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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/>.
*/
#ifndef __VCF_GENOTYPE_SAMPLE_H__
#define __VCF_GENOTYPE_SAMPLE_H__
#include "VcfGenotypeFormat.h"
/// This header file provides interface to read/write VCF files.
class VcfGenotypeSample : public VcfGenotypeField
{
public:
static const int INVALID_GT;
static const int MISSING_GT;
static const std::string MISSING_FIELD;
/// Default Constructor, initializes the variables.
VcfGenotypeSample();
/// Destructor
virtual ~VcfGenotypeSample();
/// Read this sample from the file up until the next \t,\n, or EOF.
/// \param filePtr IFILE to read from.
/// \param format the VCF Genotype Format field description.
/// \return true if a tab ended the field, false if it was \n or EOF.
bool read(IFILE filePtr, VcfGenotypeFormat& format);
virtual bool write(IFILE filePtr);
/// Get a pointer to the string containing the value associated with the
/// specified key(the pointer will be invalid if the field is
/// changed/reset).
/// \param key to find the falue for.
/// \return const pointer to the string value for this key, NULL if
/// the sample or the key was not found.
const std::string* getString(const std::string& key);
/// Set the string associated with the specified key, returns true if set,
/// false if not.
bool setString(const std::string& key, const std::string& value);
inline bool isPhased() { return(myPhased); }
inline bool isUnphased() { return(myUnphased); }
inline bool hasAllGenotypeAlleles() { return(myHasAllGenotypeAlleles); }
/// Return the integer allele at the specified index of the GT field.
/// For example, a GT of 0/3, getGT(1) returns 3 and getGT(0) returns 0.
/// Returns INVALID_GT if there is no GT at the specified index or GT was
/// not specified and returns MISSING_GT if it is '.'.
int getGT(unsigned int index);
/// Set the integer allele at the specified index of the GT field.
/// Requires the GT index to already exist.
void setGT(unsigned int index, int newGt);
/// Return the number of GT fields for this sample.
int getNumGTs();
protected:
/// reset the sample for a new entry.
virtual void internal_reset();
bool parseGT();
private:
VcfGenotypeSample(const VcfGenotypeSample& vcfGenotypeSample);
VcfGenotypeSample& operator=(const VcfGenotypeSample& vcfGenotypeSample);
void updateGTString();
VcfGenotypeFormat* myFormatPtr;
bool myPhased;
bool myUnphased;
bool myHasAllGenotypeAlleles;
bool myNewGT;
std::vector<int> myGTs;
};
#endif
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