sanity check input; contig filtering

[martinghunt]

These changes:

• sanity check input assembly (strips everything after first whitespace)
• checks all input files exist before running any of the pipeline
• adds an option to pull out a user-spcified list of contigs (--only_contigs)
• exposes the min read length parameter (--min_read_length)
• option to not use unmapped reads (--discard_unmapped)