Added memoization to FASTQ downsampling.
Run test_run downsampling in parallel.
Added quick option to downsample fastq files.

Just grabs the first N records.
Let sort_order detection work for BAM and SAM files.
Fixes to make Tophat more reliable.
Make alignment-post processing more reliable.
Remove commented out code.
Make Cufflinks output more verbose.
Add Cufflinks section to the default config.