fgvieira/ngsClean — pull request #1 by libor-m (2013-11-25 21:20:41+00:00)
Title: fix probably misplaced end bracket in SNPcleaner.pl

secondary mutation type (DNA damage) filter is using ``$opts{M}`` even when it's not initialized.

This fix encloses the filter to the previous block that is conditioned by ``$opts{M} && $t[3] =~ m/[ATCG]/i && $t[4] =~ m/[ATCG]/i``.

Is this ok?