pilon options? break contigs and local realignement #32
Description
-- fix "all, breaks"
by default fix = all but does not include option breaks (that allows opening gaps)
the option breaks should allow local reassembly to open gaps (this for me appeared to result of the break of one scaffold that was not broken othewise but with N) - I can re-test
option --dumpreads (might be interesting for local reassemblies) - or if someone want to try to re-scaffold.
Though I am not sure I get how all of this is functionning - it might be interesting to investigate (also to be sure to understand what this does). I would also for security (use all scaffolds at this stage) ... will also make some tests
- and filter the scaffolds by length after the pilon step (nb filtering before could also affect mapping to reference - as some reads might have been better mapped on parts that were filtered out - filtering before pilon could force some suboptimal reads to be mapped in regions that are similar, this might affect pilon as it uses coverage and PE insert for detecting missassembies & local reassembly - of course all is a question of how many times this happened to see an impact - but more logical to do it afterwards - on this one I now agree with myself :) - let's see if my arguments are convincing)