Prevent treatment of confidence 255 ("*" in qual field for BAM) as
confidence -1 (or 255). Instead set it to a minimal confidence of 3.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden@3712 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Further tweakage of the align_blocks function. This was necessary in
order to get alignments scoring positive when using very weakly
aligning data.

It doesn't seem to overly harm my other tests for Illumina.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden@3713 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Fasta data now has a default quality of 3 instead of 0, as this was
causing problems with my experimental consensus algorithm.  It makes
more sense at 3 anyway. Confidence 0 implies it is 100% chance of
being incorrect.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden@3714 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1