Catch length-2 filtering arguments when processing single-end data

And provide an informative error message to help users fix the function call. Fixes benjjneb#388
leholman · Mar 20, 2019 · 3b6bec5 · 3b6bec5
1 parent 905dc8f
commit 3b6bec5
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Showing 4 changed files with 13 additions and 10 deletions.
diff --git a/R/filter.R b/R/filter.R
@@ -480,6 +480,9 @@ fastqFilter <- function(fn, fout, truncQ = 2, truncLen = 0, maxLen = Inf, minLen
     ompthreads <- .Call(ShortRead:::.set_omp_threads, 1L)
     on.exit(.Call(ShortRead:::.set_omp_threads, ompthreads))
   }
+  if(any(sapply(list(truncQ, truncLen, maxLen, minLen, trimLeft, trimRight, maxN, minQ, maxEE), length) > 1)) {
+    stop("Filtering and trimming arguments should be of length 1 when processing single-end (rather than paired-end) data.")
+  }
 
   start <- max(1, trimLeft + 1, na.rm=TRUE)
   end <- truncLen

diff --git a/man/fastqFilter.Rd b/man/fastqFilter.Rd
diff --git a/man/fastqPairedFilter.Rd b/man/fastqPairedFilter.Rd
diff --git a/man/filterAndTrim.Rd b/man/filterAndTrim.Rd