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accessor.cpp
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accessor.cpp
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/*******************************************************************************
* Copyright (C) 2021 Rick Wertenbroek, University of Lausanne (UNIL),
* University of Applied Sciences and Arts Western Switzerland (HES-SO),
* School of Management and Engineering Vaud (HEIG-VD).
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
******************************************************************************/
#include "accessor.hpp"
Accessor::Accessor(std::string& filename) : filename(filename) {
std::fstream s(filename, s.binary | s.in);
if (!s.is_open()) {
std::cerr << "Failed to open file " << filename << std::endl;
throw "Failed to open file";
}
// Read the header
s.read((char *)(&(this->header)), sizeof(header_t));
// Check magic
if ((header.first_magic != MAGIC) or (header.last_magic != MAGIC)) {
std::cerr << "Bad magic" << std::endl;
std::cerr << "Expected : " << MAGIC << " got : " << header.first_magic << ", " << header.last_magic << std::endl;
throw "Bad magic";
}
// Check version
if (header.version != 2 and header.version != 3) {
if (header.version == 4) {
//std::cerr << "Experimental version" << std::endl;
} else {
std::cerr << "Bad version" << std::endl;
throw "Bad version";
}
}
// Extract the sample list
sample_list.clear();
s.seekg(header.samples_offset);
std::string str;
while(std::getline(s, str, '\0').good() and (sample_list.size() < (header.hap_samples/header.ploidy))) {
sample_list.push_back(str);
}
s.close();
if (header.aet_bytes == 2) {
if (header.version == 4) {
internals = make_unique<AccessorInternalsNewTemplate<uint16_t> >(filename);
} else {
std::cerr << "Unsupported version : " << header.version << std::endl;
throw "Unsupported version";
}
} else if (header.aet_bytes == 4) {
if (header.version == 4) {
internals = make_unique<AccessorInternalsNewTemplate<uint32_t> >(filename);
} else {
std::cerr << "Unsupported version : " << header.version << std::endl;
throw "Unsupported version";
}
} else {
std::cerr << "Unsupported access type" << std::endl;
throw "Unsupported A_T";
}
values = (int*)malloc(sizeof(int));
}
Accessor::~Accessor() {
if (values) {
free(values);
values = NULL;
}
}