instead of "https://github.com/bioperl/bioperl-live/issues/" (since the first is the dominant form in the other hundreds files)
… yn00 reported by Volker Brendel
Use COLLATE NOCASE instead of LOWER() for Bio::DB::SeqFeature::Store::DBI::SQLite
…egex' error, Species.t and genbank.t pass
flexibility to the ID field in the ID line, to allow custom IDs
attribute.attribute_value, and typelist.tag; and remove the user of the LOWER() function; to allow the use of indexes instead of full-table scans. Add the COLLATE NOCASE opterator to affected queries for backwards compatibility with Bio::DB::SeqFeature::Store databases created without the COLLATE NOCASE constraints.
except inside map/grep blocks. Also extensive cleanup of tabs, parenthesis, indentation, etc. Test suite pass.
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.
"_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.
and 'HSP-hit_length' in "end_hsp" subroutine. Also fixed an undefined value warning for $hit_bits in "_add_hit"
"to_string" method, and cleaned indentation and tabs from test file
to the more portable File::Copy. Tested and works fine.
to lexical with three-argument opens calls, added die/throw and reason of failure $! where missing, and made error messages more uniform and consistent with Florent Angly messages for Root (like quoting of filenames). Also deleted a few unused open filehandles and some unnecessary parenthesis. Tests pass.
Add reason for failure of file IO
Should be ">$o_file" and not "> $o_file" Also did miscellaneous cleaning (tabs, parentheses)
Was "sample_dataset.tigr " instead of "sample_dataset.tigr" (no trailing space) Also made style more consistent
1/ their documentation was less than clear 2/ they seem to have been broken for quite some time 3/ tests disagree that STDIN should be used this way