Fixed contig_export_sam (used for SAM, BAM and CRAM formats) to be
much faster in excessively deep regions where soft-clipping is being
used.

Gap5 has to convert from coordinates sorted by object start including
soft-clipped bases, to coordinates sorted by first unclipped site
(SAM).  This sorting could become O(N^2) in the worst case, but is now
O(NlogN) - possibly better if soft-clip lengths co-locate.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3758 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
The popup listbox from the combobox now shares the width from the
entry box.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3759 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Added the option to view the readings/haplotype lists on the ednames
right click menu.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3760 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Delete old haplotype_* lists when creating new ones, so as not to
confuse people as to how many haplotypes are present.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3761 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1