pileupRead: Read pileup file
In EricArcher/swfscGenetics: Miscellaneous functions for genetic data manipulation

Reads a pileup format file created by samtools mpileup.

1	pileupRead(fname, all.columns = FALSE)

`fname`	filename of pileup file
`all.columns`	If `FALSE` (default), only the first 6 columns are returned. If `TRUE`, all columns are returned, but only the six are informatively named.

data frame representing the pileup file with the following columns:

`chrom`	Chromosome name.
`pos`	1-based position on the chromosome.
`ref`	Reference base at this position.
`cov`	Number of reads covering this position.
`bases`	Read bases.
`quals`	Base qualities, encoded as ASCII characters.