Bio/Index/Abstract: Fixed uninitialized warning from pack_record
Bio/Assembly/Singlet: Get End from parent sequence when locatable sequence
can't figure it out in _seq_to_singlet
Bio/SearchIO/blasttable: Recover conserved value from %positives
when possible, so the program don't assume "conserved == identical"
Bio/Index/Blast: Fixed _index_file to adjust filehandle position
when reading '\r\n' lines in Windows (length() differs from byte length)
Big Windows compatibility fixes. Now all tests pass in Linux AND Windows!!!
Almost every bug was caused because Perl in Windows hide the '\r' character
from the user when reading the line in text mode, so text length()
is 1 less than the byte length for '\r\n' files, which caused trouble
when the code relied on the byte position of 'tell' and 'seek'.
Now the code check this situation and apply a correction if necessary.
Untabified 't/LocalDB/Index/Index.t' and deleted some empty lines at the
end of a few test files
Bio/SimpleAlign.pm: Fixed a TODO, allowed the use of mask characters
in 'slice'. Related to Bug #2842.
Removed tabs from previous commit
Bio/SeqIO/interpro.pm: Recognition of '<protein>' is now more specific,
related to bug #3452. Also removed some tabs from the test file.
Bio::SimpleAlign - follow some perl best practices

* use warnings
* use parent instead of base
* declare variable with "our" instead of use vars
* remove unecessary BEGIN block
Bio::Align::Utilities - new function most_common_sequences

* adds a new subroutine that takes a Bio::AlignI object and finds the sequence
that appears repeated most often.
Bio::Align::Utilities - follow some perl best practices.

* use warnings;
* declare variables with "our" instead of "use vars"
* don't set Exporter at runtime and make things simpler
* drop unecessary BEGIN block
Fix nonsense in code comments.
Bio::Align::Utilities - remove usage of /r option to support pre 5.14 perl
see if we can get travis-ci notifications working
test Bio::ASN1::EntrezGene
test failing build
Revert "test failing build"

This reverts commit 0fdeb6d2892f2f731cc6e5c8dc14879e304cf858.
Bio/SearchIO/blast.pm: Fixed bug #2978. Added a code to guess 'report_type'
as BLASTX or TBLASTN based on the start/end values from Query in the
alignment. Now the Frame value can be correctly assigned to $queryframe
or $hitframe and the Bio::LocatableSeq objects have the correct locations.
Also added tests using the bug report example.
Bio/SearchIO/Blast.pm: Removed tabs