From dba3ff5c4877bf492daaa488270028bdd3abb484 Mon Sep 17 00:00:00 2001
From: Gael <Gael@WL20-0067.corp.pasteur.fr>
Date: Sun, 4 Jul 2021 13:22:36 +0200
Subject: [PATCH] release v19.0.0
---
README.md | 5 +++++
cnr_curation_voc_qc.R | 2 +-
.../{20210626_critical_pos.txt => 20210704_critical_pos.txt} | 2 ++
3 files changed, 8 insertions(+), 1 deletion(-)
rename dataset/{20210626_critical_pos.txt => 20210704_critical_pos.txt} (88%)
diff --git a/README.md b/README.md
index 1b2d6e62..70ee6a10 100644
--- a/README.md
+++ b/README.md
@@ -199,6 +199,11 @@ Hub-CDB and Institut Pasteur
<br /><br />
## WHAT'S NEW IN
+### v19.0.0
+
+1) S13I and W152C positions added as critical because of https://science.sciencemag.org/content/early/2021/06/30/science.abi7994.full
+
+
### v18.0.0
1) S:K417N position added as critical because of https://www.reuters.com/business/healthcare-pharmaceuticals/what-is-delta-variant-coronavirus-with-k417n-mutation-2021-06-23/
diff --git a/cnr_curation_voc_qc.R b/cnr_curation_voc_qc.R
index e557296e..6fc31a38 100644
--- a/cnr_curation_voc_qc.R
+++ b/cnr_curation_voc_qc.R
@@ -1023,7 +1023,7 @@ for(i0 in 1:nrow(res)){
# end tempo.qc positions converted to nextclade positions
# coverage QC of all the voc variants using the .cov file
- # cov file use the MN908947_Ampliseq positions
+ # cov file uses the MN908947_Ampliseq positions
var.range <- paste0(tempo.qc$pos - dcov.ext, ":", tempo.qc$pos + dcov.ext)
var.range.list <- lapply(as.list(var.range), FUN = function(x){eval(parse(text = x))})
range.cov <- lapply(var.range.list, FUN = function(x){cov[x, 3]})
diff --git a/dataset/20210626_critical_pos.txt b/dataset/20210704_critical_pos.txt
similarity index 88%
rename from dataset/20210626_critical_pos.txt
rename to dataset/20210704_critical_pos.txt
index 96053f2e..c402a32b 100644
--- a/dataset/20210626_critical_pos.txt
+++ b/dataset/20210704_critical_pos.txt
@@ -1,6 +1,8 @@
# GATK positions for the deletions
chr begin_pos end_pos codon_ref orf name ini_concern_name
+MN908947_Ampliseq 21545 21547 AGT S S:S13 S:S13I
MN908947_Ampliseq 21563 21565 ACA S S:T19 S:T19R
+MN908947_Ampliseq 21962 21964 TGG S S:W152 S:W152C
MN908947_Ampliseq 22757 22759 AAG S S:K417 S:K417N
MN908947_Ampliseq 22826 22828 AAT S S:N440 S:N440K
MN908947_Ampliseq 22862 22864 CTG S S:L452 S:L452R
--
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