Update demo

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: igvShiny
 Title: igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive
     tool for visualization and exploration integrated genomic data)
-Version: 0.99.2
+Version: 0.99.3
 Date: 2024-02-08
 Authors@R: c(
     person("Paul","Shannon", role = c("aut"), 
@@ -20,14 +20,6 @@ Depends:
     GenomicRanges,
     methods,
     shiny
-Suggests: 
-    BiocStyle,
-    GenomicAlignments,
-    knitr,
-    rtracklayer,
-    RUnit,
-    shinytest2,
-    VariantAnnotation
 Imports: 
     BiocGenerics,
     checkmate,
@@ -39,6 +31,15 @@ Imports:
     randomcoloR,
     RCurl,
     utils
+Suggests: 
+    BiocStyle,
+    GenomicAlignments,
+    knitr,
+    Rsamtools,
+    rtracklayer,
+    RUnit,
+    shinytest2,
+    VariantAnnotation
 biocViews: Software, ShinyApps, Sequencing, Coverage
 License: MIT + file LICENSE
 Encoding: UTF-8

NEWS.md

@@ -1,9 +1,13 @@
-## 0.99.2 (2024-02-09)
-- fix some Bioconductor NOTEs
+## igvShiny 0.99.3 - 2024-02-16
+* fix bug in function loadBamTrackFromLocalData
+* improvge way of loading BAM files - show mismatches
 
-## 0.99.1 (2024-02-05)
-- fix some Bioconductor NOTEs
+## igvShiny 0.99.2 - 2024-02-09
+* fix some Bioconductor NOTEs
 
-## 0.99.0 (2024-02-04)
-- make the first Bioconductor release
+## igvShiny 0.99.1 - 2024-02-05
+* fix some Bioconductor NOTEs
+
+## igvShiny 0.99.0 - 2024-02-04
+* make the first Bioconductor release
 

R/igvShiny.R

@@ -926,17 +926,19 @@ loadBamTrackFromLocalData <-
            displayMode = "EXPANDED") {
     if (!requireNamespace("rtracklayer"))
       stop("install rtracklayer to use loadBamTrackFromLocalData")
+    if (!requireNamespace("Rsamtools"))
+      stop("install Rsamtools to use loadBamTrackFromLocalData")
     if (deleteTracksOfSameName) {
       removeTracksByName(session, id, trackName)
 
     }
-    
+
     t_dir <- get_tracks_dir()
     fpath <- tempfile(tmpdir = t_dir, fileext = ".bam")
 
     lmsg <-
       sprintf("igvShiny::load bam from local data, about to write to file '%s'",
-              file.path)
+              fpath)
     flog.debug(lmsg)
     rtracklayer::export(data, fpath, format = "BAM")
 

inst/demos/igvShinyDemo.R

@@ -146,7 +146,7 @@ server = function(input, output, session) {
     printf("---- addBamLocalFileButton")
     showGenomicRegion(session, id="igvShiny_0", "chr21:10,397,614-10,423,341")
     bamFile <- system.file(package="igvShiny", "extdata", "tumor.bam")
-    x <- readGAlignments(bamFile)
+    x <- readGAlignments(bamFile, param = Rsamtools::ScanBamParam(what="seq"))
     loadBamTrackFromLocalData(session, id="igvShiny_0", trackName="tumor.bam", data=x)
   })
 
@@ -261,4 +261,4 @@ if(grepl("hagfish", Sys.info()[["nodename"]]) & !interactive()){
   runApp(shinyApp(ui, server), port=6867)
 } else {
   shinyApp(ui, server)
-}
+}