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/*
* Copyright (C) 2011 Regents of the University of Michigan,
* Hyun Min Kang, Matthew Flickenger, Matthew Snyder,
* and Goncalo Abecasis
*
* 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 <string>
#include "VcfRecordFilter.h"
#include "VcfHelper.h"
bool VcfRecordFilter::ourParseFilter = false;
bool VcfRecordFilter::read(IFILE filePtr)
{
static const std::string fieldStopCharsNoParse = "\n\t";
static const int tabPos = 1;
static std::string fieldStopChars = fieldStopCharsNoParse;
fieldStopChars += FILTER_DELIM;
// The start of the first character in stopChars that means there is more
// filter info in the format field, so continue reading the format field.
static const int contPos = fieldStopCharsNoParse.length();
// Clear out any previously set values.
reset();
if(ifeof(filePtr))
{
// End of file, just return false.
return(false);
}
// Check how much the filter should be parsed.
int stopPos = 0;
if(!ourParseFilter)
{
// Do not need to parse the filter, so just read until the tab.
stopPos = filePtr->readTilChar(fieldStopCharsNoParse, myFilterString);
}
else
{
// Parse the filter as we go.
stopPos = contPos;
std::string* nextFilter;
while(stopPos >= contPos)
{
nextFilter = &(myFilterVector.getNextEmpty());
stopPos = filePtr->readTilChar(fieldStopChars, *nextFilter);
}
}
return(stopPos == tabPos);
}
void VcfRecordFilter::reset()
{
myFilterString.clear();
myFilterVector.reset();
}
bool VcfRecordFilter::passedAllFilters()
{
static std::string pass("PASS");
return(pass.compare(getString()) == 0);
}
const std::string& VcfRecordFilter::getString()
{
// Check if the filter string needs to be set.
if(myFilterString.size() == 0)
{
// Filter string is not yet set, so set it.
for(int i = 0; i < myFilterVector.size(); i++)
{
if(i != 0)
{
myFilterString += ';';
}
myFilterString += myFilterVector.get(i);
}
}
return(myFilterString);
}
int VcfRecordFilter::getNumFilters()
{
// Check if the filter has been parsed.
if(myFilterVector.size() == 0)
{
// Filter is not parsed, so parse the filter.
VcfHelper::parseString(myFilterString, FILTER_DELIM, myFilterVector);
}
return(myFilterVector.size());
}
const std::string& VcfRecordFilter::getString(int index)
{
// Check if the filter has been parsed yet.
if(myFilterVector.size() == 0)
{
// Filter has not yet been parsed, so parse it.
VcfHelper::parseString(myFilterString, FILTER_DELIM, myFilterVector);
}
return(myFilterVector.get(index));
}
void VcfRecordFilter::setFilter(const char* filter)
{
reset();
myFilterString = filter;
}
void VcfRecordFilter::addFilter(const char* filter)
{
// If both are empty, add to both.
if((myFilterString.size() == 0) &&
(myFilterVector.size() == 0))
{
myFilterString += filter;
myFilterVector.getNextEmpty() = filter;
}
else
{
// Either filter (or both) have contents, so append
// as appropriate.
if(myFilterString.size() != 0)
{
// String is set, so add the filter to the string.
myFilterString += ';';
myFilterString += filter;
}
if(myFilterVector.size() != 0)
{
// Vector is set, so add the filter to the vector.
myFilterVector.getNextEmpty() = filter;
}
}
}
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