Cull some of the old malign scoring methods in scale_malign_scores().

Switched to a new version that scores based on log(count) instead of
count. This allows for better multiple sequence alignments within
heterozygous regions, so that we don't overly penalise the rare allele
but still prefer to align correctly.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden@3649 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Now more rigorous bounds checking in rewrite_soft_clips(), curing some
crashes.

concordant_soft_clips() is now more liberal with the scoring when
extending into cutoff, to allow for misalignments of the cutoff data.
The final assessment post re-alignment within rewrite_soft_clips() is
still using the original scores so this shouldn't cause problems.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden@3650 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1