bugfix: issue with VCF files

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: igvShiny
 Title: igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive
     tool for visualization and exploration integrated genomic data)
-Version: 1.0.1
-Date: 2024-08-10
+Version: 1.0.2
+Date: 2024-08-16
 Authors@R: c(
     person("Paul","Shannon", role = c("aut"), 
     email = "[email protected]"),

NEWS.md

@@ -1,3 +1,6 @@
+## igvShiny 1.0.2 - 2024-08-16
+* fix issue with VCF files
+
 ## igvShiny 1.0.1 - 2024-08-10
 * fix issue with custom files not working properly
 

R/igvShiny.R

@@ -741,15 +741,16 @@ loadVcfTrack <- function(session,
 
   state[["userAddedTracks"]] <-
     unique(c(state[["userAddedTracks"]], trackName))
-  path <- file.path(get_tracks_dir(), "tmp.vcf")
-  lmsg <- sprintf("igvShiny::loadVcfTrack, about to write to file '%s'", path)
+  temp.file <- tempfile(tmpdir = get_tracks_dir(), fileext = ".vcf")
+  lmsg <- sprintf("igvShiny::loadVcfTrack, about to write to file '%s'", temp.file)
   flog.debug(lmsg)
-  VariantAnnotation::writeVcf(vcfData, path)
+  VariantAnnotation::writeVcf(vcfData, temp.file)
   lmsg2 <- sprintf("igvShiny::loadVcfTrack, file.exists(%s)? %s",
-                   path,
-                   file.exists(path))
+                   temp.file,
+                   file.exists(temp.file))
   flog.debug(lmsg2)
 
+  path <- file.path("tracks", basename(temp.file))
   message <-
     list(
       elementID = id,