Fixed @SQ line LN: field to use the clipped contig length instead of
unclipped.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden@3645 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Fixed missing output of print_malign (unused unless uncommented out).

Changed the cutoff evaluation and extension to align against
heterozygous calls rather than single base consensus call. This allows
it to extend reads into cutoffs in more situations.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden@3646 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Renamed coherent to concordant for the soft-clipping strategy. This is
the more appropriate English word.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden@3647 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Bug fix to the recent update to look at consensus heterozygous bases
(typo leading to crash).

Make the concordant clip detection more liberal to start with (it'll
filter out those with turn out to be incorrect).

Remove pad columns both both and after rewriting the clips, as
series of pads left in the consensus was causing the seq-matches-cons
check to fail early.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden@3648 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1