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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_SUBSET_SAMPLES_H__
#define __VCF_SUBSET_SAMPLES_H__
#include <vector>
#include <set>
#include <string>
#include "VcfHeader.h"
class VcfSubsetSamples
{
public:
VcfSubsetSamples()
: mySampleSubsetIndicator(),
mySampleNames()
{}
~VcfSubsetSamples()
{
mySampleSubsetIndicator.clear();
}
void reset();
/// Read the samples from the header initiallizing them all to be
/// included/excluded based on the include paramater. The header is
/// not stored or updated based on any include/excludes. The mapping
/// between sampleNames & indexes is stored to be used for addIncludeSample
/// and addExcludeSample.
void init(const VcfHeader& header, bool include);
/// Include the specified sample. initSample must first be called to
/// specify the header mapping between index and sample.
/// \return true if the sample could be included, false if the sample
/// was not found in the sample list so cannot be included.
bool addIncludeSample(const char* sampleName);
/// Exclude the specified sample. initSample must first be called to
/// specify the header mapping between index and sample.
/// \return true if the sample was found in teh sample list and could be
/// excluded, false if the sample was not found in the sample list.
bool addExcludeSample(const char* sampleName);
/// Initialize this object based on the sample names found in sampleFileName
/// delimited by any of the characters in delims or '\n' and update the
/// header to only include the specified samples.
/// This also initializes this class to identify which samples should
/// be kept/removed when reading records.
bool init(VcfHeader& header, const char* sampleFileName,
const char* excludeSample, const char* excludeFileName,
const char* delims = "\n");
/// Return if the specified original sample index should be kept.
/// This is only applicable after calling init.
/// If the index is out of range, it will return false (do not keep).
/// \param sampleIndex index into the original sample set to check if
/// it should be kept.
/// \return true if the sample index should be kept, false if not or if
/// the index is out of range.
bool keep(unsigned int sampleIndex);
private:
VcfSubsetSamples(const VcfSubsetSamples& vcfSubsetSamples);
VcfSubsetSamples& operator=(const VcfSubsetSamples& vcfSubsetSamples);
// Read a list of samples from the specified file delimited by any of the
// characters in delims or '\n' and store them in the specified container.
bool readSamplesFromFile(const char* fileName,
std::set<std::string>& sampleList,
const char* delims="\n");
std::vector<bool> mySampleSubsetIndicator;
// Used for initSample & addIncludeSample & addExcludeSample for
// mapping between original sample names and indexes in
// mySampleSubsetIndicator.
std::vector<std::string>mySampleNames;
};
#endif
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