## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>"
)

## ----eval=FALSE---------------------------------------------------------------
#  if (!requireNamespace("BiocManager", quietly = TRUE))
#      install.packages("BiocManager")
#  
#  BiocManager::install("ompBAM")

## ----eval=FALSE---------------------------------------------------------------
#  install.packages(c("devtools", "usethis"))

## -----------------------------------------------------------------------------
library(ompBAM)
pkg_path = file.path(tempdir(), "MyPkg")
use_ompBAM(pkg_path)

## -----------------------------------------------------------------------------
devtools::document(pkg_path)

## -----------------------------------------------------------------------------
devtools::load_all(pkg_path)

## -----------------------------------------------------------------------------
library(MyPkg)

## -----------------------------------------------------------------------------
idxstats(ompBAM::example_BAM("Unsorted"), 2)

## -----------------------------------------------------------------------------
idxstats(ompBAM::example_BAM("scRNAseq"), 2)

## ----eval=FALSE---------------------------------------------------------------
#  library(ompBAM)
#  project_path = "\path\to\MyPkg"
#  use_ompBAM(project_path)

## ----eval=FALSE---------------------------------------------------------------
#  devtools::document()

## -----------------------------------------------------------------------------
library(ompBAM)
pkg_path = file.path(tempdir(), "myPkgName")
use_ompBAM(pkg_path)

## ----eval=FALSE---------------------------------------------------------------
#  use_ompBAM("/path/to/myPkgName")

## ----eval=FALSE---------------------------------------------------------------
#  #' @useDynLib myPkgName, .registration = TRUE
#  #' @import Rcpp
#  NULL
#  
#  #' @export
#  idxstats <- function(bam_file, n_threads) {
#      idxstats_pbam(bam_file, n_threads)
#  }

## ----eval=FALSE---------------------------------------------------------------
#  idxstats(ompBAM::example_BAM("Unsorted"), 2)

## ----eval=FALSE---------------------------------------------------------------
#  # this is added to R/ompBAM_imports.R by use_ompBAM()
#  
#  #' @export
#  idxstats <- function(bam_file, n_threads) {
#    idxstats_pbam(bam_file, n_threads)
#  }

## ----eval=FALSE---------------------------------------------------------------
#  source_path = system.file("examples", "ompBAMExample", "src",
#      package = "ompBAM")

## -----------------------------------------------------------------------------
sessionInfo()