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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
*/
#ifndef SAMHEADER_H_
#define SAMHEADER_H_
#include<cstdlib>
#include<string>
#include<set>
#include<map>
#include "htslib/sam.h"
class SamHeader {
public:
SamHeader(const char* text = NULL) {
if (text != NULL) parse_text(text);
}
void replaceSQ(const char* faiF);
void insertPG(const std::string& pid, const std::string& command = "") {
if (pids.find(pid) == pids.end()) {
pids.insert(pid);
PGstr += "@PG\tID:" + pid;
if (command != "") PGstr += "\tCL:" + command;
PGstr += "\n";
}
}
void addComment(const std::string& comment) {
COstr += "@CO\t" + comment + "\n";
}
bam_hdr_t* create_header() {
std::string text = HDstr + SQstr + RGstr + PGstr + COstr + other;
bam_hdr_t *h = sam_hdr_parse(text.length(), text.c_str());
h->l_text = text.length();
h->text = (char*)calloc(h->l_text + 1, 1);
strcpy(h->text, text.c_str());
return h;
}
private:
std::string HDstr, SQstr, RGstr, PGstr, COstr, other;
std::set<std::string> pids;
std::map<std::string, std::string> parse_line(const std::string& line);
void parse_text(const char* text);
};
#endif
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