Not really an issue but something to remember. MagicBlast version 1.2 by default does not return unaligned reads. HOWEVER, version 1.3 does return unaligned reads by default. To turn this off, use the '-no_unaligned' option. See https://gist.github.com/pcantalupo/fe755e79d5b195573f80ec9ef179e562 for comparsion of v1.2 vs v1.3 options.
Not really an issue but something to remember. MagicBlast version 1.2 by default does not return unaligned reads. HOWEVER, version 1.3 does return unaligned reads by default. To turn this off, use the '-no_unaligned' option. See https://gist.github.com/pcantalupo/fe755e79d5b195573f80ec9ef179e562 for comparsion of v1.2 vs v1.3 options.