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package App::Fasops;

our $VERSION = '0.6.4';

use strict;
use warnings;
use App::Cmd::Setup -app;

1;

__END__

=head1 NAME

App::Fasops - operating blocked fasta files

=head1 SYNOPSIS

    fasops <command> [-?h] [long options...]
            -? -h --help  show help

    Available commands:

       commands: list the application's commands
           help: display a command's help screen

        axt2fas: convert axt to blocked fasta
          check: check genome locations in (blocked) fasta headers
         concat: concatenate sequence pieces in blocked fasta files
      consensus: create consensus from blocked fasta file
         covers: scan blocked fasta files and output covers on chromosomes
           join: join multiple blocked fasta files by common target
          links: scan blocked fasta files and output bi/multi-lateral range links
        maf2fas: convert maf to blocked fasta
       mergecsv: merge csv files based on @fields
          names: scan blocked fasta files and output all species names
         refine: realign blocked fasta file with external programs
        replace: replace headers from a blocked fasta
       separate: separate blocked fasta files by species
          slice: extract alignment slices from a blocked fasta
          split: split blocked fasta files to per-alignment files
           stat: basic statistics on alignments
         subset: extract a subset of species from a blocked fasta
           xlsx: paint substitutions and indels to an excel file


See C<fasops commands> for usage information.

=head1 AUTHOR

Qiang Wang <wang-q@outlook.com>

=head1 COPYRIGHT AND LICENSE

This software is copyright (c) 2014 by Qiang Wang.

This is free software; you can redistribute it and/or modify it under
the same terms as the Perl 5 programming language system itself.

=cut