string alignment_to_sam(const Alignment& alignment,
const string& refseq,
const int32_t refpos,
const string& cigar,
const string& mateseq,
const int32_t matepos,
const int32_t tlen) {
stringstream sam;
sam << (!alignment.name().empty() ? alignment.name() : "*") << "\t"
<< sam_flag(alignment) << "\t"
<< (refseq.empty() ? "*" : refseq) << "\t"
<< refpos + 1 << "\t"
//<< (alignment.path().mapping_size() ? refpos + 1 : 0) << "\t" // positions are 1-based in SAM, 0 means unmapped
<< alignment.mapping_quality() << "\t"
<< (alignment.has_path() && alignment.path().mapping_size() ? cigar : "*") << "\t"
<< (mateseq == refseq ? "=" : mateseq) << "\t"
<< matepos + 1 << "\t"
<< tlen << "\t"
<< (!alignment.sequence().empty() ? alignment.sequence() : "*") << "\t";
// hack much?
if (!alignment.quality().empty()) {
const string& quality = alignment.quality();
for (int i = 0; i < quality.size(); ++i) {
sam << quality_short_to_char(quality[i]);
}
} else {
sam << "*";
//sam << string(alignment.sequence().size(), 'I');
}
//<< (alignment.has_quality() ? string_quality_short_to_char(alignment.quality()) : string(alignment.sequence().size(), 'I'));
if (!alignment.read_group().empty()) sam << "\tRG:Z:" << alignment.read_group();
sam << "\n";
return sam.str();
}
bool want_entry(T const& e) const {
int mapq = mapping_quality(e);
int flag = sam_flag(e);
return mapq >= opts_.min_mapq
&& (flag & opts_.required_flags) == opts_.required_flags
&& (flag & opts_.forbidden_flags) == 0;
}
