Commit 994df707 authored by Mathieu Giraud's avatar Mathieu Giraud

core/output.cpp: add {v,j}_support and {v,d,j}_sequence_{start,end}

see #3569
parent b8d1062f
......@@ -167,6 +167,18 @@ map <string, string> CloneOutputAIRR::fields()
fields["d_call"] = get(KEY_SEG, "4", "name");
fields["j_call"] = get(KEY_SEG, "3", "name");
fields["v_sequence_start"] = get(KEY_SEG, "5", "start");
fields["v_sequence_end"] = get(KEY_SEG, "5", "stop");
fields["d_sequence_start"] = get(KEY_SEG, "4", "start");
fields["d_sequence_end"] = get(KEY_SEG, "4", "stop");
fields["j_sequence_start"] = get(KEY_SEG, "3", "start");
fields["j_sequence_end"] = get(KEY_SEG, "3", "stop");
fields["cdr3_sequence_start"] = get(KEY_SEG, "cdr3", "start");
fields["cdr3_sequence_end"] = get(KEY_SEG, "cdr3", "stop");
fields["v_support"] = get(KEY_SEG, "evalue_left", "val");
fields["j_support"] = get(KEY_SEG, "evalue_right", "val");
fields["cdr3_aa"] = get(KEY_SEG, "cdr3", "aa");
fields["junction"] = NULL_VAL;
fields["junction_aa"] = get(KEY_SEG, "junction", "aa");
......@@ -192,6 +204,15 @@ void SampleOutputAIRR::out(ostream &s)
"junction",
"cdr3_aa",
"warnings",
"v_sequence_start", "v_sequence_end",
"d_sequence_start", "d_sequence_end",
"j_sequence_start", "j_sequence_end",
"cdr3_sequence_start", "cdr3_sequence_end",
"v_support", "j_support",
"rev_comp",
"sequence_alignment",
"germline_alignment",
......
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