From 28c4684c58a30a82429c38e72dc27cd4c773220a Mon Sep 17 00:00:00 2001
From: bcallah <bcallah@PHPMB13.local>
Date: Sat, 12 Aug 2017 20:30:51 -0400
Subject: [PATCH] Added warning when no reads pass filterAndTrim

---
 R/filter.R | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/R/filter.R b/R/filter.R
index 189c022..1f1db97 100644
--- 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.