Merge branch 'dev' into 'master'

dev to master

See merge request tron/bnt_neoants/splice2neo!117

.gitignore

@@ -4,3 +4,5 @@
 .Ruserdata
 docs
 fix_issue_*.R
+vignettes/*.html
+vignettes/*.R

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: splice2neo
 Title: Aberrant splice junction analysis with associated mutations
-Version: 0.6.5
+Version: 0.6.6
 Authors@R: 
     c(
     person(given = "Jonas",
@@ -29,7 +29,8 @@ Suggests:
     knitr,
     testthat (>= 3.0.0),
     covr,
-    ggbio
+    ggbio,
+    rmarkdown
 Config/testthat/edition: 3
 Language: en-US
 Imports: 
@@ -39,7 +40,7 @@ Imports:
     GenomeInfoDb,
     magrittr,
     tibble,
-    stringr,
+    stringr (>= 1.5.0),
     dplyr,
     readr,
     tidyr,

NEWS.md

@@ -1,3 +1,9 @@
+# splice2neo 0.6.6
+
+* add vignette with example workflow
+* fix parsing of pangolin results
+* simplify README
+
 # splice2neo 0.6.5
 
 * Fixed bug while parsing VCF files containing only a single variant

R/parse_gtf.R

@@ -3,6 +3,7 @@
 #' Parse a GFF/GTF file as \code{\link[GenomicRanges]{GRangesList}} of exons
 #'
 #' @param file path to a GFF or GTF file (See \code{\link[GenomicFeatures]{makeTxDbFromGFF}}))
+#' @param ... other options passed to file path to \code{\link[GenomicFeatures]{makeTxDbFromGFF}})
 #' @return A \code{\link[GenomicRanges]{GRangesList}} of exons grouped by transcripts
 #'
 #' @examples
@@ -11,9 +12,9 @@
 #' parse_gtf(gff_file)
 #'
 #' @export
-parse_gtf <- function(file){
+parse_gtf <- function(file, ...){
 
-  txdb <- suppressWarnings(GenomicFeatures::makeTxDbFromGFF(file))
+  txdb <- suppressWarnings(GenomicFeatures::makeTxDbFromGFF(file, ...))
   transcripts <- GenomicFeatures::exonsBy(txdb, by = c("tx"), use.names = TRUE)
 
   return(transcripts)

R/parse_pangolin.R

@@ -57,8 +57,7 @@ parse_pangolin <- function(vcf_file){
     unnest(annot_gene) %>%
     # pares individual annotation values
     mutate(
-      gene_id = annot_gene %>%
-        str_replace("([^|]*)\\|-?\\d+:-?\\d\\.+\\d+\\|-?\\d+:-?\\d\\.+\\d+\\|", "\\1"),
+      gene_id = gsub("\\|.*", "", annot_gene),
       # extract all annotations per variant - gene
       annot = annot_gene %>%
         str_extract_all("-?\\d+:-?\\d\\.+\\d+")