bam2GRanges: Import BAM file into GRanges
In drashley/InversionAnalysis_HGSVC: Find breakpoints in Strand-seq data

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

1 2	bam2GRanges(file, bamindex = file, chromosomes = NULL, pairedEndReads = FALSE, min.mapq = 10, keep.duplicate.reads = TRUE)

`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.
`keep.duplicate.reads`	A logical indicating whether or not duplicate reads should be kept.