Count stop codons as coverage for #336.

cfe-lab · Jul 22, 2016 · 964fe58 · 964fe58
1 parent d18538e
commit 964fe58
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/micall/monitor/coverage_plots.R b/micall/monitor/coverage_plots.R
@@ -225,7 +225,7 @@ data <- read.csv(file=input.csv, header=TRUE, sep=',')
 #seed,region,q-cutoff,query.aa.pos,refseq.aa.pos,A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*
 #HCV1A-H77-core-seed,HCV1A-H77-core,0,0,1,0,0,0,0,0,0,0,3,0,0,1542,0,0,0,0,0,0,0,0,0,0
 
-alphabet <- c('A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y')  # X. represents stop codon '*'
+alphabet <- c('A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y', 'X.')  # X. represents stop codon '*'
 
 data$coverage <- apply(data[ , which(is.element(names(data), alphabet))], 1, sum)