Commit 018a24a0 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

doc/warnings.md, js/warnings_data.js: bikeshedding, more simple descriptions

parent f938acda
Pipeline #735702 failed with stages
in 41 minutes and 50 seconds
......@@ -91,7 +91,7 @@ var warnings_data = {
"visibility": 0
}
},
"Clone quality (KmerSegmenter in vidjil-algo)":
"Clonotype quality":
{
"W50":
{
......@@ -115,7 +115,7 @@ var warnings_data = {
{
"title": "Bad e-value",
"level": 1,
"visibility": 1,
"visibility": 0,
"reference": "W5a"
},
"W53":
......@@ -131,7 +131,7 @@ var warnings_data = {
"visibility": 0
}
},
"Strange recombination (FineSegmenter in vidjil-algo), V and J genes":
"Uncommon recombination":
{
"W6a":
{
......@@ -203,7 +203,7 @@ var warnings_data = {
"visibility": 0
}
},
"Comparisons between several samples or patients (such as with clonedb)":
"Clonotypes across samples":
{
"W8x":
{
......@@ -219,13 +219,13 @@ var warnings_data = {
},
"W81":
{
"title": "Merged clone has different V(D)J designation in some samples",
"title": "Clonotype with different V(D)J designations in some samples",
"level": 2,
"visibility": 1
},
"W82":
{
"title": "Merged clone has different productivities in some samples",
"title": "Clonotype with different productivities in some samples",
"level": 2,
"visibility": 1
}
......
......@@ -28,16 +28,16 @@ Warnings which were implemented ([x]) have a fixed code that should not be chang
- [ ] W2x CDR3 detection without gapped germlines #2187 (ou bien par clone ?)
## Output of an analysis, warnings on some clones
## Output of an analysis, warnings on some clonotypes
### Read quality
- [ ] W40 Low quality #1544
### Clone quality (KmerSegmenter in vidjil-algo)
### Clonotype quality (KmerSegmenter in vidjil-algo)
- [x] W50 Short or shifted window in vidjil-algo
- [x] W51 Low coverage (0.112)
- [ ] Bad e-value (0.xxx) #1437/#1566/#1889
- [x] W53 Similar to another clone
- [x] W53 Similar to another clonotype
- [ ] Possible strand ambiguity
### Strange recombination (FineSegmenter in vidjil-algo), V and J genes
......@@ -46,7 +46,7 @@ Warnings which were implemented ([x]) have a fixed code that should not be chang
- [ ] Potential di-mer #2820
- [ ] Very large deletion (xxx bp) #2909
- [ ] Unexpected recombination
- [ ] High probability clone ?
- [ ] High probability clonotype ?
- [x] W68 V(D)J designation failed, possibly complex or not recombined sequence #4818
- [x] W69 Several V/J candidate genes with equal probability #3575
......@@ -58,7 +58,7 @@ Warnings which were implemented ([x]) have a fixed code that should not be chang
## Comparisons between several samples or patients (such as with clonedb)
- [ ] W8x Potential contamination or public clone #1744
- [ ] Known public clone
- [x] W81 Merged clone has different V(D)J designation in some samples #4566
- [x] W82 Merged clone has different productivities in some samples #4578
- [ ] Known public clonotype
- [x] W81 Clonotyoe with different V(D)J designations in some samples #4566
- [x] W82 Clonotype with different productivities in some samples #4578
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