bam2GRanges: Import BAM file into GRanges
In AneuFinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Description Usage Arguments Value Examples

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

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bam2GRanges(bamfile, bamindex = bamfile, chromosomes = NULL,
  pairedEndReads = FALSE, remove.duplicate.reads = FALSE, min.mapq = 10,
  max.fragment.width = 1000, blacklist = NULL, what = "mapq")

`bamfile`	A sorted BAM file.
`bamindex`	BAM index file. Can be specified without the .bai ending. If the index file does not exist it will be created and a warning is issued.
`chromosomes`	If only a subset of the chromosomes should be imported, specify them here.
`pairedEndReads`	Set to `TRUE` if you have paired-end reads in your BAM files (not implemented for BED files).
`remove.duplicate.reads`	A logical indicating whether or not duplicate reads should be removed.
`min.mapq`	Minimum mapping quality when importing from BAM files. Set `min.mapq=NA` to keep all reads.
`max.fragment.width`	Maximum allowed fragment length. This is to filter out erroneously wrong fragments due to mapping errors of paired end reads.
`blacklist`	A `GRanges-class` or a bed(.gz) file with blacklisted regions. Reads falling into those regions will be discarded.
`what`	A character vector of fields that are returned. Uses the `Rsamtools::scanBamWhat` function. See `Rsamtools::ScanBamParam` to see what is available.

A GRanges-class object containing the reads.

## Get an example BAM file with single-cell-sequencing reads
bamfile <- system.file("extdata", "BB150803_IV_074.bam", package="AneuFinderData")
## Read the file into a GRanges object
reads <- bam2GRanges(bamfile, chromosomes=c(1:19,'X','Y'), pairedEndReads=FALSE,
                    min.mapq=10, remove.duplicate.reads=TRUE)
print(reads)