Allow bowtie index/reference files to be gzipped

[amatchan]

For the Tophat-fusion RNA-Seq pipeline, there are many bowtie reference and transcriptome index files that need to be in place (three sets altogether when including tophat fusion post).
Currently the pipeline checks for the existence of the index files using the precise, uncompressed name e.g. GRCh37.genome.1.ebwt for bowtie or GRCh37.genome.1.bt2 for bowtie2, the script will stop if they can't be found so if the files are gzipped the script stops.
Steps should be added to the setup subroutine to allow checking and decompression of the index files.