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

        for my $line ( $tempdir->child("$basename.db")->lines ) {
            if ( $line =~ /^blocks\s+=\s+(\d+)/ ) {
                $block_number = $1;
                last;
            }
        }

        my $cmd;
        $cmd
            .= "HPC.daligner $basename -M16 -T$opt->{parallel} -e$opt->{idt} -l$opt->{len} -s$opt->{len} -mdust";
        $cmd .= " | sed 's/ -vS / -S /'";    # don't show LAcheck prompts
        $cmd .= " | bash";
        App::Dazz::Common::exec_cmd( $cmd, { verbose => $opt->{verbose}, } );

        if ( defined $block_number and $block_number > 1 ) {
            $cmd = "LAcat $basename.\@.las > $basename.las";
            App::Dazz::Common::exec_cmd( $cmd, { verbose => $opt->{verbose}, } );
        }

        if ( !$tempdir->child("$basename.las")->is_file ) {
            Carp::croak "Failed: daligner\n";