Corrected a bug in computePred.R when there is only one mutation in the mut file.

computePred.R

@@ -110,6 +110,7 @@ wt = wt[[1]][1:n]
 if(simple==FALSE){
   print("reading selected mutations...")
   res=readMut(fname)
+  #print(res)
   pos = res[[1]]
   subsaa = res[[2]]
   rawMut = res[[3]]
@@ -122,8 +123,8 @@ nbSeqs = computeNbSeqs(ali)
 # compute gap counts for each position
 nbGaps = N[1] - apply(nbSeqs,2,sum)
 # output the conservation values
-dat=rbind(trace,KL=res[[1]][[2]],SE=res[[1]][[1]],gap=nbGaps/N[1],KL60=res[[2]][[2]],SE60=res[[2]][[1]],KL80=res[[3]][[2]],SE80=res[[3]][[1]])
-write.table(dat,paste0(prot,"_conservation.txt"))
+# dat=rbind(trace,KL=res[[1]][[2]],SE=res[[1]][[1]],gap=nbGaps/N[1],KL60=res[[2]][[2]],SE60=res[[2]][[1]],KL80=res[[3]][[2]],SE80=res[[3]][[1]])
+# write.table(dat,paste0(prot,"_conservation.txt"))
 # compute log-odd ratios between mutated and wt sequence counts
 predInd = computePredNbSeqs(wt,nbSeqs)
 rownames(predInd)=aa