[ADD] Tophat argument parser setup, initial function names.
[REFACT] syntax follows PEP8
[ADD] Sample mode
[ADD] out_dir, ref search
[FIX] out_dir
[FIX] out_dir
[FIX] paired sample and out_dir
[ADD] single-read mode
[FIX] input fastq accepted, correct typo
[ADD] project mode
[FIX] project mode, output to sample subdir
[FIX] reference for nickname in SampleSheet.csv
[FIX] use unix pipeline to unzip fastq.gz
[MOD] remove the FCID mode