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.
Fixed bug in move_id_to_bootstrap where supportvalues of 0 where
silently dropped.
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.
Add unit test for SearchIO::Exonerate negative score case

Exonerate can return negative scores.
We need to have a unit test case for that.

- Add example output file with a negative score

- Add test case, which parses the example output file and looks for
  the score of the first hit of the first result.
  Test succeeds if the value found matches the expected one.
  If the negative score is not parsed (as before the bugfix), the
  test is not run, meaning a failure per the test plan.

The handling of failure could be improved to have a more meaningful
error than the catch-all "Bad plan".
FastAlign.pl

I did a bioperl script which uses the heuristic method of tfasty.
The query string is in amino acids and the hit string is in nucleotides.
There are extra nucleotides at the end of the hit string (option -diff and by
default = 10), that allow to verify if the intron start with common rules
(5'-GTGCGA-... for group II intron and after an exonic T for group I intron).

I'm glad to help the bioperl community!
Added script for breaking sequence files into equal sized parts.
Added script to cut subsequences out of a set of sequence files.
fix POD syntax
Merge branch 'master' of git://github.com/viklund/bioperl-live into topic/viklund-master
Merge branch 'bugfix-exonerate' of git://github.com/JeanFred/bioperl-live into topic/JeanFred-bugfix-exonerate
Merge pull request #60 from MattOates/master

Some sequence manipulation scripts wrapping SeqIO.  All tests are passing.
Merge branch 'master' of git://github.com/adsj/bioperl-live into topic/pull_request47_adsj

Now with long label support

Conflict resolved:
	t/SeqIO/genbank.t
Merge branch 'topic/pull_request47_adsj'
move hard-coded FT line length to a global
Merge branch 'master' of git://github.com/fschwach/bioperl-live into topic/pull_request33

Conflicts fixed (and perltidied):
	Bio/SeqUtils.pm
	t/SeqTools/SeqUtils.t
fix for hash randomization bug in Bio::Map for perl 5.18.0