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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.

jkbonfield 2014-05-02

changed /staden/trunk/src/gap5/shuffle_pads.c
/staden/trunk/src/gap5/shuffle_pads.c Diff Switch to side-by-side view
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