First draft of a new haplotype finder.  It replaces the Sort By
Sequence mode in the contig editor as well as generating lists of read
IDs per haplotype and creating a master "haplotypes" list of lists.

Disassemble readings now knows how to handle list of lists, so that it
disassembles each sub-list into its own set of contigs.

There is more to do on this to tidy it up: handling read-pairs,
optimising it for larger contigs, improving the consensus algorithm to
label more things as SNPs by avoiding the dominance of depth.  However
it's a good starting point and users are already wanting to use it so
we'll see how it goes in the current state.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden@3750 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Made contig_insert_base2() more robust with respect to corrupted data
or other sources of errors.

Previously it just bailed out of the recursion, leaving a half
inserted column. This is complicated to deal with and often turns a
small problem into a bigger problem.

Now it boldly carries on regardless, completing as much as it can,
before then returning -1 to the calling function to indicate the
failure.  Ideally the calling function would execute this in a child
io so it can be backed out of to revert the change, but in the absence
of this we have at least maintained consistency where able.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden@3751 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1