#!/usr/bin/perl
use strict;
use warnings;
use App::Egaz;

App::Egaz->run;

=head1 OVERVIEW

For help with App::Egaz, run "egaz help"

=cut

__END__

perl -I lib/ script/egaz help

lastz t/pseudocat.fa t/pseudopig.fa > t/default.lav
lavToPsl t/default.lav t/default.psl

perl -I lib/ script/egaz exactmatch t/pig2.fa t/pseudopig.fa --debug
perl -I lib/ t/03-exactmatch.t

perl -I lib/ script/egaz lav2axt t/default.lav
perl -I lib/ t/04-lav2axt.t

perl -I lib/ script/egaz lav2psl t/default.lav
perl -I lib/ t/05-lav2psl.t

perl -I lib/ script/egaz formats
perl -I lib/ t/06-formats.t

perl -I lib/ t/07-maskfasta.t

perl -I lib/ script/egaz masked <(echo -e ">1\nNNNN\n")
perl -I lib/ t/08-masked.t

perl -I lib/ script/egaz partition
perl -I lib/ t/09-partition.t

touch 't/pseudocat.fa[5001,10100]'
lastz 't/pseudocat.fa[5001,10100]' t/pseudopig.fa > t/partition.t.lav
cat t/partition.t.lav | perl ~/Downloads/blastz-normalizeLav 18803 0 > t/partition.t.norm.lav

touch 't/pig2.fa[10001,18000]'
lastz t/pseudocat.fa 't/pig2.fa[10001,18000]' > t/partition.q.lav
cat t/partition.q.lav | perl ~/Downloads/blastz-normalizeLav 18803 22929 > t/partition.q.norm.lav

perl -I lib/ script/egaz normalize t/partition.t.lav --tlen 18803
perl -I lib/ t/10-normalize.t

perl -I lib/ script/egaz raxml t/YDL184C.fas --verbose
perl -I lib/ t/11-raxml.t

blastn

sortaxt

