Author:         Martin Asser Hansen - Copyright (C) - All rights reserved

Contact:        mail@maasha.dk

Date:           August 2007

License:        GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)

Description:    Inverts an alignment showing only non-mathing residues using the first sequence as reference.

Usage:          ... | $script [options]

Options:        [-s          | --soft]               -  Use soft inversion instead of hard inversion.
Options:        [-I <file>   | --stream_in=<file>]   -  Read input from stream file  -  Default=STDIN
Options:        [-O <file>   | --stream_out=<file>]  -  Write output to stream file  -  Default=STDOUT

Examples:       ... | $script     -  Invert alignment in stream.
Examples:       ... | $script -s  -  Soft invert alignment in stream.