Fixed a bug in r3655 caused by failure to save bin ranges after
modifying.  This causes thousands of errors after inserting columns of
bases (eg via shuffle_pads).


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3698 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Added an interface to save heterozygous bases in the consensus.

Internally there are some new functions for this too (eg
calculate_consensus_simple_het) as well as some experimental only
functions for evaluation of SNP calling. (It is not expected that Gap5
will perform well here.)


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3699 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Remove the code attempting to set GRANGE_FLAG_REFPOS_HAVE_* fields.

These are used internally in tg_iface_g.c to determine whether we need
to store the Position, Size or ID fields via a simplistic delta
mechanism.  Outside of that file they should never be set or queried.

This fix removes a warning about the in-memory and on-disc
representations differing, which is bogus as these bit fields are
zeroed after reading anyway.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3700 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Added explanatory note to GRANGE_FLAG_REFPOS_HAVE_* fields so we don't
accidentally recreate the same bug as before. (Fake warnings from
Check Database.)


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3701 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1