*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.