Good things to do if time

[rmcolq]

1. Allow bam file (or sorted, or sorted indexed bam file) to be input and skip the relevant steps in cortex_polish.pl, where the bam is a map of the reads to the draft assembly
2. Allow a bam file to be input where the reads are mapped to a mysterious reference (as in our JR samples)
3. Sort out changes in default parameters if "ont" input
4. Make the cleanfile given threshold parameter for manual cleaning.