Changed the simple consensus qualities to be Phred scores instead of
log-odds scores.  This fixes a bug where negative consensus qualities
were appearing in CAF and ACE outputs.

The change also impacts some other code, such as searching for
consensus quality in the editor and fastq outputs, but only at the
very low end as log-odds and phred scales rapidly converge. It is only
very poor quality data that changes.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden@3719 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Bug fixes the insertion/deletion counting in List Base Confidence
(they were reversed). Also updated it to report percentages.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden@3721 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Switched to using older method of handling ONT consensus (based on a
one-liner perl/awk combo).  It just has a single parameter for how
much more likely it is to have overcall vs undercall. This is simple
to understand and more robust.

It corrects issues with the old system, which was causing * in
columns of illumina data to be downweighted too much.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden@3722 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1