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SAM.cpp
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SAM.cpp
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/*
* Part of SMITHLAB_CPP software
*
* Copyright (C) 2013 University of Southern California and
* Andrew D. Smith
*
* Authors: Meng Zhou, Qiang Song, Andrew Smith
*
* 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/>.
*/
#include <string>
#include <vector>
#include <fstream>
#include <iostream>
#include "SAM.hpp"
#include "smithlab_utils.hpp"
#include "MappedRead.hpp"
#include "sam.h"
using std::string;
using std::vector;
using std::cerr;
using std::endl;
SAMReader::SAMReader(const string fn, const string mapper_used) :
filename(fn), mapper(mapper_used), file_handler(NULL),
algn_p(NULL), GOOD(false)
{
if (mapper != "bsmap" && mapper != "bismark"
&& mapper != "bs_seeker" && mapper != "general")
throw SMITHLABException("Mapper unsupported:" + mapper);
const string ext_name = filename.substr(filename.find_last_of('.'));
mode = ext_name == ".bam" ? "rb" : "r";
if ((file_handler = samopen(filename.c_str(), mode.c_str(), NULL))
== NULL)
{
cerr << "Fail to open SAM/BAM file " << filename << endl;
exit(-1);
}
algn_p = bam_init1();
GOOD = true;
}
SAMReader::~SAMReader()
{
close();
}
void
SAMReader::close()
{
if (algn_p)
{
bam_destroy1(algn_p);
algn_p = NULL;
}
if (file_handler)
{
samclose(file_handler);
file_handler = NULL;
filename = "";
mode = "";
GOOD = false;
}
}
bool
SAMReader::get_SAMRecord(const string &str, SAMRecord &samr)
{
if (mapper == "bsmap")
return get_SAMRecord_bsmap(str, samr);
else if (mapper == "bismark")
return get_SAMRecord_bismark(str, samr);
else if (mapper == "bs_seeker")
return get_SAMRecord_bsseeker(str, samr);
else if (mapper == "general")
return get_SAMRecord_general(str, samr);
else
GOOD = false;
return false;
}
SAMReader&
operator>>(SAMReader &sam_stream, SAMRecord& samr)
{
if (samread(sam_stream.file_handler, sam_stream.algn_p) >= 0)
{
char *str = bam_format1_core(sam_stream.file_handler->header,
sam_stream.algn_p,
sam_stream.file_handler->type>>2&3);
sam_stream.GOOD = sam_stream.get_SAMRecord(str, samr);
free(str);
}
else
sam_stream.GOOD = false;
return sam_stream;
}
/////////////////////////////////////////////
//// general facility for SAM format
/////////////////////////////////////////////
void static
apply_CIGAR(const string &seq, const string &qual,
const string &CIGAR, string &new_seq, string &new_qual)
{
assert(seq.size() == qual.size());
assert(new_seq.size() == 0 && new_qual.size() == 0);
size_t n;
char op;
size_t i = 0;
std::istringstream iss(CIGAR);
while (iss >> n >> op)
{
switch (op)
{
case 'M':
new_seq += seq.substr(i, n);
new_qual += qual.substr(i, n);
i += n;
break;
case 'I':
i += n;
break;
case 'D':
new_seq += string(n, 'N');
new_qual += string(n, 'B');
break;
case 'S':
i += n;
break;
case 'H':
;
break;
case 'P':
;
break;
case '=':
new_seq += seq.substr(i, n);
new_qual += qual.substr(i, n);
i += n;
break;
case 'X':
new_seq += seq.substr(i, n);
new_qual += qual.substr(i, n);
i += n;
break;
}
}
// Sum of lengths of the M/I/S/=/X operations
// shall equal the length of seq.
assert(i == seq.length());
assert(new_seq.size() == new_qual.size());
}
class FLAG
{
public:
FLAG(const size_t f) : flag(f) {}
bool is_pairend() const {return flag & 0x1;}
bool is_singlend() const {return !(is_pairend());}
bool is_mapping_paired() const {return flag & 0x2;}
bool is_unmapped() const {return flag & 0x4;}
bool is_mapped() const {return !(is_unmapped());}
bool is_revcomp() const {return flag & 0x10;}
bool is_Trich() const {return flag & 0x40;}
bool is_Arich() const {return flag & 0x80;}
bool is_secondary() const {return flag & 0x100;}
bool is_primary() const {return !(is_secondary());}
private:
size_t flag;
};
////////////////////////////////////////
// BSMAP
////////////////////////////////////////
class BSMAPFLAG : public FLAG
{
public:
BSMAPFLAG(const size_t f) : FLAG(f) {}
};
inline static void
bsmap_get_strand(const string &strand_str, string &strand, string &bs_forward)
{
strand = strand_str.substr(5, 1);
bs_forward = strand_str.substr(6, 1);
if (bs_forward == "-") strand = strand == "+" ? "-" : "+";
}
bool
SAMReader::get_SAMRecord_bsmap(const string &str, SAMRecord &samr)
{
/////
cerr << "WARNING: "<< "[BSMAP Converter] test version: may contain bugs" << endl;
/////
string name, chrom, CIGAR, mate_name, seq, qual, strand_str, mismatch_str;
size_t flag, start, mapq_score, mate_start;
int seg_len;
std::istringstream iss(str);
if (!(iss >> name >> flag >> chrom >> start >> mapq_score >> CIGAR
>> mate_name >> mate_start >> seg_len >> seq >> qual
>> mismatch_str >> strand_str))
{
GOOD = false;
throw SMITHLABException("malformed line in bsmap SAM format:\n" + str);
}
BSMAPFLAG Flag(flag);
samr.mr.r.set_chrom(chrom);
samr.mr.r.set_start(start - 1);
samr.mr.r.set_name(name);
samr.mr.r.set_score(atoi(mismatch_str.substr(5).c_str()));
string strand, bs_forward;
bsmap_get_strand(strand_str, strand, bs_forward);
samr.mr.r.set_strand(strand[0]);
string new_seq, new_qual;
apply_CIGAR(seq, qual, CIGAR, new_seq, new_qual);
samr.mr.r.set_end(samr.mr.r.get_start() + new_seq.size());
samr.mr.seq = new_seq;
samr.mr.scr = new_qual;
samr.is_Trich = Flag.is_Trich();
samr.is_mapping_paired = Flag.is_mapping_paired();
return GOOD;
}
////////////////////////////////////////
// Bismark
////////////////////////////////////////
class BISMARKFLAG : public FLAG
{
public:
BISMARKFLAG(const size_t f) : FLAG(f) {}
bool is_Trich() const {return is_pairend() ? FLAG::is_Trich() : true;}
};
static size_t
get_mismatch_bismark(const string &edit_distance_str,
const string &meth_call_str)
{
/*
the result of this function might not be accurate, because if a sequencing
error occurs on a cytosine, then it probably will be reported as a convertion
*/
size_t edit_distance;
edit_distance = atoi(edit_distance_str.substr(5).c_str());
int convert_count = 0;
const char *temp = meth_call_str.substr(5).c_str();
while(*temp != '\0') {
if (*temp == 'x' || *temp == 'h' || *temp == 'z')
++convert_count;
++temp;
}
return edit_distance - convert_count;
}
bool
SAMReader::get_SAMRecord_bismark(const string &str, SAMRecord &samr)
{
string name, chrom, CIGAR, mate_name, seq, qual, strand_str,
edit_distance_str, mismatch_str, meth_call_str,
read_conv_str, genome_conv_str;
size_t flag, start, mapq_score, mate_start;
int seg_len;
std::istringstream iss(str);
if (!(iss >> name >> flag >> chrom >> start >> mapq_score >> CIGAR
>> mate_name >> mate_start >> seg_len >> seq >> qual
>> edit_distance_str >> mismatch_str >> meth_call_str
>> read_conv_str >> genome_conv_str))
{
GOOD = false;
throw SMITHLABException("malformed line in bismark SAM format:\n" + str);
}
BISMARKFLAG Flag(flag);
samr.mr.r.set_chrom(chrom);
samr.mr.r.set_start(start - 1);
samr.mr.r.set_name(name);
samr.mr.r.set_score(get_mismatch_bismark(edit_distance_str, meth_call_str));
samr.mr.r.set_strand(Flag.is_revcomp() ? '-' : '+');
string new_seq, new_qual;
apply_CIGAR(seq, qual, CIGAR, new_seq, new_qual);
if (Flag.is_revcomp())
{
revcomp_inplace(new_seq);
std::reverse(new_qual.begin(), new_qual.end());
}
samr.mr.r.set_end(samr.mr.r.get_start() + new_seq.size());
samr.mr.seq = new_seq;
samr.mr.scr = new_qual;
samr.is_Trich = Flag.is_Trich();
samr.is_mapping_paired = Flag.is_mapping_paired();
// /////
// cerr << "check 1: "<< (samr.is_Trich ? "T-rich" : "A-rich") << "\t"
// << samr.is_mapping_paired << endl
// << samr.mr << endl;
// /////
return GOOD;
}
////////////////////////////////////////
// BS Seeker
////////////////////////////////////////
class BSSEEKERFLAG : public FLAG
{
public:
BSSEEKERFLAG(const size_t f) : FLAG(f) {}
// pair-end:
// if T-rich mate is +, then both mates are +;
// if T-rich mate is -, then both mates are -;
// single-end:
// 0 for +; 16 for -.
bool is_Trich() const {
return FLAG::is_pairend() ? FLAG::is_Trich() : true;
}
bool is_Arich() const {
return FLAG::is_pairend() && FLAG::is_Arich();
}
bool is_revcomp() const {
if (FLAG::is_pairend())
return FLAG::is_revcomp() ? is_Trich() : is_Arich();
else
return FLAG::is_revcomp();
}
};
bool
SAMReader::get_SAMRecord_bsseeker(const string &str, SAMRecord &samr)
{
string name, chrom, CIGAR, mate_name, seq, qual, orientation_str,
conversion_str, mismatch_str, mismatch_type_str, seq_genome_str;
size_t flag, start, mapq_score, mate_start;
int seg_len;
std::istringstream iss(str);
if (!(iss >> name >> flag >> chrom >> start >> mapq_score >> CIGAR
>> mate_name >> mate_start >> seg_len >> seq >> qual
>> orientation_str >> conversion_str >> mismatch_str
>> mismatch_type_str >> seq_genome_str))
{
GOOD = false;
throw SMITHLABException("malformed line in bs_seeker SAM format:\n" + str);
}
// bs_seeker also doesn't keep sequencing quality information?
qual = string(seq.size(), 'h');
BSSEEKERFLAG Flag(flag);
samr.mr.r.set_chrom(chrom);
samr.mr.r.set_start(start - 1);
samr.mr.r.set_name(name);
samr.mr.r.set_score(atoi(mismatch_str.substr(5).c_str()));
samr.mr.r.set_strand(Flag.is_revcomp() ? '-' : '+');
string new_seq, new_qual;
apply_CIGAR(seq, qual, CIGAR, new_seq, new_qual);
if (Flag.is_revcomp())
{
revcomp_inplace(new_seq);
std::reverse(new_qual.begin(), new_qual.end());
}
samr.mr.r.set_end(samr.mr.r.get_start() + new_seq.size());
samr.mr.seq = new_seq;
samr.mr.scr = new_qual;
samr.is_Trich = Flag.is_Trich();
samr.is_mapping_paired = Flag.is_mapping_paired();
return GOOD;
}
////////////////////////////////////////
// general: for non-BSseq mappers
////////////////////////////////////////
class GENERALFLAG : public FLAG
{
public:
GENERALFLAG(const size_t f) : FLAG(f) {}
bool is_Trich() const {return is_pairend() ? FLAG::is_Trich() : true;}
};
bool
SAMReader::get_SAMRecord_general(const string &str, SAMRecord &samr)
{
string name, chrom, CIGAR, mate_name, seq, qual;
size_t flag, start, mapq_score, mate_start;
int seg_len;
std::istringstream iss(str);
if (!(iss >> name >> flag >> chrom >> start >> mapq_score >> CIGAR
>> mate_name >> mate_start >> seg_len >> seq >> qual))
{
GOOD = false;
throw SMITHLABException("malformed line in SAM format:\n" + str);
}
GENERALFLAG Flag(flag);
samr.is_primary = Flag.is_primary();
samr.is_mapped = Flag.is_mapped();
samr.seg_len = seg_len;
samr.mr.r.set_name(name);
if(samr.is_primary && samr.is_mapped){
samr.mr.r.set_chrom(chrom);
samr.mr.r.set_start(start - 1);
samr.mr.r.set_score(0);
samr.mr.r.set_strand(Flag.is_revcomp() ? '-' : '+');
string new_seq, new_qual;
apply_CIGAR(seq, qual, CIGAR, new_seq, new_qual);
if (Flag.is_revcomp())
{
revcomp_inplace(new_seq);
std::reverse(new_qual.begin(), new_qual.end());
}
samr.mr.r.set_end(samr.mr.r.get_start() + new_seq.size());
samr.mr.seq = new_seq;
samr.mr.scr = new_qual;
}
samr.is_Trich = Flag.is_Trich();
samr.is_mapping_paired = Flag.is_mapping_paired();
return GOOD;
}