read.bam.tags: Read BAM alignment file
In hms-dbmi/spp: ChIP-Seq Processing Pipeline

Reads in aligned reads from BAM file. Note: no split (non-unique) alignemnts should be reported in the BAM file.

1	read.bam.tags(filename, read.tag.names = F, fix.chromosome.names = F)

`filename`	BAM file
`read.tag.names`	Whether the tag names should be read in
`fix.chromosome.names`	Whether to remove ".fa" from the end of the sequence names

`tags`	A vector of 5' tag coordinates, with negative values corresponding to tags mapped to the negative strand.
`quality`	Number of mismatches
`names`	Tag names, if `read.tag.names` was set