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Add base qualities for unaligned sequences in GAF output #88

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Add base qualities for unaligned sequences in GAF output #88

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6 changes: 6 additions & 0 deletions src/alignment_io.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -913,6 +913,12 @@ gafkluge::GafRecord alignment_to_gaf(function<size_t(nid_t)> node_to_length,
string cs_cigar_str = "+" + aln.sequence();
gaf.opt_fields["cs"] = make_pair("Z", std::move(cs_cigar_str));
}

// emit base qualities for unaligned sequences
// optional base qualities
if (base_quals && !aln.quality().empty()) {
gaf.opt_fields["bq"] = make_pair("Z", string_quality_short_to_char(aln.quality()));
}
}

// optional frag_next/prev names
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