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=item C<--sort s>

Sets sort mode to s.

=item C<--maxhits n>

Display only the n (best) hits.

=item C<--datapath p>,

Generate suffix arrays in path p. Default is 'data'


=item C<--showdesc n>,

Vmatch only (see manual). Is faster because it extracts all data
directly out of the vmatch output. Otherwise, vsubseqselect is called
for every hit.

=item C<--online>

Vmatch only (see manual). Run algorithms online without using the index.

=item C<--hxdrop n>

Vmatch only (see manual). Specifies the xdrop value for hamming distance extension.

=item C<--exdrop n>

Vmatch only (see manual). Specifies the xdrop value for edit distance extension.

=item C<--no_alignments>

Don't calculate alignments with EMBOSS.

=back  

=head1 DESCRIPTION

Bio-Grep is a collection of Perl modules for searching in 
Fasta files. It is programmed in a modular way. There are different 
back-ends available. You can filter search results.

bgrep is an example of how to use this library.

=head1 CONFIGURATION AND ENVIRONMENT

C<bgrep> does not support configuration files (but it is on my TODO list).

The environment variable C<BIOGREPDEBUG> is supported. When this variable is
set to a true value, then C<bgrep> will output A LOT OF debug text.

=head1 DEPENDENCIES

L<Bio::Grep>, L<Getopt::Long>, L<Pod::Usage>, L<File::Basename>

=head1 INCOMPATIBILITIES

None reported.

=head1 BUGS AND LIMITATIONS

No bugs have been reported. 

Please report any bugs or feature requests to
C<bug-bio-grep@rt.cpan.org>, or through the web interface at
L<http://rt.cpan.org>. 

=head1 SEE ALSO

perldoc L<Bio::Grep>

=head1 AUTHOR

Markus Riester, E<lt>mriester@gmx.deE<gt>

=head1 LICENSE AND COPYRIGHT

This program is free software; you can redistribute it and/or
modify it under the same terms as Perl itself.

=head1 DISCLAIMER OF WARRANTY

BECAUSE THIS SOFTWARE IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
FOR THE SOFTWARE, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
PROVIDE THE SOFTWARE "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER
EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE
ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE IS WITH
YOU. SHOULD THE SOFTWARE PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL
NECESSARY SERVICING, REPAIR, OR CORRECTION.

IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
REDISTRIBUTE THE SOFTWARE AS PERMITTED BY THE ABOVE LICENSE, BE
LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL,
OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE
THE SOFTWARE (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING
RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
FAILURE OF THE SOFTWARE TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF
SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.

=cut

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