From 9bca3ae4ca479af3431bea2a36cc6cf03dc3e96d Mon Sep 17 00:00:00 2001 From: chapmanb Date: Fri, 21 Sep 2018 11:59:22 -0400 Subject: [PATCH] teststrandbias.R compatibility with VarDictJava 1.5.5 New structural variant addition to VarDictJava in 1.5.5 or later has 36 columns. Fixes AstraZeneca-NGS/VarDict#83 --- teststrandbias.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/teststrandbias.R b/teststrandbias.R index eb6377f..8145809 100755 --- a/teststrandbias.R +++ b/teststrandbias.R @@ -10,7 +10,7 @@ if (length(myinput) > 0 ){ mynumcols = 0 d = matrix(0,0,0) } -if (mynumcols == 34 || mynumcols == 38){ # 34 columns for standard bed files, 38 for amplicon mode +if (mynumcols == 34 || mynumcols == 36 || mynumcols == 38){ # 34 columns for standard bed files (pre VarDictJava 1.5.5), 36 for VarDictJava >=1.5.5, 38 for amplicon mode d <- read.table( textConnection(myinput), sep = "\t", header = F, comment.char = "", colClasses=c("character", NA, NA, NA, NA, "character", "character", NA, NA, NA, NA, NA, NA, "character", NA, NA, NA, NA, NA, NA, NA, NA), col.names=c(1:mynumcols)) } else if (mynumcols > 0){ stop("Incorrect input detected in teststrandbias.R")