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/*
* Copyright (C) 2012 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 "VcfGenotypeFormat.h"
#include "VcfRecordGenotype.h"
VcfGenotypeFormat::VcfGenotypeFormat()
: VcfGenotypeField(),
myGTIndex(GENOTYPE_INDEX_NA)
{
}
VcfGenotypeFormat::~VcfGenotypeFormat()
{
}
bool VcfGenotypeFormat::read(IFILE filePtr)
{
// Clear out any previously set values.
reset();
SUBFIELD_READ_STATUS readStatus = MORE_SUBFIELDS;
std::string* nextType = &(myGenotypeSubFields.getNextEmpty());
int subFieldIndex = 0;
while(readStatus == MORE_SUBFIELDS)
{
// more subfields to read.
readStatus = readGenotypeSubField(filePtr, nextType);
// Check if this field should be read/stored.
if(!VcfRecordGenotype::storeField(*nextType))
{
// Do not read/store this field.
myStoreIndices.push_back(false);
nextType->clear();
}
else
{
// Check if this is GT.
if(*nextType == "GT")
{
myGTIndex = subFieldIndex;
}
myStoreIndices.push_back(true);
nextType = &(myGenotypeSubFields.getNextEmpty());
}
++subFieldIndex;
}
// Since we didn't use the last type that was retrieved, remove it.
myGenotypeSubFields.rmLast();
// Return true if there is a tab - it is just END_OF_FIELD.
return(readStatus == END_OF_FIELD);
}
int VcfGenotypeFormat::getIndex(const std::string& key)
{
// Search for this field of the genotypeFormat.
for(int i = 0; i < myGenotypeSubFields.size(); i++)
{
if(myGenotypeSubFields.get(i) == key)
{
// Found the type.
return(i);
}
}
// field was not found, so return null.
return(GENOTYPE_INDEX_NA);
}
bool VcfGenotypeFormat::storeIndex(unsigned int index)
{
if(index > myStoreIndices.size())
{
return(false);
}
return(myStoreIndices[index]);
}
void VcfGenotypeFormat::internal_reset()
{
myGTIndex = GENOTYPE_INDEX_NA;
myStoreIndices.clear();
}
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