update changelog

CHANGELOG.md

@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Fix singularity image pull tag for MAGeCKFlute ([#160](https://github.com/nf-core/crisprseq/pull/160))
 - Skip dolar signs on containerOptions ([#163](https://github.com/nf-core/crisprseq/pull/163))
+- Fix error in R script when adding patterns ([#170](https://github.com/nf-core/crisprseq/pull/170))
 
 ### Deprecated
 

bin/cigar_parser.R

@@ -547,7 +547,7 @@ correct_insertion_vc <- function(cut_site_position, insertion_row, gRNA){
         after_inserted <- substr(as.character(bam[[1]]$seq[bam[[1]]$qname == insertion_row$Ids]), nts_bef_nt+1+insertion_row$Length + diff, nts_bef_nt+insertion_row$Length+3 + diff)
 
         if(before_inserted == before_cut && after_inserted == after_cut){
-            return(list(Modification="ins", Start=cut_site_position+1, Length=insertion_row$Length, Ids=insertion_row$Ids, above_error_rate=insertion_row$above_error_rate, in_pick = insertion_row$in_pick, freq = insertion_row$freq, Perc=insertion_row$Perc, pre_ins_nt=before_inserted, ins_nt=inserted, post_ins_nt=after_inserted))
+            return(list(Modification="ins", Start=cut_site_position+1, Length=insertion_row$Length, Ids=insertion_row$Ids, above_error_rate=insertion_row$above_error_rate, in_pick = insertion_row$in_pick, freq = insertion_row$freq, Perc=insertion_row$Perc, patterns=insertion_row$patterns, pre_ins_nt=before_inserted, ins_nt=inserted, post_ins_nt=after_inserted))
         } else {
             return(insertion_row)
         }
@@ -900,6 +900,7 @@ if (dim(alignment_info)[1] != 0){
             separated_indels["post_ins_nt"]<-NA
         }else if(dim(separated_indels_ins_all)[1]>0){
             separated_indels <- separated_indels_ins_all
+            separated_indels["patterns"]<-NA
         }