This avoid the problem of query sequence file names randomly ending in _Z, which makes (at least) wublastp (3.0SE-AB) try to unzgip the non-gzipped temporary file, resulting in an error.
…mport extra stuff into namespace
which was failing in a test, and adjusted the mask maker programs (windowmasker, segmasker and dustmasker) to use 'maskinfo_asn1_text' output format, so it can be used with makeblastdb (all other formats fails). Removed the TODOs from the test file now that masking works.
complained about starting tree. Added test for -w option with tempdir(). Test runs now.
returned undef. This is now fixed. (2) When -quiet was set, redirection to /dev/null messed up the outfile name. This is also fixed.
…cept maybe through Bio::Root::Test; in any case should not be frozen in the distro, but tests that break due to updates should instead be updated themselves.
… removed TODO around translate_params test
to have been added by mistake
…le values (new blast+ feature); added tests for issue 12 to SABlastPlus.t
Add to documentation, reorganize code a bit
Store Bio::SeqFeature::Lite strand correctly when "+", "-", or "."
Always return undef from READLINE for EOF or failure
and cleaned format and indentation
increased significantly server waiting cycle (sleep + retries) because server was taking much longer than current setting to return results, and cleaned format and indentation