glactools/FilterVCF.h at master · grenaud/glactools · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
/*
 * FilterVCF
 * Date: Aug-22-2012
 * Author : Gabriel Renaud gabriel.reno@gmail.com
 *
 */

#ifndef FilterVCF_h
#define FilterVCF_h

#include "SimpleVCF.h"
#include "SetVCFFilters.h"

//extern int rejectIndel=0;
/* extern int rejectREFValidREF=0; */
/* extern int rejectREFValidALT=0; */
/* extern int rejectLOWCOV_REF=0; */
/* extern int rejectMap20=0; */
/* extern int rejectLOWMQ=0; */
/* extern int rejectLOWQUAL=0; */
/* extern int rejectCloseIndels=0; */
/* extern int rejectSysERR=0; */
/* extern int rejectRM=0; */
/* extern int rejectREF_unknownGeno=0; */

bool passedFilters(SimpleVCF * smvcf,const SetVCFFilters * filtersToUse);
//,int minCovcutoff,int maxCovcutoff,double minMapabilitycutoff,int minMQcutoff,int minGQcutoff);
string rejectFiltersTally();

#endif