read.maqmap.tags: Read MAQ text alignment output file
In hms-dbmi/spp: ChIP-Seq Processing Pipeline

Reads in MAQ alignment results in text format (that results from "maq mapview" command.)

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

`filename`	MAQ text output 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