more robust arg parsing in interleaved fastq files (aln module)
fixed bug in output file naming when -o flag not specified (aln module)
in aln module, do a -e file check on fastq instead of -f. this allows fastqs to be crazy mkfifo streams or pipe ins
changed mapdups to samblaster in usage descr
Merge branch 'master' into dev

pulling in mike's updates to speedseq.config
fixed bug where lumpy module would fail if passed -L command line arg