Not doing what it says on the tin

[rmcolq]

OK, so the Readme (which I know is a guideline) says:
Take as input the nanopore assembly, and sam/bam of mapping of illumina reads to the assembly
Take 50kb chunks of the assembly, and pull out the relevant reads
For each chunk, call variants against the reference, and fix up the ref.
Then take the fixed up ref and run standard WG Cortex calling, and again fix up.

At the moment, I believe the cortex_correction.pl script will do a global polishing with bam, but in windows it only works with fq so far.

So, need to:

1. Handle bam in the cortex_polish.pl script (first step is mapping these reads to the draft assembly. Can we map mapped reads? I should look some more at bwa.
2. Want do run whole thing from the 'top' script, which is the cortex_polish.pl script (can change name), so should enable it to handle --window_size global or similar, in which case skip mapping step and just do the correction.

[iqbal-lab]

I'm happy to change the READMe, wrote it ages ago. I bet bwa can handle bam input