Improve error messages.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3765 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Reduced complexity in haplotype_str_add(). With long sections this can
become over 100x less cpu, and growing more.  It is still a linear
scan though so needs futher optimisation yet, using a tree instead to
find snp overlaps.

Also amended it to consider sites with too many discrepancies rather
than pure consensus SNP call.

Finally, added a minimum count of 2 seqs to filter most of the
singleton haplotypes. The minimum count figure isn't yet user
adjustable, but should be made so before this becomes production
ready.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3766 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
The list size is now shown in the contig editor, giving an indication
of how many fragments are in each haplotype.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3767 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1