*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

**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.