NAME
    Alien::SeqAlignment::parasail

VERSION
    version 0.03

SYNOPSIS
    To execute the alignment using the commande line tool:

     use Alien::parasail;
     use Env qw( @PATH );

     unshift @PATH, Alien::SeqAlignment::parasail->bin_dir;
     system Alien::SeqAlignment::parasail->exe, (list of options);

DESCRIPTION
    This distribution provides parsail so that it can be used by other Perl
    distributions that are on CPAN. The source code will be downloaded from
    the parasail github repo, and if that fails it will use the location of
    a fork but the author of this module. Contrary to other Alien modules,
    this one will not test for a prior install of the parasail library, but
    will install from source into a private share location for the use by
    other modules. This strategy will avoid overwritting prior system
    installs of the parasail library, and is guaranteed to use the latest
    version of parasail. The build provides the static and shared libraries,
    but also the CLI aligner (parasail_aligner).

NAME
    Alien::SeqAlignment::parasail - find, build and install the parasail
    library

METHODS
  exe
     Alien::SeqAlignment::parasail->exe

    Returns the command name for running the CLI version of the parasail
    aligner.

HELPERS
    %{parasail_aligner}

  parasail_aligner
    Returns the CLI command for the parasail aligner

SEE ALSO
    parasail <https://github.com/jeffdaily/parasail>
        parasail is a SIMD C (C99) library containing implementations of the
        Smith-Waterman (local), Needleman-Wunsch (global), and various
        semi-global pairwise sequence alignment algorithms. Here,
        semi-global means insertions before the start or after the end of
        either the query or target sequence are optionally not penalized.
        parasail implements most known algorithms for vectorized pairwise
        sequence alignment, including diagonal , blocked , striped , and
        prefix scan. Therefore, parasail is a reference implementation for
        these algorithms in addition to providing an implementation of the
        best-performing algorithm(s) to date on today's most advanced CPUs.

        parasail implements the above algorithms currently in three
        variants, 1) returning the alignment score and ending locations, 2)
        additionally returning alignment statistics (number of exact matches
        , number of similarities, and alignment length), and 3) functions
        that store a traceback for later retrieval as a SAM CIGAR string.
        The three variants exist because parasail is intended to be
        high-performing; calculating additional statistics or the traceback
        will perform slower than simply calculating the alignment score.
        Select the appropriate implementation for your needs. =back

    Alien
        Documentation on the Alien concept itself.

    Alien::Base
        The base class for this Alien.

    Alien::Build::Manual::AlienUser
        Detailed manual for users of Alien classes.

AUTHOR
    Christos Argyropoulos <chrisarg@gmail.com>

COPYRIGHT AND LICENSE
    This software is copyright (c) 2023 by Christos Argyropoulos.

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

AUTHOR
    Christos Argyropoulos <chrisarg@gmail.com>

COPYRIGHT AND LICENSE
    This software is copyright (c) 2023 by Christos Argyropoulos.

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

