Alignment strip_from_start(const Alignment& aln, size_t drop) {
if (!drop) return aln;
Alignment res;
res.set_name(aln.name());
res.set_score(aln.score());
//cerr << "drop " << drop << " from start" << endl;
res.set_sequence(aln.sequence().substr(drop));
if (!aln.has_path()) return res;
*res.mutable_path() = cut_path(aln.path(), drop).second;
assert(res.has_path());
if (alignment_to_length(res) != res.sequence().size()) {
cerr << "failed!!! drop from start 轰" << endl;
cerr << pb2json(res) << endl << endl;
assert(false);
}
return res;
}
Alignment strip_from_end(const Alignment& aln, size_t drop) {
if (!drop) return aln;
Alignment res;
res.set_name(aln.name());
res.set_score(aln.score());
//cerr << "drop " << drop << " from end" << endl;
size_t cut_at = aln.sequence().size()-drop;
//cerr << "Cut at " << cut_at << endl;
res.set_sequence(aln.sequence().substr(0, cut_at));
if (!aln.has_path()) return res;
*res.mutable_path() = cut_path(aln.path(), cut_at).first;
assert(res.has_path());
if (alignment_to_length(res) != res.sequence().size()) {
cerr << "failed!!! drop from end 轰" << endl;
cerr << pb2json(res) << endl << endl;
assert(false);
}
return res;
}
int32_t sam_flag(const Alignment& alignment) {
int16_t flag = 0;
if (alignment.score() == 0) {
// unmapped
flag |= BAM_FUNMAP;
} else {
// correctly aligned
flag |= BAM_FPROPER_PAIR;
}
// HACKZ -- you can't determine orientation from a single part of the mapping
// unless the graph is a DAG
if (alignment.has_path()
&& alignment.path().mapping(0).position().is_reverse()) {
flag |= BAM_FREVERSE;
}
if (alignment.is_secondary()) {
flag |= BAM_FSECONDARY;
}
return flag;
}
