read.eland.tags: Read eland output file
In hms-dbmi/spp: ChIP-Seq Processing Pipeline

Reads in ELAND output file, returning 5'-end tag coordinates and number of mismatches associated with each mapped tag.

read.eland.tags(filename, 
  read.tag.names = F, 
  fix.chromosome.names = T, 
  max.eland.tag.length = -1,
  extended=F, 
  multi = F)

`filename`	ELAND 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
`max.eland.tag.length`	Specifies max length of the tag sequence considered by ELAND. This needs to be specified if the tags are longer than the sequences considred by ELAND during alignment.
`extended`	Whether the file is written out in "extended" format provided in GA pipeline 1.0.
`multi`	Whether the file is written in "multi" format, showing multiple alignments of the reads

`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