SeqFeatureDB Postgres: Changed the use of system("cp") command
to the more portable File::Copy. Tested and works fine.
Bio/Ontology/InterProTerm: Fixed an uninitialized warning in
"to_string" method, and cleaned indentation and tabs from test file
SearchResultEventBuilder: Simplified calculation of 'HSP-query_length'
and 'HSP-hit_length' in "end_hsp" subroutine. Also fixed an
undefined value warning for $hit_bits in "_add_hit"
SeqIO/Tinyseq.pm: Fixed an uninitialized value warning from
"_get_writer" by changing '$Bio::SeqIO::tinyseq::VERSION' to
'$Bio::Root::Version::VERSION'. Also cleaned tabs, indentation
and trailing whitespace from both module and test file.
Unflattener: Fix for Bug #3458. Incorporated Bastien Chevreux
suggestions to improve error reports from "problem" subroutine
by adding feature location and locus_tag. Also merged all
tests from 'Unflattener2.t' into 'Unflattener.t' to have
all tests in a single file.
SeqIO/Genbank: Complete elimination of the use of '$_',
except inside map/grep blocks. Also extensive cleanup of tabs,
parenthesis, indentation, etc. Test suite pass.