Commit e451edad authored by Mathieu Giraud's avatar Mathieu Giraud

doc/vidjil-algo.md: update

parent bd25e972
Pipeline #46275 failed with stages
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......@@ -644,7 +644,7 @@ See also [What is a clone ?](vidjil-format/#what-is-a-clone).
| Name | Type | AIRR 1.2 Description <br /> *vidjil-algo implementation* |
| ----- | ---- | ------------------------------------------------------- |
| locus | string | Gene locus (chain type). For example, `IGH`, `IGK`, `IGL`, `TRA`, `TRB`, `TRD`, or `TRG`.<br />*Vidjil-algo outputs all these loci. Moreover, the incomplete recombinations analyzed by vidjil-algo are reported as `IGH+`, `IGK+`, `TRA+D`, `TRB+`, `TRD+`, and `xxx` for unexpected recombinations. See [locus](locus).*
| consensus_count | number | Number of reads contributing to the (UMI) consensus for this sequence. For example, the sum of the number of reads for all UMIs that contribute to the query sequence. <br />*Number of reads gathered in the clone.*
| duplicate_count | number | Number of reads contributing to the (UMI) consensus for this sequence. For example, the sum of the number of reads for all UMIs that contribute to the query sequence. <br />*Number of reads gathered in the clone.*
| sequence_id | string | Unique query sequence identifier within the file. Most often this will be the input sequence header or a substring thereof, but may also be a custom identifier defined by the tool in cases where query sequences have been combined in some fashion prior to alignment. <br />*This identifier is the (50 bp by default) window extacted around the junction.* |
| clone_id | string | Clonal cluster assignment for the query sequence. <br />*This identifier is again the (50 bp by default) window extacted around the junction.*
| warnings (+) | string | *Warnings associated to this clone. See <https://gitlab.vidjil.org/blob/dev/doc/warnings.md>.*
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