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Commit 3158f4d4 authored by Thonier Florian's avatar Thonier Florian

doc/vidjil-algo; AIRR; add missing field junction

parent 4df0f4d1
Pipeline #44941 passed with stages
in 56 minutes and 2 seconds
......@@ -652,7 +652,8 @@ See also [What is a clone ?](vidjil-format/#what-is-a-clone).
| sequence | string | The query nucleotide sequence. Usually, this is the unmodified input sequence, which may be reverse complemented if necessary. In some cases, this field may contain consensus sequences or other types of collapsed input sequences if these steps are performed prior to alignment. <br />*This contains the consensus/representative sequence of each clone.*
| rev_comp | boolean | True if the alignment is on the opposite strand (reverse complemented) with respect to the query sequence. If True then all output data, such as alignment coordinates and sequences, are based on the reverse complement of 'sequence'. <br />*Set to null, as vidjil-algo gather reads from both strands in clones* |
| v_call, d_call, j_call | string | V/D/J gene with allele. For example, IGHV4-59\*01. <br /> *In the case of uncomplete/unexpected recombinations (locus with a `+`), we still use* `v/d/j_call`. |
| junction_aa | string | Junction region amino acid sequence. | <br />*null*
junction | string | Junction region nucleotide sequence, where the junction is defined as the CDR3 plus the two flanking conserved codons. <br />*null*
| junction_aa | string | Junction region amino acid sequence. <br />*null*
| 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* |
| 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*
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