Re-assemble reads to the reference genome and determine haplotypes

[joergi-w]

For an active region:

Create an assembly graph with the reference as template.
Take each read and match it to graph segments. Add new nodes if a part does not match.
Keep track how many reads support each path segment and determine the most likely paths.
Build haplotype sequences from likely paths.

[joergi-w]

Use T-Coffee or parts of SViper for implementing this? (both SeqAn2)