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consistency of option "--outfmt 6 qseq sseq" with blastp #818

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consistency of option "--outfmt 6 qseq sseq" with blastp #818

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23 changes: 13 additions & 10 deletions src/output/blast_tab_format.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -240,6 +240,7 @@ void Blast_tab_format::print_match(const HspContext& r, Output::Info& info)
out << ",";
out << "\n\t{\n";
}
HspContext::Iterator qi = r.begin(), si = r.begin();
for (auto i = fields.cbegin(); i != fields.cend(); ++i) {
if(is_json){
out << prepos << "\"" << field_def[*i].key << "\":";
Expand Down Expand Up @@ -277,17 +278,19 @@ void Blast_tab_format::print_match(const HspContext& r, Output::Info& info)
out << r.subject_source_range().end_;
break;
case 17:
r.query.source().print(out, r.query_source_range().begin_, r.query_source_range().end_, input_value_traits);
break;
//r.query.source().print(out, r.query_source_range().begin_, r.query_source_range().end_, input_value_traits);
while (qi.good()) { out << qi.query_char(); ++qi; }
break; // qseq
case 18:
{
vector<Letter> seq;
seq.reserve(r.subject_range().length());
for (HspContext::Iterator j = r.begin(); j.good(); ++j)
if (!(j.op() == op_insertion))
seq.push_back(j.subject());
out << Sequence(seq);
break;
//vector<Letter> seq;
//seq.reserve(r.subject_range().length());
//for (HspContext::Iterator j = r.begin(); j.good(); ++j)
//if (!(j.op() == op_insertion))
//seq.push_back(j.subject());
//out << Sequence(seq);
while (si.good()) { out << si.subject_char(); ++si; }
break; // sseq
}
case 19:
out.print_e(r.evalue());
Expand Down Expand Up @@ -670,4 +673,4 @@ void Blast_tab_format::print_footer(Consumer &f) const {
const char* s = "\n]";
f.consume(s, strlen(s));
}
}
}