Added warning when no reads pass filterAndTrim

leholman · Aug 13, 2017 · 28c4684 · 28c4684
1 parent 3271207
commit 28c4684
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/R/filter.R b/R/filter.R
@@ -199,6 +199,11 @@ filterAndTrim <- function(fwd, filt, rev=NULL, filt.rev=NULL, compress=TRUE,
                      mc.cores=ncores, mc.silent=TRUE)
   }
   colnames(rval) <- basename(fwd)
+  if(all(rval["reads.out",]==0)) {
+    warning("No reads passed the filter. Please revisit your filtering parameters.")
+  } else if(any(rval["reads.out",]==0)) {
+    message("Some input samples had no reads pass the filter.")
+  }
   return(invisible(t(rval)))
 }
 #' Filter and trim a fastq file.