Commit 81af152d authored by Mathieu Giraud's avatar Mathieu Giraud

core/output.cpp: more AIRR fields

See #3572 and #3573.
parent 8e0d1c51
......@@ -120,6 +120,13 @@ void SampleOutputVidjil::out(ostream &s)
// AIRR .tsv output
string TF_format_bool(string val)
{
if (val == "false") return "F" ;
if (val == "true") return "T" ;
return val ;
}
map <string, string> CloneOutputAIRR::fields()
{
map <string, string> fields;
......@@ -133,6 +140,12 @@ map <string, string> CloneOutputAIRR::fields()
fields["v_call"] = get(KEY_SEG, "5", "name");
fields["d_call"] = get(KEY_SEG, "4", "name");
fields["j_call"] = get(KEY_SEG, "3", "name");
fields["cdr3_aa"] = get(KEY_SEG, "cdr3", "aa");
fields["junction"] = NULL_VAL;
fields["junction_aa"] = get(KEY_SEG, "junction", "aa");
fields["productive"] = TF_format_bool(get(KEY_SEG, "junction", "productive"));
fields["rev_comp"] = NULL_VAL;
return fields;
}
......@@ -145,6 +158,12 @@ void SampleOutputAIRR::out(ostream &s)
"v_call", "d_call", "j_call",
"sequence_id",
"sequence",
"productive",
"junction_aa",
"junction",
"cdr3_aa",
"rev_comp",
"sequence_alignment",
"germline_alignment",
"v_cigar", "d_cigar", "j_cigar",
......
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