fix handling of reports for no variants

Author: pdimens

harpy/reports/leviathan_pop.Rmd

@@ -80,8 +80,8 @@ emptyfiles <- character()
 sv <- data.frame(matrix(ncol=8,nrow=0, dimnames=list(NULL, c("population",	"contig",	"position_start",	"position_end",	"length",	"type",	"n_barcodes",	"n_pairs"))))
 for(i in statsfiles){
   .df <- tryCatch(readvariants(i), error = function(e){return(0)})
-  if(length(.df)==1){
-      emptyfiles <- c(emptyfiles, i)
+  if(nrow(.df)==0){
+    emptyfiles <- c(emptyfiles, i)
   } else {
     sv <- rbind(sv, .df)
   }

harpy/reports/naibr.Rmd

@@ -36,17 +36,16 @@ samplename <- gsub(".bedpe", "", basename(infile))
 tryCatch(
   expr = {
     variants <- read.table(infile, header = T) 
+    if (nrow(variants) == 0) {
+      cat(paste0("There are no variants in the file ", "`", infile, "`"))
+      knitr::knit_exit()
+    }
   },
   error = function(e){ 
     cat(paste0("There are no variants in the file ", "`", infile, "`"))
     knitr::knit_exit()
   }
 )
-
-if (nrow(variants) == 0) {
-  cat(paste0("There are no variants in the file ", "`", infile, "`"))
-  knitr::knit_exit()
-}
 ```
 
 ```{r package_imports}

harpy/reports/naibr_pop.Rmd

@@ -99,7 +99,7 @@ emptyfiles <- character()
 sv <- data.frame(matrix(ncol=12,nrow=0, dimnames=list(NULL, c("Population", "Chr1", "Break1", "Chr2", "Break2", "SplitMolecules", "DiscordantReads", "Orientation", "Haplotype", "Score", "PassFilter", "SV"))))
 for(i in infiles){
   .df <- tryCatch(readvariants(i), error = function(e){return(0)})
-  if(length(.df)==1){
+  if(nrow(.df)==0){
       emptyfiles <- c(emptyfiles, i)
   } else {
     sv <- rbind(sv, .df)