From 8bbc46bdfff640981a5147440f5f94241e5f23a7 Mon Sep 17 00:00:00 2001 From: Peter Chovanec Date: Mon, 14 Dec 2020 20:42:04 -0800 Subject: [PATCH] pair2frgm xa filter pair2frgm if TRUE throws an error: `Error in data.first & data.last: operations are possible only for numeric, logical or complex types` --- R/importReads.R | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/R/importReads.R b/R/importReads.R index 7761213..7cfbbc8 100644 --- a/R/importReads.R +++ b/R/importReads.R @@ -93,14 +93,16 @@ readBamFileAsGRanges <- function(file, bamindex=file, chromosomes=NULL, pairedEn ## filter XA tag if (filtAlt) { - data.first <- is.na(mcols(data.first)$XA) - data.last <- is.na(mcols(data.last)$XA) - } + data.first.xa <- is.na(mcols(data.first)$XA) + data.last.xa <- is.na(mcols(data.last)$XA) - mask <- data.first & data.last + mask <- data.first.xa & data.last.xa - data.first <- data.first[mask] - data.last <- data.last[mask] + data.first <- data.first[mask] + data.last <- data.last[mask] + } + + ## Filter by mapping quality and duplicate reads if (!is.null(min.mapq)) {