Load a BAM Track from a Local File via HTTP Range Requests

Streams a local BAM file and its index directly from disk using HTTP 206 Partial Content requests handled by the Shiny session. This allows viewing multi-gigabyte BAM files without loading them into R memory.

Usage

loadBamTrackFromLocalFile(
  session,
  id,
  trackName,
  bamFile,
  indexFile = paste0(bamFile, ".bai"),
  deleteTracksOfSameName = TRUE,
  displayMode = "EXPANDED",
  trackConfig = list(),
  validateReference = TRUE,
  trackHeight = NULL
)

Arguments

session

an environment or list, provided and managed by shiny (ShinySession)

id

character string, the html element id of this widget instance

trackName

character string, display name for the track

bamFile

character string, path to an existing, readable .bam file

indexFile

character string, path to the corresponding .bai index file (default: paste0(bamFile, ".bai"))

deleteTracksOfSameName

logical, whether to delete any existing track with the same name (default: TRUE)

displayMode

character string, display mode for alignments ("EXPANDED", "COLLAPSED", or "SQUISHED"), default "EXPANDED"

trackConfig

list, additional track options passed to igv.js

validateReference

logical flag, default TRUE: checks track contigs against the active reference genome and emits warnings/toasts on mismatch.

trackHeight

numeric, track height in pixels (default: NULL, igv.js defaults to 300)

Value

None, sends a message to the browser

Examples

if (FALSE) { # \dontrun{
# Inside a Shiny server function:
bamFile <- system.file(package = "igvShiny", "extdata",
                       "A_2_A24_02_01_01.nanopore.minimap.sorted.bam")
baiFile <- paste0(bamFile, ".bai")
loadBamTrackFromLocalFile(session, "igvShiny_0", "Nanopore Reads",
                         bamFile, baiFile, displayMode = "SQUISHED",
                         trackHeight = 100)
} # }