Commit dd14adbf authored by Mikaël Salson's avatar Mikaël Salson

Merge branch 'feature-a/3575-warning-two-assignations' into 'dev'

Feature a/3575 warning two assignations

Closes #3575

See merge request !333
parents 656ddd25 021fc442
Pipeline #44866 passed with stages
in 6 minutes and 29 seconds
......@@ -1343,6 +1343,19 @@ void FineSegmenter::checkWarnings(CloneOutput *clone)
{
clone->add_warning("W61", "Non-recombined D7-27/J1 sequence", LEVEL_ERROR);
}
// Multiple candidate assignations
for (auto box: {box_V, box_J})
{
if ((box->score.size() > 1) && (box->score[0].first == box->score[1].first)) {
string genes = "";
for (auto it: box->score) {
if (it.first < box->score[0].first) break;
genes += " " + box->rep->label(it.second);
}
clone->add_warning("W69", "Several genes with equal probability:" + genes, LEVEL_WARN);
}
}
}
}
......
......@@ -10,3 +10,8 @@ $ There is a segmentation in the .vidjil, but without any D
1:"name": "TRBJ2-3.01"
0:"name": "TRBD
1:"name": "TRBV7-2.01"
$ There is a warning on multiple candidate assignations
1:"code": "W69"
1:equal probability: TRBV7-2.0[12] TRBV7-2.0[12]"
......@@ -49,6 +49,7 @@ Warnings which were implemented ([x]) have a fixed code that should not be chang
- [ ] Unexpected recombination
- [ ] High probability clone ?
- [ ] W6z Unexpected error in V(D)J analysis (FineSegmenter failed)
- [x] W69 Several V/J candidate genes with equal probability #3575
*Strange recombination (FineSegmenter in vidjil-algo), D gene, N regions*
- [ ] W7x Mutations near breakpoint #1412
......
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