makeBinnedCountsFile: makeBinnedCountsFile
In RAPIDR: Reliable Accurate Prenatal non-Invasive Diagnosis R package

This function takes in a list of bam files and creates a binned counts file. If a mask file is provided, it will also create a masked binned counts file. The output file is comma separated and the first column is the sampleID, the header is the chromosome name of each bin.

1 2	makeBinnedCountsFile(bam.file.list, sampleIDs, binned.counts.fname, mask = NULL, k = 20000)

`bam.file.list`	list of bam file names
`sampleIDs`	list of sampleIDs, assumed to be in the same order as the bam files in bam.file.list
`binned.counts.fname`	file name of the output binned counts file
`mask`	file name of a bed file with the regions to be masked out. Default is no mask file
`k`	bin size in number of bases. Default is 20,000 bp