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lib/App/Dazz/Command/cover.pm  view on Meta::CPAN

    #
    #                #@type AlignDB::IntSpan
    #                my $region = $covered_of->{$serial}{ $opt->{coverage} };
    #
    #                for my $set ( $region->sets ) {
    #                    next if $set->size < $opt->{len};
    #
    #                    my $cmd;
    #                    $cmd .= "DBshow -U $basename $serial";
    #                    $cmd .= " | faops replace -l 0 stdin first.replace.tsv stdout";
    #                    $cmd .= " | faops frag -l 0 stdin @{[$set->min]} @{[$set->max]} stdout";
    #                    $cmd .= " >> covered.fasta";
    #                    App::Dazz::Common::exec_cmd( $cmd, { verbose => $opt->{verbose}, } );
    #                }
    #            }
    #        }
    #
    #        if ( !$tempdir->child("covered.fasta")->is_file ) {
    #            Carp::croak "Failed: create covered.fasta\n";
    #        }
    #    }