fix some warnings found with valgrind

Link: https://github.com/GeneAssembly/biosal/issues/327
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
manually find memory leaks

Link: https://github.com/GeneAssembly/biosal/issues/400
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>