implement a plugin for Pilon

[levinas]

Used by Broad to post-process AllPaths-LG assemblies.

http://www.broadinstitute.org/software/pilon/reference/

HOW PILON IDENTIFIES BAD LOCATIONS AND REGIONS

Pilon determines which regions may contain contiguity breaks requiring local reassembly by looking for the following motifs:

"V-dips," or locations where coverage drops significantly as compared to flanking regions General low coverage
Large percentage of soft-clipped alignments at a specific locus
A high percentage of invalid pairs
Note that multiple such events in close proximity (~200bp) will be treated as a single suspect region.