.h
#ifndef __NONCALL_H
#define __NONCALL_H
#include <string>
#include <vector>
#include <set>
#include <map>
#include <utility>
#include "Utility.h"
#include "Allele.h"
#include "Sample.h"
using namespace std;
class NonCall {
public:
NonCall(void)
: refCount(0)
, reflnQ(0)
, altCount(0)
, altlnQ(0)
, minDepth(0)
, nCount(0)
{ }
NonCall(int rc, long double rq, int ac, long double aq, int mdp)
: refCount(rc)
, reflnQ(rq)
, altCount(ac)
, altlnQ(aq)
, minDepth(mdp)
{ }
int refCount;
int altCount;
int minDepth;
int nCount ;
long double reflnQ;
long double altlnQ;
};
class NonCalls : public map<string, map<long, map<string, NonCall> > > {
public:
void record(const string& seqName, long pos, const Samples& samples);
NonCall aggregateAll(void);
void aggregatePerSample(map<string, NonCall>& perSite);
pair<string, long> firstPos(void);
pair<string, long> lastPos(void);
};
#endif