Commit bd25e972 authored by Mathieu Giraud's avatar Mathieu Giraud

Merge branch 'feature-a/3590-airr-duplicate-count' into 'dev'

Feature a/3590 airr duplicate count

See merge request !343
parents 87719c10 6711acc0
Pipeline #46273 canceled with stages
......@@ -153,7 +153,7 @@ map <string, string> CloneOutputAIRR::fields()
map <string, string> fields;
fields["locus"] = get("germline");
fields["consensus_count"] = string_of_int(reads());
fields["duplicate_count"] = string_of_int(reads());
fields["sequence_id"] = get("id");
fields["clone_id"] = get("id");
......@@ -177,7 +177,7 @@ void SampleOutputAIRR::out(ostream &s)
{
vector <string> fields = {
"locus",
"consensus_count",
"duplicate_count",
"v_call", "d_call", "j_call",
"sequence_id",
"sequence",
......
......@@ -16,6 +16,12 @@ $ The required AIRR fields are present
:productive
:rev_comp
$ Optional AIRR fields
:duplicate_count
$ Custom AIRR fields
:warnings
$ Three clones on IGH
3:IGH
......
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