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Properly paired tag #36

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merged 3 commits into from
Mar 4, 2021
Merged

Properly paired tag #36

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a7cd3be
Add proper pairing tag to alignment message and gaf
xchang1 Mar 3, 2021
d0d39fd
Use an annotation for proper pairing instead of a separate field
xchang1 Mar 3, 2021
3483803
Set annotation value properly
xchang1 Mar 3, 2021
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14 changes: 14 additions & 0 deletions src/alignment_io.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -376,6 +376,14 @@ gafkluge::GafRecord alignment_to_gaf(function<size_t(nid_t)> node_to_length, fun
gaf.opt_fields["fp"] = make_pair("Z", aln.fragment_prev().name());
}
}

if (aln.has_annotation()) {
auto& annotation = aln.annotation();
if (annotation.fields().count("proper_pair")) {
bool is_properly_paired = (annotation.fields().at("proper_pair")).bool_value();
gaf.opt_fields["pd"] = make_pair("b", is_properly_paired ? "1" : "0");
}
}
}

return gaf;
Expand Down Expand Up @@ -515,6 +523,12 @@ void gaf_to_alignment(function<size_t(nid_t)> node_to_length, function<string(ni
} else if (opt_it.first == "fn") {
// get the fragment_next field
aln.mutable_fragment_next()->set_name(opt_it.second.second);
} else if (opt_it.first == "pd") {
//Is this read properly paired
auto* annotation = aln.mutable_annotation();
google::protobuf::Value is_properly_paired;
is_properly_paired.set_bool_value(opt_it.second.second == "1");
(*annotation->mutable_fields())["proper_pair"] = is_properly_paired;
}
}
}
Expand Down