unitigs: use the correct codec

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
performance: build in debug mode

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
thorium: improve runtime performance

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
quality: fix compilation warnings with gcc 4.8.3

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
thorium: cache some variables in main loop

Link: https://github.com/GeneAssembly/biosal/issues/720
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>