Commit a7543499 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/: precisions on 1-based positions

parent 52e352b7
Pipeline #150396 canceled with stages
in 1 minute and 6 seconds
......@@ -45,6 +45,11 @@ The algorithm follows roughly those steps:
Germline is the one that overwrites those members with the Fasta
corresponding to the affectation found by the KmerSegmenter.
## Positions on sequences
Internally, most positions are 0-based. See #4327.
However, as soon as there are exported (.vidjil, AIRR), the positions are 1-based, they start at 1.
## Tests
### Unit
......@@ -750,7 +750,7 @@ In a `.vdj.fa` format, a line starting with a \> is of the following form:
The following lines are for VDJ recombinations:
``` diff
startV endV start and end position of the V gene in the sequence (start at 1)
startV endV start and end position of the V gene in the sequence (1-based, start at 1)
startD endD ... of the D gene ...
startJ endJ ... of the J gene ...
......@@ -348,7 +348,7 @@ In the `.analysis` file, this section is intended to describe some specific clon
// on the web application, clones that are not detected will be shown on the grid with '?/?'
// positions are related to the 'sequence'
// names of V/D/J genes should match the ones in files referenced in germline/
// Positions on the sequence start at 1.
// Positions on the sequence are 1-based, they start at 1.
"5": {"name": "IGHV5*01", "start": 1, "stop": 120, "delRight": 5}, // V (or 5') segment
"4": {"name": "IGHD1*01", "start": 124, "stop": 135, "info": "unsure designation", "delRight": 5, "delLeft": 0}, // D (or middle) segment
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