From febb6b8d10ea423c40545e9855f913dc1c4b2ce5 Mon Sep 17 00:00:00 2001 From: JocelynSP Date: Wed, 10 Jan 2024 13:44:31 +1100 Subject: [PATCH] Move close bracket in fix to #615 Fix for #615:,reflect upstream BiocConductor/VariantAnnotation ALT field format changes, fails due to mis-placed ')' --- scripts/libgridss.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/libgridss.R b/scripts/libgridss.R index 35452c78..399eb265 100755 --- a/scripts/libgridss.R +++ b/scripts/libgridss.R @@ -777,7 +777,7 @@ align_breakpoints <- function(vcf, align=c("centre"), is_higher_breakend=names(v } else { stop("Only centre alignment is currently implemented.") } - isbp = str_detect(VariantAnnotation::fixed(vcf)$ALT, "[\\]\\[]") + isbp = str_detect(as.vector(VariantAnnotation::fixed(vcf)$ALT), "[\\]\\[]") is_adjusted_bp = isbp & !is.na(adjust_by) & adjust_by != 0 rowRanges(vcf) = shift(rowRanges(vcf), ifelse(!is_adjusted_bp, 0, adjust_by)) info(vcf)$CIPOS = info(vcf)$CIPOS - adjust_by