MAFFT.pm: Fixed an uninitialized warning from
"if ( $self->version =~ /^v6/ )" in "methods".
MAFFT.t : Fixed number of skipped tests to include the tests
in the nested skip, since it was warning me
"planned 23 tests but ran 17".
Untabified both files.
Hyphy/BatchFile.pm: Changed @validvals[$i] to $validvals[$i].
Hyphy.t: Fixed number of skipped tests, eliminated a duplicated "my $rel".
Removed tabs.
Blat.t: Fixed skipped tests number and removed "$blat_present",
since test_skip() already check if the executable is available,
and executing it before test_skip() make the script crash if exe
is not present. Also removed some trailing whitespaces.
BEDTools.t: Moved the file-finding lines inside the SKIP block,
this way it only looks for the files after confirming that the package
is installed. Also removed tabs and trailing whitespace
FastTree.t & Neighbor.t: Fixed number of skipped tests and removed
tabs and trailing whitespace
Vista.t: The 'java Vista 2>&1' command to determine if Vista
is installed gives me a different error message than the one
expected in the match (/NoClassDefFoundError/),
so adding another option (/^Error\:/). Also removed tabs.
SABlastPlus.t: Some bl2seq tests were giving hits even when the
blast output said 'no hits found' because of no similarity
between the sequences. After fixing SearchResultEventBuilder 'end_hit',
now I'm adapting those tests to give similarity in some cases
and no similarity in others, and expect num_hits accordingly.
Also reflowed some paragraphs
SABlastPlus.t: Added an additional $fac->cleanup for
temporal files deletion
StandAloneBlastPlus.pm: Some temporal files were not deleted
on cleanup() because of open filehandles. Added a check to $self
to close its own filehandle if its file is on the cleanup list.