From 2058fc96d796fc976afbf0062a0d0901ad62515f Mon Sep 17 00:00:00 2001 From: coolneng Date: Sat, 15 May 2021 17:49:39 +0200 Subject: [PATCH] Consider the read start in the Cys location --- src/alignment.r | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/alignment.r b/src/alignment.r index 03470d3..de1c8bf 100644 --- a/src/alignment.r +++ b/src/alignment.r @@ -110,8 +110,9 @@ get_cys_coordinates <- function(alignment) { insertion <- unlist(Biostrings::insertion(alignment)) deletion <- unlist(Biostrings::deletion(alignment)) delta_coordinates <- handle_indels(insertion, deletion, cys, alignment) - cys_start <- cys$start + delta_coordinates$start - cys_end <- cys$end + delta_coordinates$end + read_start <- unlist(start(Biostrings::Views(alignment))) + cys_start <- cys$start + delta_coordinates$start + read_start - 1 + cys_end <- cys$end + delta_coordinates$end + read_start return(list("start" = cys_start, "end" = cys_end)) }