corrected bug in features positions after delete

fixed a bug:
_coord_adjust_deletion: test for features overlapping only one end of
the deletion site had incorrect use of Bio::RangeI::contains, which led
to incorrect adjustment of positions ifor features that start at the
start of the deletion site and extend beyond the deletion's end point.
Added a new test case for this situation.
throw exception on negative positions

changed _coord_adjust to check for negative positions, which now lead to
an exception. Previous behaviour was to allow such coordinates but the
resulting adjustments were incorrect because they were treated as
positive numbers
Test that long label qualifiers can be parsed in genbank format.
Quote qualifiers that are so long that they are line wrapped in genbank format.
Fix for Bug #2936, now Split.pm/flip_strand sets guide_strand according to
sublocation strands. Also initialize the sublocations strand values
if necessary to perform the flip. Tests added.
Initialize the Strand value if missing before performing a "flip_strand"
for an Atomic location, or it will silently fail
Split/flip_strand now makes a strand consistency check in all sublocations,
and sets Guide Strand accordingly. In case of mixed strands (trans-splicing),
it reverse the sublocations order to produce the correct revcom transcript
Split/guide_strand now makes a consistency check of the sublocations
strand values to set its own value, giving undef for mixed strands
Split/to_FTstring don't need to reverse sublocations order anymore
PrimarySeq/subseq now uses "guide_strand" for Split locations to know
when to reverse the sublocations order to produce the correct sequence
Added extensive testing for the introduced changes, with many locations
and subsequences tests in t/Seq/PrimarySeq.t
Expanded some comments
Merge remote branch 'upstream/master'
Merge remote branch 'upstream/master'
PrimarySeq.pm/new: Changed $is_circular test to use "define",
since it fails to add is_circular attribute if the argument is 0
PrimarySeqI.pm: use Bio::Root::clone to make sure that copied objects
get all attributes from the original. Implemented in revcom(), trunc(),
translate(), transcribe() and rev_transcribe()
PrimarySeq.t: TODO tests are now fixed. All the other tests also pass
Fixed bug in move_id_to_bootstrap where supportvalues of 0 where
silently dropped.
Sorry about this, analyzing new output files is leading to minor changes in regex's
Fix bug with score parsing in SearchIO::Exonerate

Exonerate can return negative scores, such as:
vulgar: aly-miR169a 0 21 + contig15750__54-177 19 40 + -3 M 21 21

These were not parsed correctly, resulting in an empty hit.

Edit the corresponding regular expression to account for a
possible minus symbol '-' before the digits.