*GmapGenome doesn't yet have a method for DNAStringSet genomes

 *genome param for GmapGenome class isn't making it into the
 object. not in representation?

 *passing use_snps=NULL as an arg to GsnapParam constructor breaks it

 *fix extra() arg in gsnap method
 
 *Vignette 
 **remove all eval=FALSE. This means rolling some GmapGenome packages
 
 *cannot overwrite files from gsnap. In other words, can only run gsnap
  function once.
 
 *make sure mapping in gsnap command-line too (short form args) are
  clearly linked to in the R docs (Greg request)
 
 *get NGS seq pipeline tests working
 
 *gsnap said the distant_splice_identity args is not supported, but
  it's in the gsnap --help documention
 
 *bam_tally segfaults if the BAM file used is not indexed
 
 *cannot get seqinfo(GmapGenome) if genome created with
  DNAStringSet. Also, R issues warnings during creation about
  contigs. Currently, the unity test for seqinfo(GmapGenome) does not
  exist because of this.