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/* Copyright (c) 2016
Bo Li (University of California, Berkeley)
bli25@berkeley.edu
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, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
USA
*/
#include<cstdio>
#include<cassert>
#include<string>
#include<set>
#include<map>
#include<fstream>
#include<sstream>
#include "my_assert.h"
#include "SamHeader.hpp"
void SamHeader::replaceSQ(const char* faiF) {
std::ifstream fin(faiF);
general_assert(fin.is_open(), "Cannot open " + cstrtos(faiF) + "! It may not exist.");
std::string line;
size_t pos;
SQstr = "";
while (getline(fin, line)) {
pos = line.find_first_of('\t');
assert(pos != std::string::npos && pos > 0 && pos + 1 < line.length() && line[pos + 1] != '\t');
SQstr += "@SQ\tSN:" + line.substr(0, pos) + "\tLN:" + line.substr(pos + 1, line.find_first_of('\t', pos + 1)) + "\n";
}
fin.close();
}
std::map<std::string, std::string> SamHeader::parse_line(const std::string& line) {
size_t len = line.length();
assert(line.substr(0, 3) != "@CO" && len > 4);
size_t fr, to, colon;
std::string field;
std::map<std::string, std::string> dict;
fr = 4;
do {
to = line.find_first_of('\t', fr);
field = line.substr(fr, to);
colon = field.find_first_of(':');
if (colon != std::string::npos) {
dict[field.substr(0, colon)] = field.substr(colon + 1);
}
fr = to;
} while (fr != std::string::npos && (++fr) < len);
return dict;
}
void SamHeader::parse_text(const char* text) {
std::istringstream strin(text);
std::string line, tag;
std::map<std::string, std::string> dict;
std::map<std::string, std::string>::iterator dict_iter;
HDstr = SQstr = RGstr = PGstr = COstr = other = "";
pids.clear();
while (getline(strin, line)) {
if (line[0] != '@') continue;
tag = line.substr(1, 2);
if (tag == "HD") {
general_assert(HDstr == "", "@HD tag can only present once!");
HDstr = line; HDstr += "\n";
}
else if (tag == "SQ") {
SQstr += line; SQstr += "\n";
}
else if (tag == "RG") {
RGstr += line; RGstr += "\n";
}
else if (tag == "PG") {
dict = parse_line(line);
dict_iter = dict.find("ID");
general_assert(dict_iter != dict.end(), "\"" + line + "\" does not contain an ID!" );
general_assert(pids.find(dict_iter->second) == pids.end(), "Program record identifier " + dict_iter->second + " is not unique!");
pids.insert(dict_iter->second);
PGstr += line; PGstr += "\n";
}
else if (tag == "CO") {
COstr += line; COstr += "\n";
}
else {
other += line; line += "\n";
}
}
}
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