Various fixes to keep contig start/end correct.

tg_check.c
  In check_contig, print out start and end positions in the contig and those
from the bin walk when they disagree.

tg_bin.c
  Fixed bug in bin_remove_item_from_bin where used start/end were not swapped
for complemented bins when mapping to the position in the parent.  This could
lead to the contig unclipped start/end not being recalculated when they should
have been.

tg_sequence.c
  Add code to update contig used start/end and clipped_timestamp when
necessary in sequence_move.

tg_contig.c
  Altered the way that contig_insert_base and contig_delete_base keep track of
which ends of the contig may have changed.  This fixes several cases where the
contig start/end were not updated as they should have been.
  Modified read shifting code in contig_insert_base2 and contig_delete_base2. 
The new version moves the same reads for both complemented and uncomplemented
bins.
  Renamed some variables to make the operation of the code less obscure,
e.g. r_start, r_end to v_start,v_end in contig_insert_base2 and
contig_delete_base2; ins,no_ins to del,no_del in contig_delete_base2.
  Added some comments.

gap5_del_test.tcl
  Added test to ensure cutoff data at the start/end of the contig is handled
correctly.
  Made the test script stop but not exit on failure.  This allows the
situation to be checked manually.
  Made some tests run on complemented contigs as well.
  Temporarily disabled the pattern tests to allow a faster iteration through
the random ones.



git-svn-id: svn://svn.code.sf.net/p/staden/code/staden@3640 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1