Commit f2e35592 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/vidjil-algo.md: document AIRR fields 'vj_in_frame', 'stop_codon'

closes #3569
parent 4f05481d
Pipeline #199903 passed with stages
in 43 minutes and 26 seconds
......@@ -724,6 +724,8 @@ Using `-c designations` trigger a separate analysis for each read, but this is u
| cdr3_aa | string | Amino acid translation of the cdr3 field. <br />*implemented*
| cdr3_sequence_start, cdr3_sequence_end | number | Start/end position of the CDR3 in the query sequence (1-based closed interval). <br />*implemented* |
| productive | boolean | True if the V(D)J sequence is predicted to be productive. <br /> *true, false, or null when no CDR3 has been detected* |
| vj_in_frame | boolean | True if the V and J gene alignments are in-frame. <br /> *true, false, or null when no CDR3 has been detected* |
| stop_codon | boolean | True if the aligned sequence contains a stop codon. <br /> *true, false, or null when vj_in_frame is false* |
| sequence_alignment | string | Aligned portion of query sequence, including any indel corrections or numbering spacers, such as IMGT-gaps. Typically, this will include only the V(D)J region, but that is not a requirement. <br /> *null* |
| germline_alignment | string | Assembled, aligned, fully length inferred germline sequence spanning the same region as the sequence_alignment field (typically the V(D)J region) and including the same set of corrections and spacers (if any). <br />*null*
| v_cigar, d_cigar, j_cigar | string | CIGAR strings for the V/D/J gene <br />*null*.
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