--- a/report_clonality/RScript.r	Mon Apr 24 09:39:59 2017 -0400
+++ b/report_clonality/RScript.r	Tue May 30 07:26:33 2017 -0400
@@ -122,12 +122,17 @@
   clonalityFrame = clonalityFrame[!duplicated(clonalityFrame$clonality_clonaltype), ]
 }
 
+if(nrow(PRODF) == 0){
+	stop("No sequences left after filtering")
+}
+
 prod.unique.sample.count = data.frame(data.table(PRODF)[, list(Productive_unique=.N), by=c("Sample")])
 prod.unique.rep.count = data.frame(data.table(PRODF)[, list(Productive_unique=.N), by=c("Sample", "Replicate")])
 
 unprod.unique.sample.count = data.frame(data.table(UNPROD)[, list(Unproductive_unique=.N), by=c("Sample")])
 unprod.unique.rep.count = data.frame(data.table(UNPROD)[, list(Unproductive_unique=.N), by=c("Sample", "Replicate")])
 
+
 PRODF$freq = 1
 
 if(any(grepl(pattern="_", x=PRODF$ID))){ #the frequency can be stored in the ID with the pattern ".*_freq_.*"
@@ -176,6 +181,7 @@
 
 #create the table on the overview page with the productive/unique counts per sample/replicate
 #first for sample
+
 sample.count = merge(input.sample.count, prod.sample.count, by="Sample", all.x=T)
 sample.count$perc_prod = round(sample.count$Productive / sample.count$All * 100)
 sample.count = merge(sample.count, prod.unique.sample.count, by="Sample", all.x=T)
@@ -188,6 +194,16 @@
 
 #then sample/replicate
 rep.count = merge(input.rep.count, prod.rep.count, by=c("Sample", "Replicate"), all.x=T)
+
+print(rep.count)
+
+fltr = is.na(rep.count$Productive)
+if(any(fltr)){
+	rep.count[fltr,"Productive"] = 0
+}
+
+print(rep.count)
+
 rep.count$perc_prod = round(rep.count$Productive / rep.count$All * 100)
 rep.count = merge(rep.count, prod.unique.rep.count, by=c("Sample", "Replicate"), all.x=T)
 rep.count$perc_prod_un = round(rep.count$Productive_unique / rep.count$All * 100)