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/*
* Copyright (C) 2013 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include "VcfRecordDiscardRules.h"
void VcfRecordDiscardRules::reset()
{
myExcludeIDs.clear();
myIncludeIDs.clear();
myNumDiscarded = 0;
}
bool VcfRecordDiscardRules::setExcludeIDs(const char* filename)
{
return(setIDs(myExcludeIDs, filename));
}
bool VcfRecordDiscardRules::setIncludeIDs(const char* filename)
{
return(setIDs(myIncludeIDs, filename));
}
bool VcfRecordDiscardRules::discardForID(std::string& myID)
{
if(!myExcludeIDs.empty())
{
if(myExcludeIDs.find(myID) != myExcludeIDs.end())
{
// The ID is in the exclude list,
// so return true, discard the record.
// increment the discard counter.
++myNumDiscarded;
return(true);
}
}
else if(!myIncludeIDs.empty())
{
if(myIncludeIDs.find(myID) == myIncludeIDs.end())
{
// The ID is not in the include list,
// so return false, discard the record.
// increment the discard counter.
++myNumDiscarded;
return(true);
}
}
return(false);
}
bool VcfRecordDiscardRules::setIDs(IDList& idlist, const char* filename)
{
// Open the file nad read in all the exclude ids.
IFILE idFile = ifopen(filename, "r");
if(idFile == NULL)
{
return(false);
}
std::string line;
while(idFile->readLine(line) == 0)
{
idlist.insert(line);
line.clear();
}
if(!line.empty())
{
idlist.insert(line);
line.clear();
}
return(true);
}
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