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// $Id$ |
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/* |
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Copyright (C) 2018, 2020, 2021, 2023 Peter Johansson |
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5 |
|
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The yat library is free software; you can redistribute it and/or |
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modify it under the terms of the GNU General Public License as |
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published by the Free Software Foundation; either version 3 of the |
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License, or (at your option) any later version. |
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10 |
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The yat library is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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General Public License for more details. |
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15 |
|
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You should have received a copy of the GNU General Public License |
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along with yat. If not, see <http://www.gnu.org/licenses/>. |
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*/ |
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|
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#include <config.h> |
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|
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#include "VcfHeader.h" |
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|
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#include <yat/utility/Exception.h> |
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#include <yat/utility/split.h> |
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#include <yat/utility/utility.h> |
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|
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#include <algorithm> |
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#include <cassert> |
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#include <ctime> |
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#include <istream> |
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#include <iterator> |
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#include <ostream> |
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#include <sstream> |
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#include <utility> |
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|
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namespace theplu { |
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namespace yat { |
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namespace omic { |
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|
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VcfHeader::VcfHeader(const std::string& version) |
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{ |
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add("fileformat", "VCFv" + version); |
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std::vector<std::string> tmp; |
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samples(tmp); |
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} |
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|
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|
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VcfHeader::VcfHeader(std::istream& is) |
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{ |
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if (!is.good()) |
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throw utility::IO_error("VcfHeader: istream is not good"); |
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|
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assert(is.good()); |
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if (is.peek()!='#') { |
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std::ostringstream ss; |
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char buffer[16]; |
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is.get(buffer, 16, '\n'); |
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ss << "VcfHeader: invalid format: " << buffer; |
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throw utility::IO_error(ss.str()); |
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} |
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std::string line; |
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while (getline(is, line)) { |
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lines_.push_back(std::move(line)); |
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if (is.peek()!='#') // next line does not start with '#' |
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break; |
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} |
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} |
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|
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|
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void VcfHeader::add(const std::string& key, const std::string& value) |
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{ |
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std::string line("##"); |
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line += key; |
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line += "="; |
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line += value; |
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if (lines_.empty()) { |
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lines_.push_back(std::move(line)); |
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return; |
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} |
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typedef std::vector<std::string>::iterator iterator; |
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bool found_section = false; |
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for (iterator i = lines_.begin(); i!=lines_.end(); ++i) { |
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if (i->substr(0,2)!="##") { |
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lines_.insert(i, line); |
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return; |
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} |
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if (i->size() >= key.size()+2 && i->substr(2, key.size())==key) |
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found_section = true; |
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else if (found_section) { |
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lines_.insert(i, line); |
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return; |
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} |
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} |
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} |
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|
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|
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void VcfHeader::add(const std::string& key, const std::string& ID, int number, |
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const std::string& type, const std::string& description) |
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{ |
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remove(key, ID); |
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std::stringstream value; |
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value << "<ID=" << ID << ",Number="; |
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if (number) |
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value << number; |
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else |
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value << "."; |
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value << ",Type=" << type << ",Description=\"" << description << "\">"; |
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add(key, value.str()); |
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} |
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|
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|
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void VcfHeader::add(const std::string& key, |
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const std::string& ID, const std::string& number, |
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const std::string& type, |
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const std::string& description) |
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{ |
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remove(key, ID); |
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std::stringstream value; |
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value << "<ID=" << ID << ",Number=" << number |
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<< ",Type=" << type << ",Description=\"" << description << "\">"; |
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add(key, value.str()); |
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} |
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|
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|
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void VcfHeader::add_info(const std::string& ID, const std::string& number, |
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const std::string& type, |
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const std::string& description) |
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{ |
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add("INFO", ID, number, type, description); |
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} |
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|
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|
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void VcfHeader::add_format(const std::string& ID, const std::string& number, |
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const std::string& type, |
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const std::string& description) |
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{ |
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add("FORMAT", ID, number, type, description); |
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} |
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|
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|
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void VcfHeader::add_program_command(int argc, char* argv[]) |
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{ |
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std::string key = utility::basename(argv[0]) + "Command"; |
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std::stringstream ss; |
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|
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for (int i=1; i<argc; ++i) { |
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if (i!=1) |
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ss << ' '; |
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ss << argv[i]; |
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} |
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ss << "; Date="; |
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std::time_t time = std::time(nullptr); |
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ss << std::asctime(std::localtime(&time)); |
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|
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std::string val; |
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getline(ss, val); |
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|
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add(key, val); |
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} |
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|
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|
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void VcfHeader::add_program_version(const std::string& prog, |
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const std::string& version) |
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{ |
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add(prog + "Version", version); |
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} |
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|
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|
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void VcfHeader::erase(size_t i) |
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{ |
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assert(i+1 < lines_.size()); |
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lines_.erase(lines_.begin()+i); |
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} |
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|
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|
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const std::string& VcfHeader::header(void) const |
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{ |
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assert(lines_.size()); |
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return lines_.back(); |
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} |
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|
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|
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void VcfHeader::header(const std::string& line) |
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{ |
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assert(lines_.size()); |
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lines_.back() = line; |
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} |
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|
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|
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const std::string& VcfHeader::line(size_t i) const |
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{ |
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assert(i<lines_.size()); |
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return lines_[i]; |
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} |
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|
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|
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void VcfHeader::key_value(size_t line, std::string& key, |
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std::string& value) const |
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{ |
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assert(line<size()); |
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const std::string& str = lines_[line]; |
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if (str.size()<3 || str[0]!='#' || str[1]!='#') |
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return; |
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size_t end = str.find_first_of('=', 2); |
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if (end==std::string::npos) |
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return; |
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key = str.substr(2, end-2); |
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209 |
value = str.substr(end+1); |
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210 |
} |
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|
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|
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std::string VcfHeader::key(size_t line) const |
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{ |
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215 |
std::string key; |
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216 |
std::string val; |
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key_value(line, key, val); |
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17 Oct 18 |
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return key; |
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} |
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|
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|
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222 |
void VcfHeader::nicify(void) |
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{ |
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224 |
std::stable_sort(lines_.begin(), lines_.end(), Compare()); |
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} |
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|
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|
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228 |
void VcfHeader::remove(const std::string& KEY, const std::string& ID) |
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17 Oct 18 |
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229 |
{ |
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17 Oct 18 |
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230 |
for (size_t i=0; i<lines_.size(); ++i) { |
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17 Oct 18 |
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231 |
if (key(i) == KEY && value(i, "ID") == ID) { |
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17 Oct 18 |
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232 |
lines_.erase(lines_.begin()+i); |
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233 |
--i; |
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234 |
} |
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235 |
} |
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236 |
} |
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|
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238 |
|
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239 |
std::string VcfHeader::value(size_t line) const |
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17 Oct 18 |
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240 |
{ |
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17 Oct 18 |
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241 |
std::string key; |
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17 Oct 18 |
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242 |
std::string val; |
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17 Oct 18 |
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key_value(line, key, val); |
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17 Oct 18 |
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return val; |
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} |
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246 |
|
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|
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248 |
std::string VcfHeader::value(size_t line, const std::string& key) const |
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17 Oct 18 |
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249 |
{ |
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250 |
const std::string& str = lines_[line]; |
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17 Oct 18 |
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251 |
std::string::const_iterator begin = str.begin(); |
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begin = std::find(begin, str.end(), '='); |
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253 |
begin = std::find(begin, str.end(), '<'); |
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17 Oct 18 |
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254 |
++begin; // '<' |
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255 |
|
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256 |
while (begin < str.end()) { |
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17 Oct 18 |
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257 |
std::string::const_iterator middle = std::find(begin, str.end(), '='); |
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17 Oct 18 |
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258 |
std::string::const_iterator end(middle+1); |
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17 Oct 18 |
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259 |
bool quoted = false; |
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17 Oct 18 |
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260 |
while (end < str.end()) { |
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261 |
if (*end == '"') |
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17 Oct 18 |
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262 |
quoted = !quoted; |
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17 Oct 18 |
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263 |
else if (!quoted && *end == ',') |
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17 Oct 18 |
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264 |
break; |
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265 |
++end; |
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17 Oct 18 |
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266 |
} |
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17 Oct 18 |
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267 |
if (*(end-1) == '>') |
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17 Oct 18 |
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268 |
--end; |
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17 Oct 18 |
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269 |
if (static_cast<size_t>(middle - begin) == key.size() && |
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17 Oct 18 |
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270 |
std::equal(begin,middle,key.begin())) |
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17 Oct 18 |
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271 |
return std::string(middle+1,end); |
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272 |
begin = end + 1; |
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17 Oct 18 |
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273 |
} |
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17 Oct 18 |
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274 |
return ""; |
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275 |
} |
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276 |
|
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|
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278 |
const std::vector<std::string>& VcfHeader::samples(void) const |
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279 |
{ |
3750 |
17 Oct 18 |
peter |
280 |
if (samples_.empty()) { |
3750 |
17 Oct 18 |
peter |
281 |
utility::split(samples_, header(), '\t'); |
3750 |
17 Oct 18 |
peter |
282 |
if (samples_.size()>9) |
3750 |
17 Oct 18 |
peter |
283 |
samples_.erase(samples_.begin(), samples_.begin()+9); |
3750 |
17 Oct 18 |
peter |
284 |
else |
3750 |
17 Oct 18 |
peter |
285 |
samples_.clear(); |
3750 |
17 Oct 18 |
peter |
286 |
} |
3750 |
17 Oct 18 |
peter |
287 |
return samples_; |
3750 |
17 Oct 18 |
peter |
288 |
} |
3750 |
17 Oct 18 |
peter |
289 |
|
3750 |
17 Oct 18 |
peter |
290 |
|
3750 |
17 Oct 18 |
peter |
291 |
void VcfHeader::samples(const std::vector<std::string>& s) |
3750 |
17 Oct 18 |
peter |
292 |
{ |
3750 |
17 Oct 18 |
peter |
293 |
samples_ = s; |
3750 |
17 Oct 18 |
peter |
294 |
std::string hdr("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"); |
3750 |
17 Oct 18 |
peter |
295 |
if (lines_.size() && lines_.back().size()>1 && lines_.back()[1]!='#') |
4040 |
15 Feb 21 |
peter |
296 |
lines_.back() = std::move(hdr); |
3750 |
17 Oct 18 |
peter |
297 |
else |
4040 |
15 Feb 21 |
peter |
298 |
lines_.push_back(std::move(hdr)); |
3750 |
17 Oct 18 |
peter |
299 |
|
3750 |
17 Oct 18 |
peter |
300 |
for (size_t i=0; i<s.size(); ++i) { |
3750 |
17 Oct 18 |
peter |
301 |
lines_.back() += "\t"; |
3750 |
17 Oct 18 |
peter |
302 |
lines_.back() += s[i]; |
3750 |
17 Oct 18 |
peter |
303 |
} |
3750 |
17 Oct 18 |
peter |
304 |
} |
3750 |
17 Oct 18 |
peter |
305 |
|
3750 |
17 Oct 18 |
peter |
306 |
|
3750 |
17 Oct 18 |
peter |
307 |
size_t VcfHeader::size(void) const |
3750 |
17 Oct 18 |
peter |
308 |
{ |
3750 |
17 Oct 18 |
peter |
309 |
return lines_.size(); |
3750 |
17 Oct 18 |
peter |
310 |
} |
3750 |
17 Oct 18 |
peter |
311 |
|
3750 |
17 Oct 18 |
peter |
312 |
|
3750 |
17 Oct 18 |
peter |
313 |
std::ostream& operator<<(std::ostream& os, const VcfHeader& header) |
3750 |
17 Oct 18 |
peter |
314 |
{ |
3750 |
17 Oct 18 |
peter |
315 |
std::copy(header.lines_.begin(), header.lines_.end(), |
3750 |
17 Oct 18 |
peter |
316 |
std::ostream_iterator<std::string>(os, "\n")); |
3750 |
17 Oct 18 |
peter |
317 |
return os; |
3750 |
17 Oct 18 |
peter |
318 |
} |
3750 |
17 Oct 18 |
peter |
319 |
|
3760 |
18 Oct 18 |
peter |
320 |
|
3760 |
18 Oct 18 |
peter |
321 |
bool VcfHeader::Compare::operator()(const std::string& lhs, |
3760 |
18 Oct 18 |
peter |
322 |
const std::string& rhs) const |
3760 |
18 Oct 18 |
peter |
323 |
{ |
3760 |
18 Oct 18 |
peter |
324 |
return index(lhs) < index(rhs); |
3760 |
18 Oct 18 |
peter |
325 |
} |
3760 |
18 Oct 18 |
peter |
326 |
|
3760 |
18 Oct 18 |
peter |
327 |
|
3760 |
18 Oct 18 |
peter |
328 |
int VcfHeader::Compare::index(const std::string& s) const |
3760 |
18 Oct 18 |
peter |
329 |
{ |
3760 |
18 Oct 18 |
peter |
330 |
if (match(s, "##fileformat=")) |
3760 |
18 Oct 18 |
peter |
331 |
return 0; |
3760 |
18 Oct 18 |
peter |
332 |
if (match(s, "#CHROM")) |
3760 |
18 Oct 18 |
peter |
333 |
return 99; |
3760 |
18 Oct 18 |
peter |
334 |
|
3760 |
18 Oct 18 |
peter |
335 |
if (match(s, "##reference=")) |
3760 |
18 Oct 18 |
peter |
336 |
return 4; |
3760 |
18 Oct 18 |
peter |
337 |
if (match(s, "##contig=")) |
3760 |
18 Oct 18 |
peter |
338 |
return 4; |
3760 |
18 Oct 18 |
peter |
339 |
if (match(s, "##INFO=")) |
3760 |
18 Oct 18 |
peter |
340 |
return 5; |
3760 |
18 Oct 18 |
peter |
341 |
if (match(s, "##FILTER=")) |
3760 |
18 Oct 18 |
peter |
342 |
return 6; |
3760 |
18 Oct 18 |
peter |
343 |
if (match(s, "##FORMAT=")) |
3760 |
18 Oct 18 |
peter |
344 |
return 7; |
3760 |
18 Oct 18 |
peter |
345 |
|
3760 |
18 Oct 18 |
peter |
346 |
return 9; |
3760 |
18 Oct 18 |
peter |
347 |
} |
3760 |
18 Oct 18 |
peter |
348 |
|
3760 |
18 Oct 18 |
peter |
349 |
|
3760 |
18 Oct 18 |
peter |
350 |
bool VcfHeader::Compare::match(const std::string& s, |
3760 |
18 Oct 18 |
peter |
351 |
const std::string& prefix) const |
3760 |
18 Oct 18 |
peter |
352 |
{ |
4041 |
15 Feb 21 |
peter |
353 |
return s.size() >= prefix.size() && |
4041 |
15 Feb 21 |
peter |
354 |
std::equal(prefix.begin(), prefix.end(), s.begin()); |
3760 |
18 Oct 18 |
peter |
355 |
} |
3760 |
18 Oct 18 |
peter |
356 |
|
3750 |
17 Oct 18 |
peter |
357 |
}}} |