
=pod

=head1 NAME

=over 4

=item B<squizz> - Sequence format checker

=back

=head1 SYNOPSIS

=over 4

=item B<squizz> [B<-AShlns>] [B<-c> F<format>] [B<-f> F<format>]
F<file>

=back

=head1 OPTIONS

Following command line options are allowed:

=over 4

=item -A

Restrict detection/verification to alignment formats (conflict with
B<-S> option).

=item -S

Restrict detection/verification to sequence formats (conflict with
B<-A> option).

=item -c F<format>

Convert detected sequence/alignment into F<format>. This option
implies strict alignment checking.

=item -f F<format>

Assume input format is F<format>. Do not try to detect the format,
just verify that the given one is correct.

=item -h

Usage display.

=item -l

List all supported formats.

=item -n

Count and report detected entries. This option is only available when
the detection is restricted to a single type (with B<-A> or B<-S>
options) and strict checks (without B<-s> option) are enabled.

=item -s

Disable strict format checks (enabled by default).

=back

=head1 DESCRIPTION

B<squizz> is a sequence format file checker, but it has some
conversion capabilities too.

B<squizz> can detect the most common sequence and alignment formats :

* B<CODATA>, B<EMBL>, B<FASTA>, B<GCG>, B<GDE>, B<GENBANK>, B<IG>,
B<NBRF> (pir), B<RAW>, and B<SWISSPROT>.

* B<CLUSTAL>, B<FASTA>, B<MSF>, B<NEXUS>, B<PHYLIP> (interleaved and
sequential) and B<STOCKHOLM>.

B<squizz> can do some conversions too, if the format the input format
is supported. Only 3 types are available : sequence to sequence,
alignment to alignment, and alignment to sequence (the last one,
sequence to alignment, require multiple alignments algorithms and
cannot be handled with formatting tools).

Strict format checks validate the previously detected objects, by
making some sanity checks:

=over 4

=item - sequence strings must exists.

=item - alignment is made of more than one sequence.

=item - alignment sequence strings must have the same length.

=item - alignment sequence names must exists, and be unique.

=back

=head1 SEE ALSO

=over 4

=item B<seqfmt>(5), B<alifmt>(5)

=back

=head1 AUTHOR

Nicolas Joly (njoly@pasteur.fr), Institut Pasteur.

=cut
