development commit

Things are halfway working.  Still, there is a bug with the ordering of the
nodes in the graph or the graph traversal in alignment.  This leads to a crash.
incremental commit

Seem to have solved major issue with construction related to DAG with multiple
starting nodes.  However, this is an unusable commit due to the enormous number
of debugging messages.
correct major bug in reference mapping bookkeeping

Edges in the reference map were not updated correctly when reference nodes were
split.  The cigar was always written as 0M, which is not correct for deletions.
This led to rather nasty results.
average quality for inserted sequence
added option to not decompose variants in DAG

Testing shows that decomposing actually generates fewer false-positives.  But
it is possible to test this now thanks to the new command-line option
--flat-input-vcf.
major cleanup, now usable

Lots of debugging flags were pulled out.

The check for alignment acceptibility has been refined to allow acceptance only
when the sum of mismatches and softclip qualities is >= before realignmnet than
after, or if gaps are introduced the strictly reduce this sum, implying better
alignment to the graph.  If gaps are reduced while overall qsum of mismatches
and softclips does not increase, the realignment is accepted.