readBamFileAsGRanges: Import BAM file into GRanges
In breakpointR: Find breakpoints in Strand-seq data

Description Usage Arguments Value Author(s) Examples

Import aligned reads from a BAM file into a GRanges-class object.

readBamFileAsGRanges(
  file,
  bamindex = file,
  chromosomes = NULL,
  pairedEndReads = FALSE,
  min.mapq = 10,
  remove.duplicate.reads = TRUE,
  pair2frgm = FALSE,
  filtAlt = FALSE
)

`file`	Bamfile with aligned reads.
`bamindex`	Bam-index file with or without the .bai ending. If this file does not exist it will be created and a warning is issued.
`chromosomes`	If only a subset of the chromosomes should be binned, specify them here.
`pairedEndReads`	Set to `TRUE` if you have paired-end reads in your file.
`min.mapq`	Minimum mapping quality when importing from BAM files.
`remove.duplicate.reads`	A logical indicating whether or not duplicate reads should be kept.
`pair2frgm`	Set to `TRUE` if every paired-end read should be merged into a single fragment.
`filtAlt`	Set to `TRUE` if you want to filter out alternative alignments defined in 'XA' tag.

A GRanges-class object.

David Porubsky, Aaron Taudt, Ashley Sanders

## Get an example file 
exampleFolder <- system.file("extdata", "example_bams", package="breakpointRdata")
exampleFile <- list.files(exampleFolder, full.names=TRUE)[1]
## Load the file
fragments <- readBamFileAsGRanges(exampleFile, pairedEndReads=FALSE, chromosomes='chr22')