% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/igvShiny.R
\name{loadCramTrackFromLocalData}
\alias{loadCramTrackFromLocalData}
\title{load a cram file sitting on the same machine as the shiny app}
\usage{
loadCramTrackFromLocalData(
  session,
  id,
  trackName,
  cramFile,
  indexFile = paste0(cramFile, ".crai"),
  deleteTracksOfSameName = TRUE,
  trackConfig = list()
)
}
\arguments{
\item{session}{an environment or list, provided and managed by shiny}

\item{id}{character string, the html element id of this widget instance}

\item{trackName}{character string}

\item{cramFile}{character string, path to a cram file}

\item{indexFile}{character string, path to its crai index,
by default the cram file with ".crai" appended}

\item{deleteTracksOfSameName}{logical, default TRUE}

\item{trackConfig}{a named list of additional igv.js track configuration
options, \code{sort} among them; see \code{\link{loadBamTrackFromURL}}.}
}
\value{
nothing
}
\description{
load a local cram track. Unlike \code{loadBamTrackFromLocalData}
this loader takes file paths, not an R object: no bioconductor package parses
cram, so the file and its index are handed to igv.js untouched, through the
directory shiny serves as "tracks".
}
\examples{
library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "showcase", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

}
\keyword{track_loaders}
