Spades and Introns

Changed: SPAdes now used to assemble contigs. Much more reliable than Velvet/CAP3.
Changed: GNU Parallel now reads gene list from a file, to avoid too-long command lines.

Added support for intron retrieval via interonerate.py, separately and as "supercontigs" containing exons.
Added depth_calculator.py, which uses samtools to map reads to exon or supercontig sequences.
Added cleanup.py, which removes the bulky assembly files.
Added fasta_merge.py, which can create a concatenated alignment and RAxML partition file.
Added output file exonerate_stats.csv, indicating which contigs were used in final exon recovery.

Fixed bug using bait files with lowercase DNA.
Fixed bug in sorting sequences in Biopython (NotImplementedError)
Fixed GNU parallel overwrite collision.