release v19.0.0

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/

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]})

dataset/20210626_critical_pos.txt → dataset/20210704_critical_pos.txt

 # 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