fixes whitespace
fixes method argument
documents clusterTranscripts
now uses match.arg instead of ugly if/stop statements
documents collapseTranscripts
documents gffRead
adds link for where I found this function - TODO: cite properly
deletes getRefSeq function
adds getRefSeq to gitignore because it is completely deprecated
documents getsamp
documents gettype
documents gffRead
makes inequality strict in clustering function
documents last
adds bpset.R to gitignore (bpset is helper for deprecated transcriptOverlaps)
remove bpset from github
documents pctOverlap
documents plotMeans
small doc change for plotTranscripts
adds authorship to several function docs