NAME

    App::Rangeops - operates ranges and links of ranges on chromosomes

SYNOPSIS

        rangeops <command> [-?h] [long options...]
            -? -h --help    show help
    
        Available commands:
    
          commands: list the application's commands
              help: display a command's help screen
    
            circos: range links to circos links or highlight file
             clean: replace ranges within links, incorporate hit strands and remove nested links
           connect: connect bilaterial links into multilateral ones
            create: create blocked fasta files from range links
            filter: filter links by numbers of ranges or length difference
             merge: merge overlapped ranges via overlapping graph
           replace: replace ranges within links and incorporate hit strands
              sort: sort links and ranges within links

    See rangeops commands for usage information.

DESCRIPTION

    Types of links:

    Bilateral links

          I(+):13063-17220    I(-):215091-219225
          I(+):139501-141431  XII(+):95564-97485

    Bilateral links with hit strand

          I(+):13327-17227    I(+):215084-218967      -
          I(+):139501-141431  XII(+):95564-97485      +

    Multilateral links

          II(+):186984-190356 IX(+):12652-16010       X(+):12635-15993

    Merge files aren't links

          I(-):13327-17227    I(+):13327-17227

    Steps:

        sort
          |
          v
        clean -> merge
          |     /
          |  /
          v
        clean
          |
          V
        connect
          |
          v
        filter

AUTHOR

    Qiang Wang <wang-q@outlook.com>

COPYRIGHT AND LICENSE

    This software is copyright (c) 2016 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.

